0s autopkgtest [03:16:47]: starting date: 2024-03-19 0s autopkgtest [03:16:47]: git checkout: d9c0295b adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [03:16:47]: host juju-7f2275-prod-proposed-migration-environment-4; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.7shf0slf/out --timeout-copy=6000 --setup-commands 'sed -i "s/ports.ubuntu.com/ftpmaster.internal/; s/ubuntu-ports/ubuntu/" /etc/apt/sources.list `ls /etc/apt/sources.list.d/*.list 2>/dev/null || true`; 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/7.2.6-5 python3-defaults/3.12.2-0ubuntu1' -- lxd -r lxd-armhf-10.44.124.112 lxd-armhf-10.44.124.112:autopkgtest/ubuntu/noble/armhf 57s autopkgtest [03:17:44]: @@@@@@@@@@@@@@@@@@@@ test bed setup 60s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 61s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 61s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3756 kB] 64s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.6 kB] 64s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [486 kB] 64s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf Packages [587 kB] 64s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf c-n-f Metadata [2492 B] 64s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf Packages [1372 B] 64s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf c-n-f Metadata [116 B] 64s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf Packages [3620 kB] 66s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf c-n-f Metadata [7776 B] 66s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf Packages [35.6 kB] 66s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf c-n-f Metadata [116 B] 75s Fetched 8673 kB in 8s (1148 kB/s) 75s Reading package lists... 86s tee: /proc/self/fd/2: Permission denied 120s Hit:1 http://ports.ubuntu.com/ubuntu-ports noble InRelease 120s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 120s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 120s Hit:4 http://ports.ubuntu.com/ubuntu-ports noble-updates InRelease 120s Hit:5 http://ports.ubuntu.com/ubuntu-ports noble-backports InRelease 120s Hit:6 http://ftpmaster.internal/ubuntu noble-security InRelease 120s Hit:7 http://ports.ubuntu.com/ubuntu-ports noble-security InRelease 120s Hit:8 http://ftpmaster.internal/ubuntu noble-proposed InRelease 128s Reading package lists... 128s Reading package lists... 129s Building dependency tree... 129s Reading state information... 131s Calculating upgrade... 133s The following packages were automatically installed and are no longer required: 133s libatasmart4 libblockdev-crypto3 libblockdev-fs3 libblockdev-loop3 133s libblockdev-mdraid3 libblockdev-nvme3 libblockdev-part3 libblockdev-swap3 133s libblockdev-utils3 libblockdev3 libbytesize-common libbytesize1 libnspr4 133s libnss3 libnvme1t64 libpolkit-agent-1-0 libvolume-key1 133s linux-headers-6.8.0-11 python3-lib2to3 133s Use 'apt autoremove' to remove them. 134s The following packages will be REMOVED: 134s libapt-pkg6.0 libarchive13 libatm1 libcurl3-gnutls libcurl4 libdb5.3 libelf1 134s libext2fs2 libgdbm-compat4 libgdbm6 libglib2.0-0 libgnutls30 libgpgme11 134s libhogweed6 libmagic1 libnetplan0 libnettle8 libnpth0 libnvme1 libparted2 134s libpcap0.8 libperl5.38 libpng16-16 libpsl5 libreadline8 libreiserfscore0 134s libssl3 libtirpc3 libudisks2-0 libuv1 linux-headers-6.8.0-11-generic 134s linux-headers-generic python3-distutils udisks2 134s The following NEW packages will be installed: 134s libapt-pkg6.0t64 libarchive13t64 libatm1t64 libcurl3t64-gnutls libcurl4t64 134s libdb5.3t64 libelf1t64 libext2fs2t64 libgdbm-compat4t64 libgdbm6t64 134s libglib2.0-0t64 libgnutls30t64 libgpgme11t64 libhogweed6t64 libmagic1t64 134s libnetplan1 libnettle8t64 libnpth0t64 libnvme1t64 libparted2t64 134s libpcap0.8t64 libperl5.38t64 libpng16-16t64 libpsl5t64 libreadline8t64 134s libreiserfscore0t64 libssl3t64 libtirpc3t64 libuv1t64 xdg-user-dirs 134s The following packages have been kept back: 134s multipath-tools 134s The following packages will be upgraded: 134s apparmor apt apt-utils bind9-dnsutils bind9-host bind9-libs bolt 134s bsdextrautils bsdutils btrfs-progs coreutils cryptsetup-bin curl dbus 134s dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common 134s dbus-user-session debianutils dhcpcd-base dirmngr dmsetup dpkg dpkg-dev 134s e2fsprogs e2fsprogs-l10n eject fdisk file ftp fwupd gawk gcc-13-base 134s gcc-14-base gir1.2-girepository-2.0 gir1.2-glib-2.0 gnupg gnupg-l10n 134s gnupg-utils gpg gpg-agent gpg-wks-client gpgconf gpgsm gpgv groff-base 134s ibverbs-providers inetutils-telnet info initramfs-tools initramfs-tools-bin 134s initramfs-tools-core install-info iproute2 jq keyboxd kmod kpartx 134s krb5-locales libapparmor1 libaudit-common libaudit1 libblkid1 134s libblockdev-crypto3 libblockdev-fs3 libblockdev-loop3 libblockdev-mdraid3 134s libblockdev-nvme3 libblockdev-part3 libblockdev-swap3 libblockdev-utils3 134s libblockdev3 libbpf1 libbrotli1 libbsd0 libc-bin libc6 libcap-ng0 134s libcom-err2 libcryptsetup12 libdbus-1-3 libdebconfclient0 libdevmapper1.02.1 134s libdpkg-perl libevent-core-2.1-7 libexpat1 libfdisk1 libfido2-1 libftdi1-2 135s libfwupd2 libgcc-s1 libgirepository-1.0-1 libglib2.0-data libgssapi-krb5-2 135s libgudev-1.0-0 libgusb2 libibverbs1 libjcat1 libjq1 libjson-glib-1.0-0 135s libjson-glib-1.0-common libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 135s libldap-common libldap2 liblocale-gettext-perl liblzma5 libmagic-mgc 135s libmbim-glib4 libmbim-proxy libmm-glib0 libmount1 libnghttp2-14 libnsl2 135s libnss-systemd libpam-modules libpam-modules-bin libpam-runtime 135s libpam-systemd libpam0g libplymouth5 libpolkit-agent-1-0 135s libpolkit-gobject-1-0 libpython3-stdlib libpython3.11-minimal 135s libpython3.11-stdlib libpython3.12-minimal libpython3.12-stdlib libqmi-glib5 135s libqmi-proxy libqrtr-glib0 librtmp1 libsasl2-2 libsasl2-modules 135s libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsemanage2 135s libslang2 libsmartcols1 libsqlite3-0 libss2 libssh-4 libstdc++6 135s libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl 135s libtirpc-common libudev1 libusb-1.0-0 libuuid1 libvolume-key1 libxml2 135s libxmlb2 libxmuu1 locales logsave lshw lsof man-db mount mtr-tiny 135s netplan-generator netplan.io openssh-client openssh-server 135s openssh-sftp-server openssl parted perl perl-base perl-modules-5.38 135s pinentry-curses plymouth plymouth-theme-ubuntu-text psmisc python-apt-common 135s python3 python3-apt python3-cryptography python3-dbus python3-gdbm 135s python3-gi python3-lib2to3 python3-markupsafe python3-minimal 135s python3-netplan python3-openssl python3-pkg-resources python3-pyrsistent 135s python3-setuptools python3-typing-extensions python3-yaml python3.11 135s python3.11-minimal python3.12 python3.12-minimal readline-common rsync 135s shared-mime-info sudo systemd systemd-dev systemd-resolved systemd-sysv 135s systemd-timesyncd tcpdump telnet tnftp ubuntu-pro-client 135s ubuntu-pro-client-l10n udev util-linux uuid-runtime vim-common vim-tiny wget 135s xxd xz-utils zlib1g 135s 225 upgraded, 30 newly installed, 34 to remove and 1 not upgraded. 135s Need to get 87.1 MB of archives. 135s After this operation, 9051 kB disk space will be freed. 135s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bsdutils armhf 1:2.39.3-9ubuntu2 [102 kB] 135s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc-14-base armhf 14-20240315-1ubuntu1 [47.0 kB] 135s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgcc-s1 armhf 14-20240315-1ubuntu1 [41.5 kB] 135s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libstdc++6 armhf 14-20240315-1ubuntu1 [714 kB] 136s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc6 armhf 2.39-0ubuntu6 [2827 kB] 136s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssl armhf 3.0.13-0ubuntu2 [975 kB] 137s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf zlib1g armhf 1:1.3.dfsg-3.1ubuntu1 [49.2 kB] 137s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2build6 [51.3 kB] 137s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.12 armhf 3.12.2-4build3 [645 kB] 137s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libexpat1 armhf 2.6.1-2 [65.9 kB] 137s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.12-minimal armhf 3.12.2-4build3 [1942 kB] 137s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.12-stdlib armhf 3.12.2-4build3 [1906 kB] 138s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.12-minimal armhf 3.12.2-4build3 [816 kB] 138s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main armhf parted armhf 3.6-3.1build2 [39.4 kB] 138s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblkid1 armhf 2.39.3-9ubuntu2 [160 kB] 138s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libselinux1 armhf 3.5-2build3 [70.5 kB] 138s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-dev all 255.4-1ubuntu5 [103 kB] 138s Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-timesyncd armhf 255.4-1ubuntu5 [36.0 kB] 138s Get:19 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-session-bus-common all 1.14.10-4ubuntu2 [80.3 kB] 138s Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libaudit-common all 1:3.1.2-2.1 [5674 B] 138s Get:21 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcap-ng0 armhf 0.8.4-2build1 [13.5 kB] 138s Get:22 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libaudit1 armhf 1:3.1.2-2.1 [44.3 kB] 138s Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam0g armhf 1.5.3-5ubuntu3 [62.0 kB] 138s Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main armhf liblzma5 armhf 5.6.0-0.2 [117 kB] 138s Get:25 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libldap2 armhf 2.6.7+dfsg-1~exp1ubuntu6 [172 kB] 138s Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libglib2.0-0t64 armhf 2.79.3-3ubuntu5 [1414 kB] 139s Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libvolume-key1 armhf 0.3.12-7build1 [38.4 kB] 139s Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgpgme11t64 armhf 1.18.0-4.1ubuntu3 [120 kB] 139s Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjcat1 armhf 0.2.0-2build2 [30.4 kB] 139s Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libarchive13t64 armhf 3.7.2-1.1ubuntu1 [330 kB] 139s Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main armhf fwupd armhf 1.9.15-1 [4349 kB] 140s Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ubuntu-pro-client-l10n armhf 31.2 [19.4 kB] 140s Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ubuntu-pro-client armhf 31.2 [216 kB] 140s Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.11 armhf 3.11.8-1build4 [589 kB] 141s Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.11-minimal armhf 3.11.8-1build4 [1795 kB] 141s Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.11-minimal armhf 3.11.8-1build4 [826 kB] 141s Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-4ubuntu4 [19.2 kB] 141s Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtext-iconv-perl armhf 1.7-8build2 [12.7 kB] 141s Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtext-charwidth-perl armhf 0.04-11build2 [8962 B] 141s Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl-base armhf 5.38.2-3.2 [1671 kB] 142s Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main armhf liblocale-gettext-perl armhf 1.07-6ubuntu3 [15.0 kB] 142s Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl-modules-5.38 all 5.38.2-3.2 [3110 kB] 143s Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-gdbm armhf 3.12.2-3ubuntu2 [17.1 kB] 143s Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main armhf man-db armhf 2.12.0-3build4 [1196 kB] 143s Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgdbm6t64 armhf 1.23-5.1 [30.3 kB] 143s Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgdbm-compat4t64 armhf 1.23-5.1 [6208 B] 143s Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libperl5.38t64 armhf 5.38.2-3.2 [4101 kB] 144s Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl armhf 5.38.2-3.2 [231 kB] 144s Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdb5.3t64 armhf 5.3.28+dfsg2-5build1 [661 kB] 144s Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.11-stdlib armhf 3.11.8-1build4 [1810 kB] 145s Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main armhf keyboxd armhf 2.4.4-2ubuntu15 [111 kB] 145s Get:52 http://ftpmaster.internal/ubuntu noble/main armhf libnpth0t64 armhf 1.6-3.1 [6940 B] 145s Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpgv armhf 2.4.4-2ubuntu15 [224 kB] 145s Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpg armhf 2.4.4-2ubuntu15 [524 kB] 145s Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpg-wks-client armhf 2.4.4-2ubuntu15 [87.4 kB] 145s Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gnupg-utils armhf 2.4.4-2ubuntu15 [158 kB] 145s Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpg-agent armhf 2.4.4-2ubuntu15 [235 kB] 145s Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpgsm armhf 2.4.4-2ubuntu15 [241 kB] 145s Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libreadline8t64 armhf 8.2-3.1 [129 kB] 145s Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gawk armhf 1:5.2.1-2build2 [415 kB] 146s Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main armhf fdisk armhf 2.39.3-9ubuntu2 [135 kB] 146s Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpgconf armhf 2.4.4-2ubuntu15 [115 kB] 146s Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dirmngr armhf 2.4.4-2ubuntu15 [346 kB] 146s Get:64 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gnupg all 2.4.4-2ubuntu15 [359 kB] 146s Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-apt armhf 2.7.6build1 [162 kB] 146s Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apt-utils armhf 2.7.13ubuntu1 [210 kB] 146s Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libapt-pkg6.0t64 armhf 2.7.13ubuntu1 [986 kB] 147s Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnettle8t64 armhf 3.9.1-2.2 [187 kB] 147s Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libhogweed6t64 armhf 3.9.1-2.2 [187 kB] 147s Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgnutls30t64 armhf 3.8.3-1.1ubuntu2 [1046 kB] 147s Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apt armhf 2.7.13ubuntu1 [1367 kB] 147s Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcurl3t64-gnutls armhf 8.5.0-2ubuntu7 [290 kB] 148s Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfwupd2 armhf 1.9.15-1 [123 kB] 148s Get:74 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpsl5t64 armhf 0.21.2-1.1 [55.7 kB] 148s Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main armhf wget armhf 1.21.4-1ubuntu2 [317 kB] 148s Get:76 http://ftpmaster.internal/ubuntu noble-proposed/main armhf tnftp armhf 20230507-2build1 [98.6 kB] 148s Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpcap0.8t64 armhf 1.10.4-4.1ubuntu1 [137 kB] 148s Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main armhf tcpdump armhf 4.99.4-3ubuntu2 [425 kB] 148s Get:79 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsystemd-shared armhf 255.4-1ubuntu5 [2009 kB] 149s Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-resolved armhf 255.4-1ubuntu5 [289 kB] 149s Get:81 http://ftpmaster.internal/ubuntu noble-proposed/main armhf sudo armhf 1.9.15p5-3ubuntu3 [936 kB] 149s Get:82 http://ftpmaster.internal/ubuntu noble-proposed/main armhf rsync armhf 3.2.7-1build1 [413 kB] 149s Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-cryptography armhf 41.0.7-4build2 [788 kB] 149s Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssh-sftp-server armhf 1:9.6p1-3ubuntu10 [35.5 kB] 149s Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssh-client armhf 1:9.6p1-3ubuntu10 [890 kB] 150s Get:86 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssh-server armhf 1:9.6p1-3ubuntu10 [503 kB] 150s Get:87 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libssl3t64 armhf 3.0.13-0ubuntu2 [1558 kB] 150s Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libudev1 armhf 255.4-1ubuntu5 [166 kB] 150s Get:89 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd armhf 255.4-1ubuntu5 [3502 kB] 151s Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main armhf udev armhf 255.4-1ubuntu5 [1852 kB] 152s Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-sysv armhf 255.4-1ubuntu5 [11.9 kB] 152s Get:92 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnss-systemd armhf 255.4-1ubuntu5 [148 kB] 152s Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-systemd armhf 255.4-1ubuntu5 [216 kB] 152s Get:94 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsystemd0 armhf 255.4-1ubuntu5 [410 kB] 152s Get:95 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-modules-bin armhf 1.5.3-5ubuntu3 [47.0 kB] 152s Get:96 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-modules armhf 1.5.3-5ubuntu3 [261 kB] 152s Get:97 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-runtime all 1.5.3-5ubuntu3 [40.8 kB] 152s Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-user-session armhf 1.14.10-4ubuntu2 [9962 B] 152s Get:99 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libapparmor1 armhf 4.0.0~beta2-0ubuntu3 [44.8 kB] 152s Get:100 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-bin armhf 1.14.10-4ubuntu2 [37.1 kB] 152s Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-system-bus-common all 1.14.10-4ubuntu2 [81.5 kB] 152s Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus armhf 1.14.10-4ubuntu2 [28.1 kB] 152s Get:103 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-daemon armhf 1.14.10-4ubuntu2 [109 kB] 153s Get:104 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdbus-1-3 armhf 1.14.10-4ubuntu2 [190 kB] 153s Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main armhf kmod armhf 31+20240202-2ubuntu4 [91.8 kB] 153s Get:106 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkmod2 armhf 31+20240202-2ubuntu4 [44.9 kB] 153s Get:107 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmount1 armhf 2.39.3-9ubuntu2 [171 kB] 153s Get:108 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libseccomp2 armhf 2.5.5-1ubuntu2 [49.5 kB] 153s Get:109 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libuuid1 armhf 2.39.3-9ubuntu2 [34.4 kB] 153s Get:110 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcryptsetup12 armhf 2:2.7.0-1ubuntu2 [238 kB] 153s Get:111 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfdisk1 armhf 2.39.3-9ubuntu2 [196 kB] 153s Get:112 http://ftpmaster.internal/ubuntu noble-proposed/main armhf mount armhf 2.39.3-9ubuntu2 [134 kB] 153s Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdevmapper1.02.1 armhf 2:1.02.185-3ubuntu2 [135 kB] 153s Get:114 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libparted2t64 armhf 3.6-3.1build2 [143 kB] 153s Get:115 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsqlite3-0 armhf 3.45.1-1ubuntu1 [599 kB] 153s Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main armhf pinentry-curses armhf 1.2.1-3ubuntu4 [36.7 kB] 153s Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsmartcols1 armhf 2.39.3-9ubuntu2 [117 kB] 153s Get:118 http://ftpmaster.internal/ubuntu noble-proposed/main armhf readline-common all 8.2-3.1 [56.4 kB] 153s Get:119 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-yaml armhf 6.0.1-2build1 [117 kB] 153s Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python-apt-common all 2.7.6build1 [19.8 kB] 153s Get:121 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-setuptools all 68.1.2-2ubuntu1 [396 kB] 153s Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-pkg-resources all 68.1.2-2ubuntu1 [168 kB] 153s Get:123 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dpkg armhf 1.22.6ubuntu4 [1229 kB] 154s Get:124 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-minimal armhf 3.12.2-0ubuntu1 [27.1 kB] 154s Get:125 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3 armhf 3.12.2-0ubuntu1 [24.1 kB] 154s Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3-stdlib armhf 3.12.2-0ubuntu1 [9802 B] 154s Get:127 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bsdextrautils armhf 2.39.3-9ubuntu2 [78.7 kB] 154s Get:128 http://ftpmaster.internal/ubuntu noble-proposed/main armhf groff-base armhf 1.23.0-3build1 [946 kB] 154s Get:129 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsasl2-2 armhf 2.1.28+dfsg1-4ubuntu4 [49.7 kB] 154s Get:130 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjson-glib-1.0-common all 1.8.0-2build1 [4210 B] 154s Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjson-glib-1.0-0 armhf 1.8.0-2build1 [61.2 kB] 154s Get:132 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libxml2 armhf 2.9.14+dfsg-1.3ubuntu2 [595 kB] 154s Get:133 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgudev-1.0-0 armhf 1:238-3ubuntu2 [13.6 kB] 154s Get:134 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libusb-1.0-0 armhf 2:1.0.27-1 [48.7 kB] 154s Get:135 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgusb2 armhf 0.4.8-1build1 [34.6 kB] 154s Get:136 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmbim-proxy armhf 1.31.2-0ubuntu2 [5748 B] 154s Get:137 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmbim-glib4 armhf 1.31.2-0ubuntu2 [216 kB] 154s Get:138 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmm-glib0 armhf 1.23.4-0ubuntu1 [214 kB] 154s Get:139 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpolkit-agent-1-0 armhf 124-1ubuntu1 [15.3 kB] 154s Get:140 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpolkit-gobject-1-0 armhf 124-1ubuntu1 [44.1 kB] 154s Get:141 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libqmi-proxy armhf 1.35.2-0ubuntu1 [5732 B] 154s Get:142 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libqrtr-glib0 armhf 1.2.2-1ubuntu3 [15.4 kB] 154s Get:143 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libqmi-glib5 armhf 1.35.2-0ubuntu1 [908 kB] 154s Get:144 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libxmlb2 armhf 0.3.15-1build1 [57.0 kB] 154s Get:145 http://ftpmaster.internal/ubuntu noble-proposed/main armhf shared-mime-info armhf 2.4-1build1 [470 kB] 154s Get:146 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbrotli1 armhf 1.1.0-2build1 [319 kB] 154s Get:147 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgssapi-krb5-2 armhf 1.20.1-5.1build3 [119 kB] 154s Get:148 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkrb5-3 armhf 1.20.1-5.1build3 [321 kB] 155s Get:149 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkrb5support0 armhf 1.20.1-5.1build3 [31.4 kB] 155s Get:150 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libk5crypto3 armhf 1.20.1-5.1build3 [78.6 kB] 155s Get:151 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcom-err2 armhf 1.47.0-2.4~exp1ubuntu2 [21.9 kB] 155s Get:152 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnghttp2-14 armhf 1.59.0-1build1 [68.1 kB] 155s Get:153 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libssh-4 armhf 0.10.6-2build1 [169 kB] 155s Get:154 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libibverbs1 armhf 50.0-2build1 [57.9 kB] 155s Get:155 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfido2-1 armhf 1.14.0-1build1 [75.8 kB] 155s Get:156 http://ftpmaster.internal/ubuntu noble-proposed/main armhf coreutils armhf 9.4-3ubuntu3 [1280 kB] 155s Get:157 http://ftpmaster.internal/ubuntu noble-proposed/main armhf debianutils armhf 5.17 [88.9 kB] 155s Get:158 http://ftpmaster.internal/ubuntu noble-proposed/main armhf util-linux armhf 2.39.3-9ubuntu2 [1216 kB] 155s Get:159 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc-bin armhf 2.39-0ubuntu6 [530 kB] 155s Get:160 http://ftpmaster.internal/ubuntu noble-proposed/main armhf curl armhf 8.5.0-2ubuntu7 [219 kB] 155s Get:161 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcurl4t64 armhf 8.5.0-2ubuntu7 [296 kB] 155s Get:162 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbpf1 armhf 1:1.3.0-2build1 [146 kB] 155s Get:163 http://ftpmaster.internal/ubuntu noble-proposed/main armhf iproute2 armhf 6.1.0-1ubuntu5 [1060 kB] 155s Get:164 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libelf1t64 armhf 0.190-1.1build2 [49.9 kB] 155s Get:165 http://ftpmaster.internal/ubuntu noble-proposed/main armhf lsof armhf 4.95.0-1build2 [248 kB] 155s Get:166 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnsl2 armhf 1.3.0-3build2 [36.5 kB] 155s Get:167 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtirpc-common all 1.3.4+ds-1.1 [8018 B] 155s Get:168 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtirpc3t64 armhf 1.3.4+ds-1.1 [73.2 kB] 155s Get:169 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-utils3 armhf 3.1.0-1build1 [16.9 kB] 155s Get:170 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-fs3 armhf 3.1.0-1build1 [34.4 kB] 155s Get:171 http://ftpmaster.internal/ubuntu noble-proposed/main armhf logsave armhf 1.47.0-2.4~exp1ubuntu2 [21.9 kB] 155s Get:172 http://ftpmaster.internal/ubuntu noble-proposed/main armhf initramfs-tools all 0.142ubuntu22 [9056 B] 155s Get:173 http://ftpmaster.internal/ubuntu noble-proposed/main armhf initramfs-tools-core all 0.142ubuntu22 [50.0 kB] 155s Get:174 http://ftpmaster.internal/ubuntu noble-proposed/main armhf e2fsprogs-l10n all 1.47.0-2.4~exp1ubuntu2 [5996 B] 155s Get:175 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libext2fs2t64 armhf 1.47.0-2.4~exp1ubuntu2 [201 kB] 155s Get:176 http://ftpmaster.internal/ubuntu noble-proposed/main armhf e2fsprogs armhf 1.47.0-2.4~exp1ubuntu2 [571 kB] 155s Get:177 http://ftpmaster.internal/ubuntu noble-proposed/main armhf btrfs-progs armhf 6.6.3-1.1build1 [852 kB] 155s Get:178 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dhcpcd-base armhf 1:10.0.6-1ubuntu2 [186 kB] 155s Get:179 http://ftpmaster.internal/ubuntu noble-proposed/main armhf initramfs-tools-bin armhf 0.142ubuntu22 [20.1 kB] 155s Get:180 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libreiserfscore0t64 armhf 1:3.6.27-7.1 [66.2 kB] 155s Get:181 http://ftpmaster.internal/ubuntu noble-proposed/main armhf file armhf 1:5.45-3 [21.1 kB] 156s Get:182 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmagic-mgc armhf 1:5.45-3 [307 kB] 156s Get:183 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmagic1t64 armhf 1:5.45-3 [81.4 kB] 156s Get:184 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnetplan1 armhf 1.0-1 [113 kB] 156s Get:185 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-netplan armhf 1.0-1 [22.5 kB] 156s Get:186 http://ftpmaster.internal/ubuntu noble-proposed/main armhf netplan-generator armhf 1.0-1 [58.7 kB] 156s Get:187 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-dbus armhf 1.3.2-5build2 [94.7 kB] 156s Get:188 http://ftpmaster.internal/ubuntu noble-proposed/main armhf netplan.io armhf 1.0-1 [64.3 kB] 156s Get:189 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-nvme3 armhf 3.1.0-1build1 [17.5 kB] 156s Get:190 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnvme1t64 armhf 1.8-3 [67.5 kB] 156s Get:191 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libplymouth5 armhf 24.004.60-1ubuntu4 [139 kB] 156s Get:192 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpng16-16t64 armhf 1.6.43-3 [166 kB] 156s Get:193 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bind9-host armhf 1:9.18.24-0ubuntu3 [47.4 kB] 156s Get:194 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bind9-dnsutils armhf 1:9.18.24-0ubuntu3 [149 kB] 156s Get:195 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bind9-libs armhf 1:9.18.24-0ubuntu3 [1148 kB] 156s Get:196 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libuv1t64 armhf 1.48.0-1.1 [82.9 kB] 156s Get:197 http://ftpmaster.internal/ubuntu noble-proposed/main armhf uuid-runtime armhf 2.39.3-9ubuntu2 [41.7 kB] 156s Get:198 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdebconfclient0 armhf 0.271ubuntu2 [10.8 kB] 156s Get:199 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsemanage-common all 3.5-1build4 [10.1 kB] 156s Get:200 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsemanage2 armhf 3.5-1build4 [84.5 kB] 156s Get:201 http://ftpmaster.internal/ubuntu noble-proposed/main armhf install-info armhf 7.1-3build1 [60.5 kB] 156s Get:202 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc-13-base armhf 13.2.0-19ubuntu1 [47.7 kB] 156s Get:203 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libss2 armhf 1.47.0-2.4~exp1ubuntu2 [14.7 kB] 156s Get:204 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dmsetup armhf 2:1.02.185-3ubuntu2 [81.1 kB] 156s Get:205 http://ftpmaster.internal/ubuntu noble-proposed/main armhf eject armhf 2.39.3-9ubuntu2 [43.2 kB] 156s Get:206 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gir1.2-girepository-2.0 armhf 1.79.1-1ubuntu6 [24.8 kB] 156s Get:207 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gir1.2-glib-2.0 armhf 2.79.3-3ubuntu5 [182 kB] 156s Get:208 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgirepository-1.0-1 armhf 1.79.1-1ubuntu6 [106 kB] 156s Get:209 http://ftpmaster.internal/ubuntu noble-proposed/main armhf krb5-locales all 1.20.1-5.1build3 [13.8 kB] 156s Get:210 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbsd0 armhf 0.12.1-1 [36.6 kB] 157s Get:211 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 157s Get:212 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libslang2 armhf 2.3.3-3build1 [478 kB] 157s Get:213 http://ftpmaster.internal/ubuntu noble-proposed/main armhf locales all 2.39-0ubuntu6 [4232 kB] 157s Get:214 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-gi armhf 3.47.0-3build1 [219 kB] 157s Get:215 http://ftpmaster.internal/ubuntu noble-proposed/main armhf vim-tiny armhf 2:9.1.0016-1ubuntu5 [665 kB] 157s Get:216 http://ftpmaster.internal/ubuntu noble-proposed/main armhf vim-common all 2:9.1.0016-1ubuntu5 [385 kB] 157s Get:217 http://ftpmaster.internal/ubuntu noble/main armhf xdg-user-dirs armhf 0.18-1 [17.3 kB] 157s Get:218 http://ftpmaster.internal/ubuntu noble-proposed/main armhf xxd armhf 2:9.1.0016-1ubuntu5 [62.4 kB] 157s Get:219 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apparmor armhf 4.0.0~beta2-0ubuntu3 [557 kB] 158s Get:220 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ftp all 20230507-2build1 [4724 B] 158s Get:221 http://ftpmaster.internal/ubuntu noble-proposed/main armhf inetutils-telnet armhf 2:2.5-3ubuntu3 [90.7 kB] 158s Get:222 http://ftpmaster.internal/ubuntu noble-proposed/main armhf info armhf 7.1-3build1 [127 kB] 158s Get:223 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libxmuu1 armhf 2:1.1.3-3build1 [8004 B] 158s Get:224 http://ftpmaster.internal/ubuntu noble-proposed/main armhf lshw armhf 02.19.git.2021.06.19.996aaad9c7-2build2 [310 kB] 158s Get:225 http://ftpmaster.internal/ubuntu noble-proposed/main armhf mtr-tiny armhf 0.95-1.1build1 [51.7 kB] 158s Get:226 http://ftpmaster.internal/ubuntu noble-proposed/main armhf plymouth-theme-ubuntu-text armhf 24.004.60-1ubuntu4 [9828 B] 158s Get:227 http://ftpmaster.internal/ubuntu noble-proposed/main armhf plymouth armhf 24.004.60-1ubuntu4 [143 kB] 158s Get:228 http://ftpmaster.internal/ubuntu noble-proposed/main armhf psmisc armhf 23.7-1 [176 kB] 158s Get:229 http://ftpmaster.internal/ubuntu noble-proposed/main armhf telnet all 0.17+2.5-3ubuntu3 [3682 B] 158s Get:230 http://ftpmaster.internal/ubuntu noble-proposed/main armhf xz-utils armhf 5.6.0-0.2 [271 kB] 158s Get:231 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bolt armhf 0.9.6-2build1 [138 kB] 158s Get:232 http://ftpmaster.internal/ubuntu noble-proposed/main armhf cryptsetup-bin armhf 2:2.7.0-1ubuntu2 [214 kB] 158s Get:233 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dpkg-dev all 1.22.6ubuntu4 [1074 kB] 158s Get:234 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdpkg-perl all 1.22.6ubuntu4 [268 kB] 158s Get:235 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gnupg-l10n all 2.4.4-2ubuntu15 [65.8 kB] 158s Get:236 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ibverbs-providers armhf 50.0-2build1 [27.4 kB] 158s Get:237 http://ftpmaster.internal/ubuntu noble-proposed/main armhf jq armhf 1.7.1-3 [65.2 kB] 158s Get:238 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjq1 armhf 1.7.1-3 [156 kB] 158s Get:239 http://ftpmaster.internal/ubuntu noble/main armhf libatm1t64 armhf 1:2.5.1-5.1 [20.0 kB] 158s Get:240 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-crypto3 armhf 3.1.0-1build1 [20.3 kB] 158s Get:241 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-loop3 armhf 3.1.0-1build1 [6502 B] 158s Get:242 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-mdraid3 armhf 3.1.0-1build1 [13.3 kB] 158s Get:243 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-part3 armhf 3.1.0-1build1 [16.4 kB] 158s Get:244 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-swap3 armhf 3.1.0-1build1 [8894 B] 158s Get:245 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev3 armhf 3.1.0-1build1 [42.9 kB] 158s Get:246 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-9build1 [82.3 kB] 158s Get:247 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libftdi1-2 armhf 1.5-6build4 [25.7 kB] 158s Get:248 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libldap-common all 2.6.7+dfsg-1~exp1ubuntu6 [31.3 kB] 158s Get:249 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsasl2-modules armhf 2.1.28+dfsg1-4ubuntu4 [61.4 kB] 158s Get:250 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-lib2to3 all 3.12.2-3ubuntu2 [79.3 kB] 158s Get:251 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-markupsafe armhf 2.1.5-1build1 [12.1 kB] 158s Get:252 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-openssl all 24.0.0-4 [47.9 kB] 158s Get:253 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-pyrsistent armhf 0.20.0-1build1 [53.0 kB] 158s Get:254 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-typing-extensions all 4.10.0-1 [60.7 kB] 158s Get:255 http://ftpmaster.internal/ubuntu noble-proposed/main armhf kpartx armhf 0.9.4-5ubuntu4 [31.4 kB] 164s Preconfiguring packages ... 165s Fetched 87.1 MB in 24s (3689 kB/s) 165s (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.) 165s Preparing to unpack .../bsdutils_1%3a2.39.3-9ubuntu2_armhf.deb ... 165s Unpacking bsdutils (1:2.39.3-9ubuntu2) over (1:2.39.3-6ubuntu2) ... 166s Setting up bsdutils (1:2.39.3-9ubuntu2) ... 166s (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.) 166s Preparing to unpack .../gcc-14-base_14-20240315-1ubuntu1_armhf.deb ... 166s Unpacking gcc-14-base:armhf (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ... 166s Setting up gcc-14-base:armhf (14-20240315-1ubuntu1) ... 166s (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.) 166s Preparing to unpack .../libgcc-s1_14-20240315-1ubuntu1_armhf.deb ... 166s Unpacking libgcc-s1:armhf (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ... 166s Setting up libgcc-s1:armhf (14-20240315-1ubuntu1) ... 166s (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.) 166s Preparing to unpack .../libstdc++6_14-20240315-1ubuntu1_armhf.deb ... 167s Unpacking libstdc++6:armhf (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ... 167s Setting up libstdc++6:armhf (14-20240315-1ubuntu1) ... 167s (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.) 167s Preparing to unpack .../libc6_2.39-0ubuntu6_armhf.deb ... 167s Unpacking libc6:armhf (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 168s Setting up libc6:armhf (2.39-0ubuntu6) ... 170s (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.) 170s Preparing to unpack .../openssl_3.0.13-0ubuntu2_armhf.deb ... 170s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 171s Preparing to unpack .../zlib1g_1%3a1.3.dfsg-3.1ubuntu1_armhf.deb ... 171s Unpacking zlib1g:armhf (1:1.3.dfsg-3.1ubuntu1) over (1:1.3.dfsg-3ubuntu1) ... 171s Setting up zlib1g:armhf (1:1.3.dfsg-3.1ubuntu1) ... 171s (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.) 171s Preparing to unpack .../0-librtmp1_2.4+20151223.gitfa8646d.1-2build6_armhf.deb ... 171s Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build6) over (2.4+20151223.gitfa8646d.1-2build4) ... 171s Preparing to unpack .../1-python3.12_3.12.2-4build3_armhf.deb ... 172s Unpacking python3.12 (3.12.2-4build3) over (3.12.2-1) ... 172s Preparing to unpack .../2-libexpat1_2.6.1-2_armhf.deb ... 172s Unpacking libexpat1:armhf (2.6.1-2) over (2.6.0-1) ... 172s Preparing to unpack .../3-python3.12-minimal_3.12.2-4build3_armhf.deb ... 172s Unpacking python3.12-minimal (3.12.2-4build3) over (3.12.2-1) ... 173s Preparing to unpack .../4-libpython3.12-stdlib_3.12.2-4build3_armhf.deb ... 173s Unpacking libpython3.12-stdlib:armhf (3.12.2-4build3) over (3.12.2-1) ... 174s Preparing to unpack .../5-libpython3.12-minimal_3.12.2-4build3_armhf.deb ... 174s Unpacking libpython3.12-minimal:armhf (3.12.2-4build3) over (3.12.2-1) ... 175s Preparing to unpack .../6-parted_3.6-3.1build2_armhf.deb ... 175s Unpacking parted (3.6-3.1build2) over (3.6-3) ... 176s (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.) 176s Removing libparted2:armhf (3.6-3) ... 176s (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 ... 58612 files and directories currently installed.) 176s Preparing to unpack .../libblkid1_2.39.3-9ubuntu2_armhf.deb ... 176s Unpacking libblkid1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 176s Setting up libblkid1:armhf (2.39.3-9ubuntu2) ... 176s (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 ... 58612 files and directories currently installed.) 176s Preparing to unpack .../libselinux1_3.5-2build3_armhf.deb ... 176s Unpacking libselinux1:armhf (3.5-2build3) over (3.5-2build1) ... 177s Setting up libselinux1:armhf (3.5-2build3) ... 177s (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 ... 58612 files and directories currently installed.) 177s Preparing to unpack .../systemd-dev_255.4-1ubuntu5_all.deb ... 177s Unpacking systemd-dev (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 177s Preparing to unpack .../systemd-timesyncd_255.4-1ubuntu5_armhf.deb ... 177s Unpacking systemd-timesyncd (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 177s Preparing to unpack .../dbus-session-bus-common_1.14.10-4ubuntu2_all.deb ... 177s Unpacking dbus-session-bus-common (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 178s Preparing to unpack .../libaudit-common_1%3a3.1.2-2.1_all.deb ... 178s Unpacking libaudit-common (1:3.1.2-2.1) over (1:3.1.2-2) ... 178s Setting up libaudit-common (1:3.1.2-2.1) ... 178s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58612 files and directories currently installed.) 178s Preparing to unpack .../libcap-ng0_0.8.4-2build1_armhf.deb ... 178s Unpacking libcap-ng0:armhf (0.8.4-2build1) over (0.8.4-2) ... 179s Setting up libcap-ng0:armhf (0.8.4-2build1) ... 179s (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 ... 58612 files and directories currently installed.) 179s Preparing to unpack .../libaudit1_1%3a3.1.2-2.1_armhf.deb ... 179s Unpacking libaudit1:armhf (1:3.1.2-2.1) over (1:3.1.2-2) ... 179s Setting up libaudit1:armhf (1:3.1.2-2.1) ... 179s (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 ... 58612 files and directories currently installed.) 179s Preparing to unpack .../libpam0g_1.5.3-5ubuntu3_armhf.deb ... 179s Unpacking libpam0g:armhf (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ... 179s Setting up libpam0g:armhf (1.5.3-5ubuntu3) ... 180s (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 ... 58612 files and directories currently installed.) 180s Preparing to unpack .../liblzma5_5.6.0-0.2_armhf.deb ... 180s Unpacking liblzma5:armhf (5.6.0-0.2) over (5.4.5-0.3) ... 181s Setting up liblzma5:armhf (5.6.0-0.2) ... 181s (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 ... 58612 files and directories currently installed.) 181s Preparing to unpack .../libldap2_2.6.7+dfsg-1~exp1ubuntu6_armhf.deb ... 181s Unpacking libldap2:armhf (2.6.7+dfsg-1~exp1ubuntu6) over (2.6.7+dfsg-1~exp1ubuntu1) ... 182s (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 ... 58612 files and directories currently installed.) 182s Removing udisks2 (2.10.1-1ubuntu2) ... 183s dpkg: libglib2.0-0:armhf: dependency problems, but removing anyway as you requested: 183s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 183s python3-gi depends on libglib2.0-0 (>= 2.77.0). 183s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 183s netplan.io depends on libglib2.0-0 (>= 2.70.0). 183s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 183s libxmlb2:armhf depends on libglib2.0-0 (>= 2.54.0). 183s libvolume-key1:armhf depends on libglib2.0-0 (>= 2.18.0). 183s libudisks2-0:armhf depends on libglib2.0-0 (>= 2.75.3). 183s libqrtr-glib0:armhf depends on libglib2.0-0 (>= 2.56). 183s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 183s libqmi-glib5:armhf depends on libglib2.0-0 (>= 2.54.0). 183s libpolkit-gobject-1-0:armhf depends on libglib2.0-0 (>= 2.38.0). 183s libpolkit-agent-1-0:armhf depends on libglib2.0-0 (>= 2.38.0). 183s libnetplan0:armhf depends on libglib2.0-0 (>= 2.75.3). 183s libmm-glib0:armhf depends on libglib2.0-0 (>= 2.62.0). 183s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 183s libmbim-glib4:armhf depends on libglib2.0-0 (>= 2.56). 183s libjson-glib-1.0-0:armhf depends on libglib2.0-0 (>= 2.75.3). 183s libjcat1:armhf depends on libglib2.0-0 (>= 2.75.3). 183s libgusb2:armhf depends on libglib2.0-0 (>= 2.75.3). 183s libgudev-1.0-0:armhf depends on libglib2.0-0 (>= 2.38.0). 183s libgirepository-1.0-1:armhf depends on libglib2.0-0 (>= 2.79.0). 183s libfwupd2:armhf depends on libglib2.0-0 (>= 2.79.0). 183s libblockdev3:armhf depends on libglib2.0-0 (>= 2.42.2). 183s libblockdev-utils3:armhf depends on libglib2.0-0 (>= 2.75.3). 183s libblockdev-swap3:armhf depends on libglib2.0-0 (>= 2.42.2). 183s libblockdev-part3:armhf depends on libglib2.0-0 (>= 2.42.2). 183s libblockdev-nvme3:armhf depends on libglib2.0-0 (>= 2.42.2). 183s libblockdev-mdraid3:armhf depends on libglib2.0-0 (>= 2.42.2). 183s libblockdev-loop3:armhf depends on libglib2.0-0 (>= 2.42.2). 183s libblockdev-fs3:armhf depends on libglib2.0-0 (>= 2.42.2). 183s libblockdev-crypto3:armhf depends on libglib2.0-0 (>= 2.42.2). 183s gir1.2-glib-2.0:armhf depends on libglib2.0-0 (= 2.79.2-1~ubuntu1). 183s fwupd depends on libglib2.0-0 (>= 2.79.0). 183s bolt depends on libglib2.0-0 (>= 2.56.0). 183s 183s Removing libglib2.0-0:armhf (2.79.2-1~ubuntu1) ... 183s Selecting previously unselected package libglib2.0-0t64:armhf. 183s (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 ... 58560 files and directories currently installed.) 183s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_armhf.deb ... 183s 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... 183s removed '/var/lib/dpkg/info/libglib2.0-0:armhf.postrm' 183s Unpacking libglib2.0-0t64:armhf (2.79.3-3ubuntu5) ... 184s Preparing to unpack .../libvolume-key1_0.3.12-7build1_armhf.deb ... 184s Unpacking libvolume-key1:armhf (0.3.12-7build1) over (0.3.12-5build2) ... 184s dpkg: libgpgme11:armhf: dependency problems, but removing anyway as you requested: 184s libjcat1:armhf depends on libgpgme11 (>= 1.2.0). 184s 184s (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 ... 58585 files and directories currently installed.) 184s Removing libgpgme11:armhf (1.18.0-4ubuntu1) ... 184s Selecting previously unselected package libgpgme11t64:armhf. 184s (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 ... 58579 files and directories currently installed.) 184s Preparing to unpack .../libgpgme11t64_1.18.0-4.1ubuntu3_armhf.deb ... 184s Unpacking libgpgme11t64:armhf (1.18.0-4.1ubuntu3) ... 184s Preparing to unpack .../libjcat1_0.2.0-2build2_armhf.deb ... 184s Unpacking libjcat1:armhf (0.2.0-2build2) over (0.2.0-2) ... 185s dpkg: libarchive13:armhf: dependency problems, but removing anyway as you requested: 185s fwupd depends on libarchive13 (>= 3.2.1). 185s 185s (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 ... 58586 files and directories currently installed.) 185s Removing libarchive13:armhf (3.7.2-1ubuntu2) ... 185s Selecting previously unselected package libarchive13t64:armhf. 185s (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 ... 58580 files and directories currently installed.) 185s Preparing to unpack .../00-libarchive13t64_3.7.2-1.1ubuntu1_armhf.deb ... 185s Unpacking libarchive13t64:armhf (3.7.2-1.1ubuntu1) ... 185s Preparing to unpack .../01-fwupd_1.9.15-1_armhf.deb ... 186s Unpacking fwupd (1.9.15-1) over (1.9.14-1) ... 187s Preparing to unpack .../02-ubuntu-pro-client-l10n_31.2_armhf.deb ... 187s Unpacking ubuntu-pro-client-l10n (31.2) over (31.1) ... 187s Preparing to unpack .../03-ubuntu-pro-client_31.2_armhf.deb ... 189s Unpacking ubuntu-pro-client (31.2) over (31.1) ... 190s Preparing to unpack .../04-python3.11_3.11.8-1build4_armhf.deb ... 190s Unpacking python3.11 (3.11.8-1build4) over (3.11.8-1) ... 190s Preparing to unpack .../05-python3.11-minimal_3.11.8-1build4_armhf.deb ... 190s Unpacking python3.11-minimal (3.11.8-1build4) over (3.11.8-1) ... 191s Preparing to unpack .../06-libpython3.11-minimal_3.11.8-1build4_armhf.deb ... 191s Unpacking libpython3.11-minimal:armhf (3.11.8-1build4) over (3.11.8-1) ... 192s Preparing to unpack .../07-libsasl2-modules-db_2.1.28+dfsg1-4ubuntu4_armhf.deb ... 192s Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg1-4ubuntu4) over (2.1.28+dfsg1-4) ... 192s Preparing to unpack .../08-libtext-iconv-perl_1.7-8build2_armhf.deb ... 192s Unpacking libtext-iconv-perl:armhf (1.7-8build2) over (1.7-8build1) ... 192s Preparing to unpack .../09-libtext-charwidth-perl_0.04-11build2_armhf.deb ... 192s Unpacking libtext-charwidth-perl:armhf (0.04-11build2) over (0.04-11build1) ... 192s Preparing to unpack .../10-perl-base_5.38.2-3.2_armhf.deb ... 192s Unpacking perl-base (5.38.2-3.2) over (5.38.2-3) ... 194s Setting up perl-base (5.38.2-3.2) ... 195s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58587 files and directories currently installed.) 195s Preparing to unpack .../liblocale-gettext-perl_1.07-6ubuntu3_armhf.deb ... 195s Unpacking liblocale-gettext-perl (1.07-6ubuntu3) over (1.07-6build1) ... 195s Preparing to unpack .../perl-modules-5.38_5.38.2-3.2_all.deb ... 195s Unpacking perl-modules-5.38 (5.38.2-3.2) over (5.38.2-3) ... 198s Preparing to unpack .../python3-gdbm_3.12.2-3ubuntu2_armhf.deb ... 198s Unpacking python3-gdbm:armhf (3.12.2-3ubuntu2) over (3.11.5-1) ... 198s Preparing to unpack .../man-db_2.12.0-3build4_armhf.deb ... 198s Unpacking man-db (2.12.0-3build4) over (2.12.0-3) ... 199s dpkg: libgdbm-compat4:armhf: dependency problems, but removing anyway as you requested: 199s libperl5.38:armhf depends on libgdbm-compat4 (>= 1.18-3). 199s 199s (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 ... 58587 files and directories currently installed.) 199s Removing libgdbm-compat4:armhf (1.23-5) ... 199s dpkg: libgdbm6:armhf: dependency problems, but removing anyway as you requested: 199s libperl5.38:armhf depends on libgdbm6 (>= 1.21). 199s 200s Removing libgdbm6:armhf (1.23-5) ... 200s Selecting previously unselected package libgdbm6t64:armhf. 200s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58577 files and directories currently installed.) 200s Preparing to unpack .../libgdbm6t64_1.23-5.1_armhf.deb ... 200s Unpacking libgdbm6t64:armhf (1.23-5.1) ... 200s Selecting previously unselected package libgdbm-compat4t64:armhf. 200s Preparing to unpack .../libgdbm-compat4t64_1.23-5.1_armhf.deb ... 200s Unpacking libgdbm-compat4t64:armhf (1.23-5.1) ... 201s dpkg: libperl5.38:armhf: dependency problems, but removing anyway as you requested: 201s perl depends on libperl5.38 (= 5.38.2-3). 201s 201s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58589 files and directories currently installed.) 201s Removing libperl5.38:armhf (5.38.2-3) ... 201s Selecting previously unselected package libperl5.38t64:armhf. 201s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58070 files and directories currently installed.) 201s Preparing to unpack .../libperl5.38t64_5.38.2-3.2_armhf.deb ... 201s Unpacking libperl5.38t64:armhf (5.38.2-3.2) ... 203s Preparing to unpack .../perl_5.38.2-3.2_armhf.deb ... 203s Unpacking perl (5.38.2-3.2) over (5.38.2-3) ... 203s dpkg: libdb5.3:armhf: dependency problems, but removing anyway as you requested: 203s libpython3.11-stdlib:armhf depends on libdb5.3. 203s libpam-modules:armhf depends on libdb5.3. 203s iproute2 depends on libdb5.3. 203s apt-utils depends on libdb5.3. 203s 204s (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 ... 58589 files and directories currently installed.) 204s Removing libdb5.3:armhf (5.3.28+dfsg2-4) ... 204s Selecting previously unselected package libdb5.3t64:armhf. 204s (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 ... 58583 files and directories currently installed.) 204s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-5build1_armhf.deb ... 204s Unpacking libdb5.3t64:armhf (5.3.28+dfsg2-5build1) ... 204s Preparing to unpack .../libpython3.11-stdlib_3.11.8-1build4_armhf.deb ... 205s Unpacking libpython3.11-stdlib:armhf (3.11.8-1build4) over (3.11.8-1) ... 206s Preparing to unpack .../keyboxd_2.4.4-2ubuntu15_armhf.deb ... 206s Unpacking keyboxd (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 206s dpkg: libnpth0:armhf: dependency problems, but removing anyway as you requested: 206s gpgv depends on libnpth0 (>= 0.90). 206s gpgsm depends on libnpth0 (>= 0.90). 206s gpg-agent depends on libnpth0 (>= 0.90). 206s gpg depends on libnpth0 (>= 0.90). 206s dirmngr depends on libnpth0 (>= 0.90). 206s 206s (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 ... 58587 files and directories currently installed.) 206s Removing libnpth0:armhf (1.6-3build2) ... 207s Selecting previously unselected package libnpth0t64:armhf. 207s (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 ... 58582 files and directories currently installed.) 207s Preparing to unpack .../libnpth0t64_1.6-3.1_armhf.deb ... 207s Unpacking libnpth0t64:armhf (1.6-3.1) ... 207s Setting up libnpth0t64:armhf (1.6-3.1) ... 207s (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 ... 58588 files and directories currently installed.) 207s Preparing to unpack .../gpgv_2.4.4-2ubuntu15_armhf.deb ... 207s Unpacking gpgv (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 207s Setting up gpgv (2.4.4-2ubuntu15) ... 208s (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 ... 58588 files and directories currently installed.) 208s Preparing to unpack .../gpg_2.4.4-2ubuntu15_armhf.deb ... 208s Unpacking gpg (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 208s Preparing to unpack .../gpg-wks-client_2.4.4-2ubuntu15_armhf.deb ... 208s Unpacking gpg-wks-client (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 208s Preparing to unpack .../gnupg-utils_2.4.4-2ubuntu15_armhf.deb ... 208s Unpacking gnupg-utils (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 208s Preparing to unpack .../gpg-agent_2.4.4-2ubuntu15_armhf.deb ... 208s Unpacking gpg-agent (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 209s Preparing to unpack .../gpgsm_2.4.4-2ubuntu15_armhf.deb ... 209s Unpacking gpgsm (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 209s dpkg: libreadline8:armhf: dependency problems, but removing anyway as you requested: 209s gpgconf depends on libreadline8 (>= 6.0). 209s gawk depends on libreadline8 (>= 6.0). 209s fdisk depends on libreadline8 (>= 6.0). 209s 209s (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 ... 58588 files and directories currently installed.) 209s Removing libreadline8:armhf (8.2-3) ... 209s Selecting previously unselected package libreadline8t64:armhf. 209s (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 ... 58576 files and directories currently installed.) 209s Preparing to unpack .../libreadline8t64_8.2-3.1_armhf.deb ... 209s Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64' 209s 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' 209s Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64' 209s 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' 209s Unpacking libreadline8t64:armhf (8.2-3.1) ... 209s Setting up libreadline8t64:armhf (8.2-3.1) ... 210s (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 ... 58596 files and directories currently installed.) 210s Preparing to unpack .../0-gawk_1%3a5.2.1-2build2_armhf.deb ... 210s Unpacking gawk (1:5.2.1-2build2) over (1:5.2.1-2) ... 210s Preparing to unpack .../1-fdisk_2.39.3-9ubuntu2_armhf.deb ... 210s Unpacking fdisk (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 210s Preparing to unpack .../2-gpgconf_2.4.4-2ubuntu15_armhf.deb ... 210s Unpacking gpgconf (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 211s Preparing to unpack .../3-dirmngr_2.4.4-2ubuntu15_armhf.deb ... 211s Unpacking dirmngr (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 211s Preparing to unpack .../4-gnupg_2.4.4-2ubuntu15_all.deb ... 211s Unpacking gnupg (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 211s Preparing to unpack .../5-python3-apt_2.7.6build1_armhf.deb ... 212s Unpacking python3-apt (2.7.6build1) over (2.7.6) ... 212s Preparing to unpack .../6-apt-utils_2.7.13ubuntu1_armhf.deb ... 212s Unpacking apt-utils (2.7.13ubuntu1) over (2.7.12) ... 212s dpkg: libapt-pkg6.0:armhf: dependency problems, but removing anyway as you requested: 212s apt depends on libapt-pkg6.0 (>= 2.7.12). 212s 212s (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 ... 58594 files and directories currently installed.) 212s Removing libapt-pkg6.0:armhf (2.7.12) ... 212s dpkg: libnettle8:armhf: dependency problems, but removing anyway as you requested: 212s libhogweed6:armhf depends on libnettle8. 212s libgnutls30:armhf depends on libnettle8 (>= 3.9~). 212s libcurl3-gnutls:armhf depends on libnettle8. 212s 212s Removing libnettle8:armhf (3.9.1-2) ... 213s Selecting previously unselected package libapt-pkg6.0t64:armhf. 213s (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 ... 58538 files and directories currently installed.) 213s Preparing to unpack .../libapt-pkg6.0t64_2.7.13ubuntu1_armhf.deb ... 213s Unpacking libapt-pkg6.0t64:armhf (2.7.13ubuntu1) ... 213s Setting up libapt-pkg6.0t64:armhf (2.7.13ubuntu1) ... 213s Selecting previously unselected package libnettle8t64:armhf. 213s (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 ... 58588 files and directories currently installed.) 213s Preparing to unpack .../libnettle8t64_3.9.1-2.2_armhf.deb ... 213s Unpacking libnettle8t64:armhf (3.9.1-2.2) ... 214s Setting up libnettle8t64:armhf (3.9.1-2.2) ... 214s dpkg: libhogweed6:armhf: dependency problems, but removing anyway as you requested: 214s libgnutls30:armhf depends on libhogweed6 (>= 3.6). 214s 214s (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 ... 58596 files and directories currently installed.) 214s Removing libhogweed6:armhf (3.9.1-2) ... 214s Selecting previously unselected package libhogweed6t64:armhf. 214s (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 ... 58591 files and directories currently installed.) 214s Preparing to unpack .../libhogweed6t64_3.9.1-2.2_armhf.deb ... 214s Unpacking libhogweed6t64:armhf (3.9.1-2.2) ... 214s Setting up libhogweed6t64:armhf (3.9.1-2.2) ... 214s dpkg: libgnutls30:armhf: dependency problems, but removing anyway as you requested: 214s libcurl3-gnutls:armhf depends on libgnutls30 (>= 3.8.2). 214s apt depends on libgnutls30 (>= 3.8.1). 214s 215s (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 ... 58597 files and directories currently installed.) 215s Removing libgnutls30:armhf (3.8.3-1ubuntu1) ... 215s Selecting previously unselected package libgnutls30t64:armhf. 215s (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 ... 58588 files and directories currently installed.) 215s Preparing to unpack .../libgnutls30t64_3.8.3-1.1ubuntu2_armhf.deb ... 215s Unpacking libgnutls30t64:armhf (3.8.3-1.1ubuntu2) ... 215s Setting up libgnutls30t64:armhf (3.8.3-1.1ubuntu2) ... 215s (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 ... 58616 files and directories currently installed.) 215s Preparing to unpack .../apt_2.7.13ubuntu1_armhf.deb ... 216s Unpacking apt (2.7.13ubuntu1) over (2.7.12) ... 216s Setting up apt (2.7.13ubuntu1) ... 219s dpkg: libcurl3-gnutls:armhf: dependency problems, but removing anyway as you requested: 219s libfwupd2:armhf depends on libcurl3-gnutls (>= 7.63.0). 219s 219s (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 ... 58616 files and directories currently installed.) 219s Removing libcurl3-gnutls:armhf (8.5.0-2ubuntu2) ... 219s Selecting previously unselected package libcurl3t64-gnutls:armhf. 219s (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.) 219s Preparing to unpack .../libcurl3t64-gnutls_8.5.0-2ubuntu7_armhf.deb ... 219s Unpacking libcurl3t64-gnutls:armhf (8.5.0-2ubuntu7) ... 220s Preparing to unpack .../libfwupd2_1.9.15-1_armhf.deb ... 220s Unpacking libfwupd2:armhf (1.9.15-1) over (1.9.14-1) ... 220s dpkg: libpsl5:armhf: dependency problems, but removing anyway as you requested: 220s wget depends on libpsl5 (>= 0.16.0). 220s libcurl4:armhf depends on libpsl5 (>= 0.16.0). 220s 220s (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 ... 58616 files and directories currently installed.) 220s Removing libpsl5:armhf (0.21.2-1build1) ... 220s Selecting previously unselected package libpsl5t64:armhf. 220s (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 ... 58611 files and directories currently installed.) 220s Preparing to unpack .../libpsl5t64_0.21.2-1.1_armhf.deb ... 220s Unpacking libpsl5t64:armhf (0.21.2-1.1) ... 220s Preparing to unpack .../wget_1.21.4-1ubuntu2_armhf.deb ... 220s Unpacking wget (1.21.4-1ubuntu2) over (1.21.4-1ubuntu1) ... 221s Preparing to unpack .../tnftp_20230507-2build1_armhf.deb ... 221s Unpacking tnftp (20230507-2build1) over (20230507-2) ... 221s dpkg: libpcap0.8:armhf: dependency problems, but removing anyway as you requested: 221s tcpdump depends on libpcap0.8 (>= 1.9.1). 221s 221s (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 ... 58617 files and directories currently installed.) 221s Removing libpcap0.8:armhf (1.10.4-4ubuntu3) ... 221s Selecting previously unselected package libpcap0.8t64:armhf. 221s (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 ... 58606 files and directories currently installed.) 221s Preparing to unpack .../0-libpcap0.8t64_1.10.4-4.1ubuntu1_armhf.deb ... 221s Unpacking libpcap0.8t64:armhf (1.10.4-4.1ubuntu1) ... 221s Preparing to unpack .../1-tcpdump_4.99.4-3ubuntu2_armhf.deb ... 221s Unpacking tcpdump (4.99.4-3ubuntu2) over (4.99.4-3ubuntu1) ... 222s Preparing to unpack .../2-libsystemd-shared_255.4-1ubuntu5_armhf.deb ... 222s Unpacking libsystemd-shared:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 222s Preparing to unpack .../3-systemd-resolved_255.4-1ubuntu5_armhf.deb ... 222s Unpacking systemd-resolved (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 223s Preparing to unpack .../4-sudo_1.9.15p5-3ubuntu3_armhf.deb ... 223s Unpacking sudo (1.9.15p5-3ubuntu3) over (1.9.15p5-3ubuntu1) ... 223s Preparing to unpack .../5-rsync_3.2.7-1build1_armhf.deb ... 223s Unpacking rsync (3.2.7-1build1) over (3.2.7-1) ... 223s Preparing to unpack .../6-python3-cryptography_41.0.7-4build2_armhf.deb ... 224s Unpacking python3-cryptography (41.0.7-4build2) over (41.0.7-3) ... 224s Preparing to unpack .../7-openssh-sftp-server_1%3a9.6p1-3ubuntu10_armhf.deb ... 224s Unpacking openssh-sftp-server (1:9.6p1-3ubuntu10) over (1:9.6p1-3ubuntu2) ... 224s Preparing to unpack .../8-openssh-client_1%3a9.6p1-3ubuntu10_armhf.deb ... 224s Unpacking openssh-client (1:9.6p1-3ubuntu10) over (1:9.6p1-3ubuntu2) ... 225s Preparing to unpack .../9-openssh-server_1%3a9.6p1-3ubuntu10_armhf.deb ... 225s Unpacking openssh-server (1:9.6p1-3ubuntu10) over (1:9.6p1-3ubuntu2) ... 226s (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 47475 files and directories currently installed.) 246s Preparing to unpack .../libuuid1_2.39.3-9ubuntu2_armhf.deb ... 246s Unpacking libuuid1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 246s Setting up libuuid1:armhf (2.39.3-9ubuntu2) ... 246s (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 ... 47475 files and directories currently installed.) 246s Preparing to unpack .../0-libcryptsetup12_2%3a2.7.0-1ubuntu2_armhf.deb ... 246s Unpacking libcryptsetup12:armhf (2:2.7.0-1ubuntu2) over (2:2.7.0-1ubuntu1) ... 247s Preparing to unpack .../1-libfdisk1_2.39.3-9ubuntu2_armhf.deb ... 247s Unpacking libfdisk1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 247s Preparing to unpack .../2-mount_2.39.3-9ubuntu2_armhf.deb ... 247s Unpacking mount (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 247s Preparing to unpack .../3-libdevmapper1.02.1_2%3a1.02.185-3ubuntu2_armhf.deb ... 247s Unpacking libdevmapper1.02.1:armhf (2:1.02.185-3ubuntu2) over (2:1.02.185-3ubuntu1) ... 247s Selecting previously unselected package libparted2t64:armhf. 247s Preparing to unpack .../4-libparted2t64_3.6-3.1build2_armhf.deb ... 247s Unpacking libparted2t64:armhf (3.6-3.1build2) ... 247s Preparing to unpack .../5-libsqlite3-0_3.45.1-1ubuntu1_armhf.deb ... 247s Unpacking libsqlite3-0:armhf (3.45.1-1ubuntu1) over (3.45.1-1) ... 247s Preparing to unpack .../6-pinentry-curses_1.2.1-3ubuntu4_armhf.deb ... 247s Unpacking pinentry-curses (1.2.1-3ubuntu4) over (1.2.1-3ubuntu1) ... 247s Preparing to unpack .../7-libsmartcols1_2.39.3-9ubuntu2_armhf.deb ... 247s Unpacking libsmartcols1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 248s Setting up libsmartcols1:armhf (2.39.3-9ubuntu2) ... 248s (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 ... 47482 files and directories currently installed.) 248s Preparing to unpack .../0-readline-common_8.2-3.1_all.deb ... 248s Unpacking readline-common (8.2-3.1) over (8.2-3) ... 248s Preparing to unpack .../1-python3-yaml_6.0.1-2build1_armhf.deb ... 249s Unpacking python3-yaml (6.0.1-2build1) over (6.0.1-2) ... 249s Preparing to unpack .../2-python-apt-common_2.7.6build1_all.deb ... 249s Unpacking python-apt-common (2.7.6build1) over (2.7.6) ... 249s Preparing to unpack .../3-python3-setuptools_68.1.2-2ubuntu1_all.deb ... 249s Unpacking python3-setuptools (68.1.2-2ubuntu1) over (68.1.2-2) ... 250s Preparing to unpack .../4-python3-pkg-resources_68.1.2-2ubuntu1_all.deb ... 251s Unpacking python3-pkg-resources (68.1.2-2ubuntu1) over (68.1.2-2) ... 251s Preparing to unpack .../5-dpkg_1.22.6ubuntu4_armhf.deb ... 251s Unpacking dpkg (1.22.6ubuntu4) over (1.22.4ubuntu5) ... 252s Setting up dpkg (1.22.6ubuntu4) ... 253s Setting up libpython3.12-minimal:armhf (3.12.2-4build3) ... 253s Setting up libexpat1:armhf (2.6.1-2) ... 253s Setting up python3.12-minimal (3.12.2-4build3) ... 259s (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 ... 47481 files and directories currently installed.) 259s Preparing to unpack .../python3-minimal_3.12.2-0ubuntu1_armhf.deb ... 259s Unpacking python3-minimal (3.12.2-0ubuntu1) over (3.12.1-0ubuntu2) ... 259s Setting up python3-minimal (3.12.2-0ubuntu1) ... 260s (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 ... 47481 files and directories currently installed.) 260s Preparing to unpack .../00-python3_3.12.2-0ubuntu1_armhf.deb ... 260s Unpacking python3 (3.12.2-0ubuntu1) over (3.12.1-0ubuntu2) ... 261s Preparing to unpack .../01-libpython3-stdlib_3.12.2-0ubuntu1_armhf.deb ... 261s Unpacking libpython3-stdlib:armhf (3.12.2-0ubuntu1) over (3.12.1-0ubuntu2) ... 261s Preparing to unpack .../02-bsdextrautils_2.39.3-9ubuntu2_armhf.deb ... 261s Unpacking bsdextrautils (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 261s Preparing to unpack .../03-groff-base_1.23.0-3build1_armhf.deb ... 261s Unpacking groff-base (1.23.0-3build1) over (1.23.0-3) ... 262s Preparing to unpack .../04-libsasl2-2_2.1.28+dfsg1-4ubuntu4_armhf.deb ... 262s Unpacking libsasl2-2:armhf (2.1.28+dfsg1-4ubuntu4) over (2.1.28+dfsg1-4) ... 262s Preparing to unpack .../05-libjson-glib-1.0-common_1.8.0-2build1_all.deb ... 262s Unpacking libjson-glib-1.0-common (1.8.0-2build1) over (1.8.0-2) ... 262s Preparing to unpack .../06-libjson-glib-1.0-0_1.8.0-2build1_armhf.deb ... 262s Unpacking libjson-glib-1.0-0:armhf (1.8.0-2build1) over (1.8.0-2) ... 262s Preparing to unpack .../07-libxml2_2.9.14+dfsg-1.3ubuntu2_armhf.deb ... 262s Unpacking libxml2:armhf (2.9.14+dfsg-1.3ubuntu2) over (2.9.14+dfsg-1.3ubuntu1) ... 262s Preparing to unpack .../08-libgudev-1.0-0_1%3a238-3ubuntu2_armhf.deb ... 262s Unpacking libgudev-1.0-0:armhf (1:238-3ubuntu2) over (1:238-3) ... 263s Preparing to unpack .../09-libusb-1.0-0_2%3a1.0.27-1_armhf.deb ... 263s Unpacking libusb-1.0-0:armhf (2:1.0.27-1) over (2:1.0.26-1) ... 263s Preparing to unpack .../10-libgusb2_0.4.8-1build1_armhf.deb ... 263s Unpacking libgusb2:armhf (0.4.8-1build1) over (0.4.8-1) ... 263s Preparing to unpack .../11-libmbim-proxy_1.31.2-0ubuntu2_armhf.deb ... 263s Unpacking libmbim-proxy (1.31.2-0ubuntu2) over (1.30.0-1) ... 263s Preparing to unpack .../12-libmbim-glib4_1.31.2-0ubuntu2_armhf.deb ... 263s Unpacking libmbim-glib4:armhf (1.31.2-0ubuntu2) over (1.30.0-1) ... 264s Preparing to unpack .../13-libmm-glib0_1.23.4-0ubuntu1_armhf.deb ... 264s Unpacking libmm-glib0:armhf (1.23.4-0ubuntu1) over (1.22.0-3) ... 264s Preparing to unpack .../14-libpolkit-agent-1-0_124-1ubuntu1_armhf.deb ... 264s Unpacking libpolkit-agent-1-0:armhf (124-1ubuntu1) over (124-1) ... 264s Preparing to unpack .../15-libpolkit-gobject-1-0_124-1ubuntu1_armhf.deb ... 264s Unpacking libpolkit-gobject-1-0:armhf (124-1ubuntu1) over (124-1) ... 264s Preparing to unpack .../16-libqmi-proxy_1.35.2-0ubuntu1_armhf.deb ... 264s Unpacking libqmi-proxy (1.35.2-0ubuntu1) over (1.34.0-2) ... 264s Preparing to unpack .../17-libqrtr-glib0_1.2.2-1ubuntu3_armhf.deb ... 264s Unpacking libqrtr-glib0:armhf (1.2.2-1ubuntu3) over (1.2.2-1ubuntu2) ... 264s Preparing to unpack .../18-libqmi-glib5_1.35.2-0ubuntu1_armhf.deb ... 264s Unpacking libqmi-glib5:armhf (1.35.2-0ubuntu1) over (1.34.0-2) ... 265s Preparing to unpack .../19-libxmlb2_0.3.15-1build1_armhf.deb ... 265s Unpacking libxmlb2:armhf (0.3.15-1build1) over (0.3.15-1) ... 265s Preparing to unpack .../20-shared-mime-info_2.4-1build1_armhf.deb ... 265s Unpacking shared-mime-info (2.4-1build1) over (2.4-1) ... 265s Preparing to unpack .../21-libbrotli1_1.1.0-2build1_armhf.deb ... 265s Unpacking libbrotli1:armhf (1.1.0-2build1) over (1.1.0-2) ... 266s Preparing to unpack .../22-libgssapi-krb5-2_1.20.1-5.1build3_armhf.deb ... 266s Unpacking libgssapi-krb5-2:armhf (1.20.1-5.1build3) over (1.20.1-5build1) ... 266s Preparing to unpack .../23-libkrb5-3_1.20.1-5.1build3_armhf.deb ... 266s Unpacking libkrb5-3:armhf (1.20.1-5.1build3) over (1.20.1-5build1) ... 266s Preparing to unpack .../24-libkrb5support0_1.20.1-5.1build3_armhf.deb ... 266s Unpacking libkrb5support0:armhf (1.20.1-5.1build3) over (1.20.1-5build1) ... 266s Preparing to unpack .../25-libk5crypto3_1.20.1-5.1build3_armhf.deb ... 266s Unpacking libk5crypto3:armhf (1.20.1-5.1build3) over (1.20.1-5build1) ... 266s Preparing to unpack .../26-libcom-err2_1.47.0-2.4~exp1ubuntu2_armhf.deb ... 266s Unpacking libcom-err2:armhf (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 267s Preparing to unpack .../27-libnghttp2-14_1.59.0-1build1_armhf.deb ... 267s Unpacking libnghttp2-14:armhf (1.59.0-1build1) over (1.59.0-1) ... 267s Preparing to unpack .../28-libssh-4_0.10.6-2build1_armhf.deb ... 267s Unpacking libssh-4:armhf (0.10.6-2build1) over (0.10.6-2) ... 267s Preparing to unpack .../29-libibverbs1_50.0-2build1_armhf.deb ... 267s Unpacking libibverbs1:armhf (50.0-2build1) over (50.0-2) ... 267s Preparing to unpack .../30-libfido2-1_1.14.0-1build1_armhf.deb ... 267s Unpacking libfido2-1:armhf (1.14.0-1build1) over (1.14.0-1) ... 267s Preparing to unpack .../31-coreutils_9.4-3ubuntu3_armhf.deb ... 267s Unpacking coreutils (9.4-3ubuntu3) over (9.4-2ubuntu4) ... 268s Setting up coreutils (9.4-3ubuntu3) ... 268s (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 ... 47481 files and directories currently installed.) 268s Preparing to unpack .../debianutils_5.17_armhf.deb ... 269s Unpacking debianutils (5.17) over (5.16) ... 269s Setting up debianutils (5.17) ... 269s (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 ... 47481 files and directories currently installed.) 270s Preparing to unpack .../util-linux_2.39.3-9ubuntu2_armhf.deb ... 270s Unpacking util-linux (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 270s Setting up util-linux (2.39.3-9ubuntu2) ... 273s fstrim.service is a disabled or a static unit not running, not starting it. 273s (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 ... 47481 files and directories currently installed.) 273s Preparing to unpack .../libc-bin_2.39-0ubuntu6_armhf.deb ... 273s Unpacking libc-bin (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 273s Setting up libc-bin (2.39-0ubuntu6) ... 274s (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 ... 47481 files and directories currently installed.) 274s Removing libatm1:armhf (1:2.5.1-5) ... 274s (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 ... 47476 files and directories currently installed.) 275s Preparing to unpack .../curl_8.5.0-2ubuntu7_armhf.deb ... 275s Unpacking curl (8.5.0-2ubuntu7) over (8.5.0-2ubuntu2) ... 275s (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 ... 47476 files and directories currently installed.) 275s Removing libcurl4:armhf (8.5.0-2ubuntu2) ... 275s Selecting previously unselected package libcurl4t64:armhf. 275s (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 ... 47471 files and directories currently installed.) 275s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu7_armhf.deb ... 275s Unpacking libcurl4t64:armhf (8.5.0-2ubuntu7) ... 275s Preparing to unpack .../libbpf1_1%3a1.3.0-2build1_armhf.deb ... 275s Unpacking libbpf1:armhf (1:1.3.0-2build1) over (1:1.3.0-2) ... 275s Preparing to unpack .../iproute2_6.1.0-1ubuntu5_armhf.deb ... 275s Unpacking iproute2 (6.1.0-1ubuntu5) over (6.1.0-1ubuntu2) ... 276s (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 ... 47477 files and directories currently installed.) 276s Removing libelf1:armhf (0.190-1) ... 276s Selecting previously unselected package libelf1t64:armhf. 276s (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 ... 47472 files and directories currently installed.) 276s Preparing to unpack .../libelf1t64_0.190-1.1build2_armhf.deb ... 276s Unpacking libelf1t64:armhf (0.190-1.1build2) ... 276s Preparing to unpack .../lsof_4.95.0-1build2_armhf.deb ... 276s Unpacking lsof (4.95.0-1build2) over (4.95.0-1build1) ... 277s Preparing to unpack .../libnsl2_1.3.0-3build2_armhf.deb ... 277s Unpacking libnsl2:armhf (1.3.0-3build2) over (1.3.0-3) ... 277s (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 ... 47477 files and directories currently installed.) 277s Removing libtirpc3:armhf (1.3.4+ds-1build1) ... 277s (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 ... 47471 files and directories currently installed.) 277s Preparing to unpack .../0-libtirpc-common_1.3.4+ds-1.1_all.deb ... 277s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ... 277s Selecting previously unselected package libtirpc3t64:armhf. 277s Preparing to unpack .../1-libtirpc3t64_1.3.4+ds-1.1_armhf.deb ... 277s Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3 to /lib/arm-linux-gnueabihf/libtirpc.so.3.usr-is-merged by libtirpc3t64' 277s 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' 277s Unpacking libtirpc3t64:armhf (1.3.4+ds-1.1) ... 277s Preparing to unpack .../2-libblockdev-utils3_3.1.0-1build1_armhf.deb ... 277s Unpacking libblockdev-utils3:armhf (3.1.0-1build1) over (3.1.0-1) ... 278s Preparing to unpack .../3-libblockdev-fs3_3.1.0-1build1_armhf.deb ... 278s Unpacking libblockdev-fs3:armhf (3.1.0-1build1) over (3.1.0-1) ... 278s Preparing to unpack .../4-logsave_1.47.0-2.4~exp1ubuntu2_armhf.deb ... 278s Unpacking logsave (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 278s Preparing to unpack .../5-initramfs-tools_0.142ubuntu22_all.deb ... 278s Unpacking initramfs-tools (0.142ubuntu22) over (0.142ubuntu20) ... 278s Preparing to unpack .../6-initramfs-tools-core_0.142ubuntu22_all.deb ... 278s Unpacking initramfs-tools-core (0.142ubuntu22) over (0.142ubuntu20) ... 279s Preparing to unpack .../7-e2fsprogs-l10n_1.47.0-2.4~exp1ubuntu2_all.deb ... 279s Unpacking e2fsprogs-l10n (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 279s dpkg: libext2fs2:armhf: dependency problems, but removing anyway as you requested: 279s e2fsprogs depends on libext2fs2 (= 1.47.0-2ubuntu1). 279s btrfs-progs depends on libext2fs2 (>= 1.42). 279s 279s (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 ... 47483 files and directories currently installed.) 279s Removing libext2fs2:armhf (1.47.0-2ubuntu1) ... 279s Selecting previously unselected package libext2fs2t64:armhf. 279s (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 ... 47476 files and directories currently installed.) 279s Preparing to unpack .../libext2fs2t64_1.47.0-2.4~exp1ubuntu2_armhf.deb ... 279s Adding 'diversion of /lib/arm-linux-gnueabihf/libe2p.so.2 to /lib/arm-linux-gnueabihf/libe2p.so.2.usr-is-merged by libext2fs2t64' 280s 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' 280s Adding 'diversion of /lib/arm-linux-gnueabihf/libext2fs.so.2 to /lib/arm-linux-gnueabihf/libext2fs.so.2.usr-is-merged by libext2fs2t64' 280s 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' 280s Unpacking libext2fs2t64:armhf (1.47.0-2.4~exp1ubuntu2) ... 280s Setting up libcom-err2:armhf (1.47.0-2.4~exp1ubuntu2) ... 280s Setting up libext2fs2t64:armhf (1.47.0-2.4~exp1ubuntu2) ... 280s (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 ... 47492 files and directories currently installed.) 280s Preparing to unpack .../e2fsprogs_1.47.0-2.4~exp1ubuntu2_armhf.deb ... 280s Unpacking e2fsprogs (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 281s Preparing to unpack .../btrfs-progs_6.6.3-1.1build1_armhf.deb ... 281s Unpacking btrfs-progs (6.6.3-1.1build1) over (6.6.3-1.1) ... 281s Preparing to unpack .../dhcpcd-base_1%3a10.0.6-1ubuntu2_armhf.deb ... 281s Unpacking dhcpcd-base (1:10.0.6-1ubuntu2) over (1:10.0.6-1ubuntu1) ... 282s Preparing to unpack .../initramfs-tools-bin_0.142ubuntu22_armhf.deb ... 282s Unpacking initramfs-tools-bin (0.142ubuntu22) over (0.142ubuntu20) ... 282s (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 ... 47492 files and directories currently installed.) 282s Removing libreiserfscore0 (1:3.6.27-7) ... 282s Selecting previously unselected package libreiserfscore0t64. 282s (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 ... 47487 files and directories currently installed.) 282s Preparing to unpack .../libreiserfscore0t64_1%3a3.6.27-7.1_armhf.deb ... 282s Unpacking libreiserfscore0t64 (1:3.6.27-7.1) ... 282s Preparing to unpack .../file_1%3a5.45-3_armhf.deb ... 282s Unpacking file (1:5.45-3) over (1:5.45-2) ... 283s (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 ... 47493 files and directories currently installed.) 283s Removing libmagic1:armhf (1:5.45-2) ... 283s (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 ... 47483 files and directories currently installed.) 283s Preparing to unpack .../0-libmagic-mgc_1%3a5.45-3_armhf.deb ... 283s Unpacking libmagic-mgc (1:5.45-3) over (1:5.45-2) ... 283s Selecting previously unselected package libmagic1t64:armhf. 283s Preparing to unpack .../1-libmagic1t64_1%3a5.45-3_armhf.deb ... 283s Unpacking libmagic1t64:armhf (1:5.45-3) ... 283s Selecting previously unselected package libnetplan1:armhf. 283s Preparing to unpack .../2-libnetplan1_1.0-1_armhf.deb ... 283s Unpacking libnetplan1:armhf (1.0-1) ... 284s Preparing to unpack .../3-python3-netplan_1.0-1_armhf.deb ... 284s Unpacking python3-netplan (1.0-1) over (0.107.1-3) ... 284s Preparing to unpack .../4-netplan-generator_1.0-1_armhf.deb ... 284s Adding 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 284s Unpacking netplan-generator (1.0-1) over (0.107.1-3) ... 284s Preparing to unpack .../5-python3-dbus_1.3.2-5build2_armhf.deb ... 284s Unpacking python3-dbus (1.3.2-5build2) over (1.3.2-5build1) ... 285s Preparing to unpack .../6-netplan.io_1.0-1_armhf.deb ... 285s Unpacking netplan.io (1.0-1) over (0.107.1-3) ... 285s (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 ... 47498 files and directories currently installed.) 285s Removing libnetplan0:armhf (0.107.1-3) ... 285s (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 ... 47494 files and directories currently installed.) 286s Preparing to unpack .../libblockdev-nvme3_3.1.0-1build1_armhf.deb ... 286s Unpacking libblockdev-nvme3:armhf (3.1.0-1build1) over (3.1.0-1) ... 286s (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 ... 47494 files and directories currently installed.) 286s Removing libnvme1 (1.8-2) ... 286s Selecting previously unselected package libnvme1t64. 286s (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 ... 47487 files and directories currently installed.) 286s Preparing to unpack .../libnvme1t64_1.8-3_armhf.deb ... 286s Unpacking libnvme1t64 (1.8-3) ... 286s Preparing to unpack .../libplymouth5_24.004.60-1ubuntu4_armhf.deb ... 286s Unpacking libplymouth5:armhf (24.004.60-1ubuntu4) over (24.004.60-1ubuntu3) ... 287s (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 ... 47495 files and directories currently installed.) 287s Removing libpng16-16:armhf (1.6.43-1) ... 287s Selecting previously unselected package libpng16-16t64:armhf. 287s (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 ... 47485 files and directories currently installed.) 287s Preparing to unpack .../libpng16-16t64_1.6.43-3_armhf.deb ... 287s Unpacking libpng16-16t64:armhf (1.6.43-3) ... 287s (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 ... 47496 files and directories currently installed.) 287s Removing libudisks2-0:armhf (2.10.1-1ubuntu2) ... 287s (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 ... 47491 files and directories currently installed.) 287s Preparing to unpack .../bind9-host_1%3a9.18.24-0ubuntu3_armhf.deb ... 287s Unpacking bind9-host (1:9.18.24-0ubuntu3) over (1:9.18.21-0ubuntu1) ... 288s Preparing to unpack .../bind9-dnsutils_1%3a9.18.24-0ubuntu3_armhf.deb ... 288s Unpacking bind9-dnsutils (1:9.18.24-0ubuntu3) over (1:9.18.21-0ubuntu1) ... 288s Preparing to unpack .../bind9-libs_1%3a9.18.24-0ubuntu3_armhf.deb ... 288s Unpacking bind9-libs:armhf (1:9.18.24-0ubuntu3) over (1:9.18.21-0ubuntu1) ... 288s (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 ... 47491 files and directories currently installed.) 288s Removing libuv1:armhf (1.48.0-1) ... 288s Selecting previously unselected package libuv1t64:armhf. 288s (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 ... 47486 files and directories currently installed.) 288s Preparing to unpack .../libuv1t64_1.48.0-1.1_armhf.deb ... 288s Unpacking libuv1t64:armhf (1.48.0-1.1) ... 289s (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 ... 47492 files and directories currently installed.) 289s Removing python3-distutils (3.11.5-1) ... 290s (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 ... 47437 files and directories currently installed.) 290s Preparing to unpack .../uuid-runtime_2.39.3-9ubuntu2_armhf.deb ... 290s Unpacking uuid-runtime (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 290s Preparing to unpack .../libdebconfclient0_0.271ubuntu2_armhf.deb ... 290s Unpacking libdebconfclient0:armhf (0.271ubuntu2) over (0.271ubuntu1) ... 290s Setting up libdebconfclient0:armhf (0.271ubuntu2) ... 290s (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 ... 47437 files and directories currently installed.) 290s Preparing to unpack .../libsemanage-common_3.5-1build4_all.deb ... 290s Unpacking libsemanage-common (3.5-1build4) over (3.5-1build2) ... 291s Setting up libsemanage-common (3.5-1build4) ... 291s (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 ... 47437 files and directories currently installed.) 291s Preparing to unpack .../libsemanage2_3.5-1build4_armhf.deb ... 291s Unpacking libsemanage2:armhf (3.5-1build4) over (3.5-1build2) ... 291s Setting up libsemanage2:armhf (3.5-1build4) ... 291s (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 ... 47437 files and directories currently installed.) 291s Preparing to unpack .../install-info_7.1-3build1_armhf.deb ... 291s Unpacking install-info (7.1-3build1) over (7.1-3) ... 292s Setting up install-info (7.1-3build1) ... 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 ... 47437 files and directories currently installed.) 292s Preparing to unpack .../00-gcc-13-base_13.2.0-19ubuntu1_armhf.deb ... 292s Unpacking gcc-13-base:armhf (13.2.0-19ubuntu1) over (13.2.0-17ubuntu2) ... 293s Preparing to unpack .../01-libss2_1.47.0-2.4~exp1ubuntu2_armhf.deb ... 293s Unpacking libss2:armhf (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 293s Preparing to unpack .../02-dmsetup_2%3a1.02.185-3ubuntu2_armhf.deb ... 293s Unpacking dmsetup (2:1.02.185-3ubuntu2) over (2:1.02.185-3ubuntu1) ... 293s Preparing to unpack .../03-eject_2.39.3-9ubuntu2_armhf.deb ... 293s Unpacking eject (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 293s Preparing to unpack .../04-gir1.2-girepository-2.0_1.79.1-1ubuntu6_armhf.deb ... 293s Unpacking gir1.2-girepository-2.0:armhf (1.79.1-1ubuntu6) over (1.79.1-1) ... 293s Preparing to unpack .../05-gir1.2-glib-2.0_2.79.3-3ubuntu5_armhf.deb ... 293s Unpacking gir1.2-glib-2.0:armhf (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 293s Preparing to unpack .../06-libgirepository-1.0-1_1.79.1-1ubuntu6_armhf.deb ... 293s Unpacking libgirepository-1.0-1:armhf (1.79.1-1ubuntu6) over (1.79.1-1) ... 294s Preparing to unpack .../07-krb5-locales_1.20.1-5.1build3_all.deb ... 294s Unpacking krb5-locales (1.20.1-5.1build3) over (1.20.1-5build1) ... 294s Preparing to unpack .../08-libbsd0_0.12.1-1_armhf.deb ... 294s Unpacking libbsd0:armhf (0.12.1-1) over (0.11.8-1) ... 294s Preparing to unpack .../09-libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 294s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 294s Preparing to unpack .../10-libslang2_2.3.3-3build1_armhf.deb ... 294s Unpacking libslang2:armhf (2.3.3-3build1) over (2.3.3-3) ... 294s Preparing to unpack .../11-locales_2.39-0ubuntu6_all.deb ... 294s Unpacking locales (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 296s Preparing to unpack .../12-python3-gi_3.47.0-3build1_armhf.deb ... 296s Unpacking python3-gi (3.47.0-3build1) over (3.47.0-3) ... 296s Preparing to unpack .../13-vim-tiny_2%3a9.1.0016-1ubuntu5_armhf.deb ... 296s Unpacking vim-tiny (2:9.1.0016-1ubuntu5) over (2:9.1.0016-1ubuntu2) ... 296s Preparing to unpack .../14-vim-common_2%3a9.1.0016-1ubuntu5_all.deb ... 296s Unpacking vim-common (2:9.1.0016-1ubuntu5) over (2:9.1.0016-1ubuntu2) ... 296s Selecting previously unselected package xdg-user-dirs. 297s Preparing to unpack .../15-xdg-user-dirs_0.18-1_armhf.deb ... 297s Unpacking xdg-user-dirs (0.18-1) ... 297s Preparing to unpack .../16-xxd_2%3a9.1.0016-1ubuntu5_armhf.deb ... 297s Unpacking xxd (2:9.1.0016-1ubuntu5) over (2:9.1.0016-1ubuntu2) ... 297s Preparing to unpack .../17-apparmor_4.0.0~beta2-0ubuntu3_armhf.deb ... 300s Unpacking apparmor (4.0.0~beta2-0ubuntu3) over (4.0.0~alpha4-0ubuntu1) ... 301s Preparing to unpack .../18-ftp_20230507-2build1_all.deb ... 302s Unpacking ftp (20230507-2build1) over (20230507-2) ... 302s Preparing to unpack .../19-inetutils-telnet_2%3a2.5-3ubuntu3_armhf.deb ... 302s Unpacking inetutils-telnet (2:2.5-3ubuntu3) over (2:2.5-3ubuntu1) ... 302s Preparing to unpack .../20-info_7.1-3build1_armhf.deb ... 302s Unpacking info (7.1-3build1) over (7.1-3) ... 302s Preparing to unpack .../21-libxmuu1_2%3a1.1.3-3build1_armhf.deb ... 302s Unpacking libxmuu1:armhf (2:1.1.3-3build1) over (2:1.1.3-3) ... 302s Preparing to unpack .../22-lshw_02.19.git.2021.06.19.996aaad9c7-2build2_armhf.deb ... 302s Unpacking lshw (02.19.git.2021.06.19.996aaad9c7-2build2) over (02.19.git.2021.06.19.996aaad9c7-2build1) ... 302s Preparing to unpack .../23-mtr-tiny_0.95-1.1build1_armhf.deb ... 302s Unpacking mtr-tiny (0.95-1.1build1) over (0.95-1.1) ... 302s Preparing to unpack .../24-plymouth-theme-ubuntu-text_24.004.60-1ubuntu4_armhf.deb ... 302s Unpacking plymouth-theme-ubuntu-text (24.004.60-1ubuntu4) over (24.004.60-1ubuntu3) ... 303s Preparing to unpack .../25-plymouth_24.004.60-1ubuntu4_armhf.deb ... 304s Unpacking plymouth (24.004.60-1ubuntu4) over (24.004.60-1ubuntu3) ... 304s Preparing to unpack .../26-psmisc_23.7-1_armhf.deb ... 304s Unpacking psmisc (23.7-1) over (23.6-2) ... 305s Preparing to unpack .../27-telnet_0.17+2.5-3ubuntu3_all.deb ... 305s Unpacking telnet (0.17+2.5-3ubuntu3) over (0.17+2.5-3ubuntu1) ... 305s Preparing to unpack .../28-xz-utils_5.6.0-0.2_armhf.deb ... 305s Unpacking xz-utils (5.6.0-0.2) over (5.4.5-0.3) ... 305s Preparing to unpack .../29-bolt_0.9.6-2build1_armhf.deb ... 305s Unpacking bolt (0.9.6-2build1) over (0.9.6-2) ... 306s Preparing to unpack .../30-cryptsetup-bin_2%3a2.7.0-1ubuntu2_armhf.deb ... 306s Unpacking cryptsetup-bin (2:2.7.0-1ubuntu2) over (2:2.7.0-1ubuntu1) ... 306s Preparing to unpack .../31-dpkg-dev_1.22.6ubuntu4_all.deb ... 306s Unpacking dpkg-dev (1.22.6ubuntu4) over (1.22.4ubuntu5) ... 307s Preparing to unpack .../32-libdpkg-perl_1.22.6ubuntu4_all.deb ... 307s Unpacking libdpkg-perl (1.22.6ubuntu4) over (1.22.4ubuntu5) ... 308s Preparing to unpack .../33-gnupg-l10n_2.4.4-2ubuntu15_all.deb ... 308s Unpacking gnupg-l10n (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 308s Preparing to unpack .../34-ibverbs-providers_50.0-2build1_armhf.deb ... 309s Unpacking ibverbs-providers:armhf (50.0-2build1) over (50.0-2) ... 309s Preparing to unpack .../35-jq_1.7.1-3_armhf.deb ... 309s Unpacking jq (1.7.1-3) over (1.7.1-2) ... 309s Preparing to unpack .../36-libjq1_1.7.1-3_armhf.deb ... 309s Unpacking libjq1:armhf (1.7.1-3) over (1.7.1-2) ... 309s Selecting previously unselected package libatm1t64:armhf. 309s Preparing to unpack .../37-libatm1t64_1%3a2.5.1-5.1_armhf.deb ... 309s Unpacking libatm1t64:armhf (1:2.5.1-5.1) ... 309s Preparing to unpack .../38-libblockdev-crypto3_3.1.0-1build1_armhf.deb ... 309s Unpacking libblockdev-crypto3:armhf (3.1.0-1build1) over (3.1.0-1) ... 309s Preparing to unpack .../39-libblockdev-loop3_3.1.0-1build1_armhf.deb ... 310s Unpacking libblockdev-loop3:armhf (3.1.0-1build1) over (3.1.0-1) ... 310s Preparing to unpack .../40-libblockdev-mdraid3_3.1.0-1build1_armhf.deb ... 310s Unpacking libblockdev-mdraid3:armhf (3.1.0-1build1) over (3.1.0-1) ... 310s Preparing to unpack .../41-libblockdev-part3_3.1.0-1build1_armhf.deb ... 310s Unpacking libblockdev-part3:armhf (3.1.0-1build1) over (3.1.0-1) ... 310s Preparing to unpack .../42-libblockdev-swap3_3.1.0-1build1_armhf.deb ... 310s Unpacking libblockdev-swap3:armhf (3.1.0-1build1) over (3.1.0-1) ... 310s Preparing to unpack .../43-libblockdev3_3.1.0-1build1_armhf.deb ... 310s Unpacking libblockdev3:armhf (3.1.0-1build1) over (3.1.0-1) ... 311s Preparing to unpack .../44-libevent-core-2.1-7_2.1.12-stable-9build1_armhf.deb ... 311s Unpacking libevent-core-2.1-7:armhf (2.1.12-stable-9build1) over (2.1.12-stable-9) ... 311s Preparing to unpack .../45-libftdi1-2_1.5-6build4_armhf.deb ... 311s Unpacking libftdi1-2:armhf (1.5-6build4) over (1.5-6build3) ... 311s Preparing to unpack .../46-libldap-common_2.6.7+dfsg-1~exp1ubuntu6_all.deb ... 311s Unpacking libldap-common (2.6.7+dfsg-1~exp1ubuntu6) over (2.6.7+dfsg-1~exp1ubuntu1) ... 311s Preparing to unpack .../47-libsasl2-modules_2.1.28+dfsg1-4ubuntu4_armhf.deb ... 311s Unpacking libsasl2-modules:armhf (2.1.28+dfsg1-4ubuntu4) over (2.1.28+dfsg1-4) ... 311s Preparing to unpack .../48-python3-lib2to3_3.12.2-3ubuntu2_all.deb ... 312s Unpacking python3-lib2to3 (3.12.2-3ubuntu2) over (3.11.5-1) ... 312s Preparing to unpack .../49-python3-markupsafe_2.1.5-1build1_armhf.deb ... 313s Unpacking python3-markupsafe (2.1.5-1build1) over (2.1.5-1) ... 313s Preparing to unpack .../50-python3-openssl_24.0.0-4_all.deb ... 313s Unpacking python3-openssl (24.0.0-4) over (23.2.0-1) ... 313s Preparing to unpack .../51-python3-pyrsistent_0.20.0-1build1_armhf.deb ... 313s Unpacking python3-pyrsistent:armhf (0.20.0-1build1) over (0.20.0-1) ... 314s Preparing to unpack .../52-python3-typing-extensions_4.10.0-1_all.deb ... 314s Unpacking python3-typing-extensions (4.10.0-1) over (4.9.0-1) ... 314s Preparing to unpack .../53-kpartx_0.9.4-5ubuntu4_armhf.deb ... 314s Unpacking kpartx (0.9.4-5ubuntu4) over (0.9.4-5ubuntu3) ... 314s Setting up pinentry-curses (1.2.1-3ubuntu4) ... 314s Setting up libtext-iconv-perl:armhf (1.7-8build2) ... 314s Setting up libtext-charwidth-perl:armhf (0.04-11build2) ... 314s Setting up libibverbs1:armhf (50.0-2build1) ... 314s Setting up systemd-sysv (255.4-1ubuntu5) ... 314s Setting up libapparmor1:armhf (4.0.0~beta2-0ubuntu3) ... 314s Setting up libatm1t64:armhf (1:2.5.1-5.1) ... 314s Setting up libgdbm6t64:armhf (1.23-5.1) ... 314s Setting up bsdextrautils (2.39.3-9ubuntu2) ... 314s Setting up libgdbm-compat4t64:armhf (1.23-5.1) ... 314s Setting up xdg-user-dirs (0.18-1) ... 314s Setting up ibverbs-providers:armhf (50.0-2build1) ... 315s Setting up libmagic-mgc (1:5.45-3) ... 315s Setting up gawk (1:5.2.1-2build2) ... 315s Setting up psmisc (23.7-1) ... 315s Setting up libjq1:armhf (1.7.1-3) ... 315s Setting up libtirpc-common (1.3.4+ds-1.1) ... 315s Setting up libbrotli1:armhf (1.1.0-2build1) ... 315s Setting up libsqlite3-0:armhf (3.45.1-1ubuntu1) ... 315s Setting up libsasl2-modules:armhf (2.1.28+dfsg1-4ubuntu4) ... 315s Setting up libuv1t64:armhf (1.48.0-1.1) ... 315s Setting up libmagic1t64:armhf (1:5.45-3) ... 315s Setting up libpsl5t64:armhf (0.21.2-1.1) ... 315s Setting up libnghttp2-14:armhf (1.59.0-1build1) ... 315s Setting up libreiserfscore0t64 (1:3.6.27-7.1) ... 315s Setting up libnss-systemd:armhf (255.4-1ubuntu5) ... 315s Setting up krb5-locales (1.20.1-5.1build3) ... 315s Setting up file (1:5.45-3) ... 315s Setting up lshw (02.19.git.2021.06.19.996aaad9c7-2build2) ... 315s Setting up locales (2.39-0ubuntu6) ... 318s Generating locales (this might take a while)... 326s en_US.UTF-8... done 326s Generation complete. 326s Setting up libldap-common (2.6.7+dfsg-1~exp1ubuntu6) ... 326s Setting up xxd (2:9.1.0016-1ubuntu5) ... 326s Setting up libelf1t64:armhf (0.190-1.1build2) ... 326s Setting up libkrb5support0:armhf (1.20.1-5.1build3) ... 326s Setting up eject (2.39.3-9ubuntu2) ... 326s Setting up apparmor (4.0.0~beta2-0ubuntu3) ... 326s Installing new version of config file /etc/apparmor.d/abstractions/openssl ... 326s Installing new version of config file /etc/apparmor.d/code ... 327s apparmor_parser: Unable to replace "lsb_release". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 327s 327s apparmor_parser: Unable to replace "kmod". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 327s 327s apparmor_parser: Unable to replace "nvidia_modprobe". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 327s 330s sysctl: cannot stat /proc/sys/kernel/apparmor_restrict_unprivileged_userns: No such file or directory 330s Reloading AppArmor profiles 330s /sbin/apparmor_parser: Unable to replace "1password". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "Discord". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "MongoDB Compass". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "brave". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "busybox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "cam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "buildah". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "ch-checkns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "ch-run". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "chrome". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "vscode". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "crun". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "devhelp". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "element-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "epiphany". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "evolution". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "firefox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "ipa_verify". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "github-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "lc-compliance". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "linux-sandbox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "flatpak". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "libcamerify". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "lxc-execute". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "lxc-attach". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "keybase". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "lxc-stop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "lxc-usernsexec". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "lxc-destroy". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "lxc-create". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "lxc-unshare". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "mmdebstrap". /sbin/apparmor_parser: Unable to replace "msedge". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "opam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "nautilus". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "opera". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "obsidian". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "podman". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "qcam". /sbin/apparmor_parser: Unable to replace "polypane". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "rpm". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "rootlesskit". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "runc". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "sbuild". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "sbuild-abort". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "sbuild-clean". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "sbuild-adduser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "sbuild-checkpackages". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "sbuild-createchroot". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "plasmashell". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "sbuild-destroychroot". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "sbuild-unhold". /sbin/apparmor_parser: Unable to replace "sbuild-hold". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "sbuild-shell". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "sbuild-apt". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "sbuild-distupgrade". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "sbuild-update". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "signal-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "slack". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "steam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "sbuild-upgrade". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "slirp4netns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "lsb_release". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "systemd-coredump". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "toybox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "surfshark". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "stress-ng". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "thunderbird". /sbin/apparmor_parser: Unable to replace "tup". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "trinity". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "userbindmount". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "vdens". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "unprivileged_userns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "virtiofsd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "uwsgi-core". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "wpcom". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "vivaldi-bin". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "vpnns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "kmod". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "nvidia_modprobe". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "/usr/bin/man". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "ubuntu_pro_apt_news". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 330s /sbin/apparmor_parser: Unable to replace "rsyslogd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 330s 331s /sbin/apparmor_parser: Unable to replace "tcpdump". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 331s 331s Error: At least one profile failed to load 331s Setting up libglib2.0-0t64:armhf (2.79.3-3ubuntu5) ... 331s No schema files found: doing nothing. 331s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 331s Setting up vim-common (2:9.1.0016-1ubuntu5) ... 331s Setting up gcc-13-base:armhf (13.2.0-19ubuntu1) ... 331s Setting up libqrtr-glib0:armhf (1.2.2-1ubuntu3) ... 331s Setting up libslang2:armhf (2.3.3-3build1) ... 331s Setting up libnvme1t64 (1.8-3) ... 331s Setting up mtr-tiny (0.95-1.1build1) ... 331s Setting up gnupg-l10n (2.4.4-2ubuntu15) ... 331s Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build6) ... 331s Setting up libdbus-1-3:armhf (1.14.10-4ubuntu2) ... 331s Setting up xz-utils (5.6.0-0.2) ... 331s Setting up perl-modules-5.38 (5.38.2-3.2) ... 331s Setting up libpng16-16t64:armhf (1.6.43-3) ... 331s Setting up systemd-timesyncd (255.4-1ubuntu5) ... 332s Setting up libevent-core-2.1-7:armhf (2.1.12-stable-9build1) ... 332s Setting up libss2:armhf (1.47.0-2.4~exp1ubuntu2) ... 332s Setting up sudo (1.9.15p5-3ubuntu3) ... 333s Setting up dhcpcd-base (1:10.0.6-1ubuntu2) ... 333s Setting up gir1.2-glib-2.0:armhf (2.79.3-3ubuntu5) ... 333s Setting up libk5crypto3:armhf (1.20.1-5.1build3) ... 333s Setting up logsave (1.47.0-2.4~exp1ubuntu2) ... 333s Setting up libfdisk1:armhf (2.39.3-9ubuntu2) ... 333s Setting up libdb5.3t64:armhf (5.3.28+dfsg2-5build1) ... 333s Setting up libdevmapper1.02.1:armhf (2:1.02.185-3ubuntu2) ... 333s Setting up python-apt-common (2.7.6build1) ... 333s Setting up mount (2.39.3-9ubuntu2) ... 333s Setting up dmsetup (2:1.02.185-3ubuntu2) ... 333s Setting up uuid-runtime (2.39.3-9ubuntu2) ... 336s uuidd.service is a disabled or a static unit not running, not starting it. 336s Setting up libmm-glib0:armhf (1.23.4-0ubuntu1) ... 336s Setting up groff-base (1.23.0-3build1) ... 336s Setting up libplymouth5:armhf (24.004.60-1ubuntu4) ... 336s Setting up dbus-session-bus-common (1.14.10-4ubuntu2) ... 336s Setting up jq (1.7.1-3) ... 336s Setting up gpgconf (2.4.4-2ubuntu15) ... 336s Setting up libpcap0.8t64:armhf (1.10.4-4.1ubuntu1) ... 336s Setting up libcryptsetup12:armhf (2:2.7.0-1ubuntu2) ... 336s Setting up libgirepository-1.0-1:armhf (1.79.1-1ubuntu6) ... 336s Setting up libjson-glib-1.0-common (1.8.0-2build1) ... 336s Setting up libkrb5-3:armhf (1.20.1-5.1build3) ... 336s Setting up libpython3.11-minimal:armhf (3.11.8-1build4) ... 336s Setting up libusb-1.0-0:armhf (2:1.0.27-1) ... 336s Setting up libperl5.38t64:armhf (5.38.2-3.2) ... 336s Setting up tnftp (20230507-2build1) ... 336s Setting up dbus-system-bus-common (1.14.10-4ubuntu2) ... 336s Setting up libfido2-1:armhf (1.14.0-1build1) ... 336s Setting up openssl (3.0.13-0ubuntu2) ... 336s Setting up libbsd0:armhf (0.12.1-1) ... 336s Setting up readline-common (8.2-3.1) ... 336s Setting up libxml2:armhf (2.9.14+dfsg-1.3ubuntu2) ... 336s Setting up libxmuu1:armhf (2:1.1.3-3build1) ... 336s Setting up dbus-bin (1.14.10-4ubuntu2) ... 336s Setting up info (7.1-3build1) ... 336s Setting up liblocale-gettext-perl (1.07-6ubuntu3) ... 336s Setting up gpg (2.4.4-2ubuntu15) ... 336s Setting up libgudev-1.0-0:armhf (1:238-3ubuntu2) ... 336s Setting up libpolkit-gobject-1-0:armhf (124-1ubuntu1) ... 336s Setting up libbpf1:armhf (1:1.3.0-2build1) ... 336s Setting up libmbim-glib4:armhf (1.31.2-0ubuntu2) ... 336s Setting up rsync (3.2.7-1build1) ... 339s rsync.service is a disabled or a static unit not running, not starting it. 339s Setting up libkmod2:armhf (31+20240202-2ubuntu4) ... 339s Setting up bolt (0.9.6-2build1) ... 340s bolt.service is a disabled or a static unit not running, not starting it. 340s Setting up gnupg-utils (2.4.4-2ubuntu15) ... 340s Setting up initramfs-tools-bin (0.142ubuntu22) ... 340s Setting up cryptsetup-bin (2:2.7.0-1ubuntu2) ... 340s Setting up python3.11-minimal (3.11.8-1build4) ... 343s Setting up tcpdump (4.99.4-3ubuntu2) ... 344s apparmor_parser: Unable to replace "tcpdump". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 344s 344s Setting up apt-utils (2.7.13ubuntu1) ... 344s Setting up gpg-agent (2.4.4-2ubuntu15) ... 346s Setting up libpython3.12-stdlib:armhf (3.12.2-4build3) ... 346s Setting up wget (1.21.4-1ubuntu2) ... 346s Setting up libxmlb2:armhf (0.3.15-1build1) ... 346s Setting up btrfs-progs (6.6.3-1.1build1) ... 346s Setting up libpython3.11-stdlib:armhf (3.11.8-1build4) ... 346s Setting up python3.12 (3.12.2-4build3) ... 352s Setting up gpgsm (2.4.4-2ubuntu15) ... 352s Setting up inetutils-telnet (2:2.5-3ubuntu3) ... 352s Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu2) ... 352s update-initramfs: deferring update (trigger activated) 355s e2scrub_all.service is a disabled or a static unit not running, not starting it. 355s Setting up libparted2t64:armhf (3.6-3.1build2) ... 355s Setting up dbus-daemon (1.14.10-4ubuntu2) ... 355s Setting up libmbim-proxy (1.31.2-0ubuntu2) ... 355s Setting up vim-tiny (2:9.1.0016-1ubuntu5) ... 356s Setting up kmod (31+20240202-2ubuntu4) ... 357s Setting up libnetplan1:armhf (1.0-1) ... 357s Setting up man-db (2.12.0-3build4) ... 357s Updating database of manual pages ... 364s apparmor_parser: Unable to replace "/usr/bin/man". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 364s 366s man-db.service is a disabled or a static unit not running, not starting it. 367s Setting up fdisk (2.39.3-9ubuntu2) ... 367s Setting up libjson-glib-1.0-0:armhf (1.8.0-2build1) ... 367s Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-4ubuntu4) ... 367s Setting up libftdi1-2:armhf (1.5-6build4) ... 367s Setting up perl (5.38.2-3.2) ... 367s Setting up gir1.2-girepository-2.0:armhf (1.79.1-1ubuntu6) ... 367s Setting up dbus (1.14.10-4ubuntu2) ... 367s A reboot is required to replace the running dbus-daemon. 367s Please reboot the system when convenient. 368s Setting up shared-mime-info (2.4-1build1) ... 369s Setting up libblockdev-utils3:armhf (3.1.0-1build1) ... 369s Setting up libgssapi-krb5-2:armhf (1.20.1-5.1build3) ... 369s Setting up udev (255.4-1ubuntu5) ... 372s Setting up ftp (20230507-2build1) ... 372s Setting up keyboxd (2.4.4-2ubuntu15) ... 372s Setting up libdpkg-perl (1.22.6ubuntu4) ... 372s Setting up libsasl2-2:armhf (2.1.28+dfsg1-4ubuntu4) ... 372s Setting up libssh-4:armhf (0.10.6-2build1) ... 372s Setting up libblockdev-nvme3:armhf (3.1.0-1build1) ... 372s Setting up libblockdev-fs3:armhf (3.1.0-1build1) ... 372s Setting up kpartx (0.9.4-5ubuntu4) ... 372s Setting up libpam-systemd:armhf (255.4-1ubuntu5) ... 373s Setting up libpolkit-agent-1-0:armhf (124-1ubuntu1) ... 373s Setting up libgpgme11t64:armhf (1.18.0-4.1ubuntu3) ... 373s Setting up netplan-generator (1.0-1) ... 373s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 373s Setting up initramfs-tools-core (0.142ubuntu22) ... 373s Setting up libarchive13t64:armhf (3.7.2-1.1ubuntu1) ... 373s Setting up libldap2:armhf (2.6.7+dfsg-1~exp1ubuntu6) ... 373s Setting up libpython3-stdlib:armhf (3.12.2-0ubuntu1) ... 373s Setting up systemd-resolved (255.4-1ubuntu5) ... 375s Setting up python3.11 (3.11.8-1build4) ... 379s Setting up telnet (0.17+2.5-3ubuntu3) ... 379s Setting up initramfs-tools (0.142ubuntu22) ... 379s update-initramfs: deferring update (trigger activated) 379s Setting up libblockdev-mdraid3:armhf (3.1.0-1build1) ... 379s Setting up libcurl4t64:armhf (8.5.0-2ubuntu7) ... 379s Setting up bind9-libs:armhf (1:9.18.24-0ubuntu3) ... 379s Setting up libtirpc3t64:armhf (1.3.4+ds-1.1) ... 379s Setting up e2fsprogs-l10n (1.47.0-2.4~exp1ubuntu2) ... 379s Setting up libblockdev-swap3:armhf (3.1.0-1build1) ... 379s Setting up plymouth (24.004.60-1ubuntu4) ... 379s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 380s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 381s Setting up iproute2 (6.1.0-1ubuntu5) ... 381s Setting up openssh-client (1:9.6p1-3ubuntu10) ... 382s Setting up libgusb2:armhf (0.4.8-1build1) ... 382s Setting up libblockdev-loop3:armhf (3.1.0-1build1) ... 382s Setting up libcurl3t64-gnutls:armhf (8.5.0-2ubuntu7) ... 382s Setting up parted (3.6-3.1build2) ... 382s Setting up libqmi-glib5:armhf (1.35.2-0ubuntu1) ... 382s Setting up python3 (3.12.2-0ubuntu1) ... 383s Setting up python3-markupsafe (2.1.5-1build1) ... 384s Setting up libblockdev3:armhf (3.1.0-1build1) ... 384s Setting up libjcat1:armhf (0.2.0-2build2) ... 384s Setting up dpkg-dev (1.22.6ubuntu4) ... 384s Setting up libblockdev-part3:armhf (3.1.0-1build1) ... 384s Setting up dirmngr (2.4.4-2ubuntu15) ... 384s Setting up dbus-user-session (1.14.10-4ubuntu2) ... 384s Setting up plymouth-theme-ubuntu-text (24.004.60-1ubuntu4) ... 384s update-initramfs: deferring update (trigger activated) 384s Setting up python3-cryptography (41.0.7-4build2) ... 386s Setting up python3-gi (3.47.0-3build1) ... 386s Setting up python3-typing-extensions (4.10.0-1) ... 387s Setting up lsof (4.95.0-1build2) ... 387s Setting up python3-pyrsistent:armhf (0.20.0-1build1) ... 388s Setting up libnsl2:armhf (1.3.0-3build2) ... 388s Setting up gnupg (2.4.4-2ubuntu15) ... 388s Setting up python3-netplan (1.0-1) ... 388s Setting up curl (8.5.0-2ubuntu7) ... 388s Setting up libvolume-key1:armhf (0.3.12-7build1) ... 388s Setting up bind9-host (1:9.18.24-0ubuntu3) ... 388s Setting up python3-lib2to3 (3.12.2-3ubuntu2) ... 389s Setting up python3-pkg-resources (68.1.2-2ubuntu1) ... 390s Setting up openssh-sftp-server (1:9.6p1-3ubuntu10) ... 390s Setting up python3-dbus (1.3.2-5build2) ... 390s Setting up python3-setuptools (68.1.2-2ubuntu1) ... 392s Setting up gpg-wks-client (2.4.4-2ubuntu15) ... 392s Setting up openssh-server (1:9.6p1-3ubuntu10) ... 393s Replacing config file /etc/ssh/sshd_config with new version 397s Created symlink /etc/systemd/system/ssh.service.requires/ssh.socket → /usr/lib/systemd/system/ssh.socket. 400s Setting up libblockdev-crypto3:armhf (3.1.0-1build1) ... 400s Setting up python3-gdbm:armhf (3.12.2-3ubuntu2) ... 400s Setting up python3-apt (2.7.6build1) ... 401s Setting up python3-openssl (24.0.0-4) ... 401s Setting up libfwupd2:armhf (1.9.15-1) ... 401s Setting up python3-yaml (6.0.1-2build1) ... 402s Setting up libqmi-proxy (1.35.2-0ubuntu1) ... 402s Setting up netplan.io (1.0-1) ... 402s Setting up bind9-dnsutils (1:9.18.24-0ubuntu3) ... 402s Setting up ubuntu-pro-client (31.2) ... 402s apparmor_parser: Unable to replace "ubuntu_pro_apt_news". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 402s 407s Setting up fwupd (1.9.15-1) ... 409s fwupd-offline-update.service is a disabled or a static unit not running, not starting it. 409s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 409s fwupd.service is a disabled or a static unit not running, not starting it. 410s Setting up ubuntu-pro-client-l10n (31.2) ... 410s Processing triggers for ufw (0.36.2-5) ... 410s Processing triggers for install-info (7.1-3build1) ... 410s Processing triggers for libc-bin (2.39-0ubuntu6) ... 411s Processing triggers for initramfs-tools (0.142ubuntu22) ... 417s Reading package lists... 418s Building dependency tree... 418s Reading state information... 420s The following packages will be REMOVED: 420s libatasmart4* libblockdev-crypto3* libblockdev-fs3* libblockdev-loop3* 420s libblockdev-mdraid3* libblockdev-nvme3* libblockdev-part3* 420s libblockdev-swap3* libblockdev-utils3* libblockdev3* libbytesize-common* 421s libbytesize1* libnspr4* libnss3* libnvme1t64* libpolkit-agent-1-0* 421s libvolume-key1* linux-headers-6.8.0-11* python3-lib2to3* 422s 0 upgraded, 0 newly installed, 19 to remove and 1 not upgraded. 422s After this operation, 89.7 MB disk space will be freed. 422s (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 ... 47392 files and directories currently installed.) 422s Removing libatasmart4:armhf (0.19-5build2) ... 422s Removing libblockdev-crypto3:armhf (3.1.0-1build1) ... 422s Removing libblockdev-fs3:armhf (3.1.0-1build1) ... 422s Removing libblockdev-loop3:armhf (3.1.0-1build1) ... 422s Removing libblockdev-mdraid3:armhf (3.1.0-1build1) ... 422s Removing libblockdev-nvme3:armhf (3.1.0-1build1) ... 423s Removing libblockdev-part3:armhf (3.1.0-1build1) ... 423s Removing libblockdev-swap3:armhf (3.1.0-1build1) ... 423s Removing libblockdev3:armhf (3.1.0-1build1) ... 423s Removing libblockdev-utils3:armhf (3.1.0-1build1) ... 423s Removing libbytesize1:armhf (2.10-1ubuntu1) ... 423s Removing libbytesize-common (2.10-1ubuntu1) ... 423s Removing libvolume-key1:armhf (0.3.12-7build1) ... 423s Removing libnss3:armhf (2:3.98-1) ... 423s Removing libnspr4:armhf (2:4.35-1.1) ... 423s Removing libnvme1t64 (1.8-3) ... 423s Removing libpolkit-agent-1-0:armhf (124-1ubuntu1) ... 423s Removing linux-headers-6.8.0-11 (6.8.0-11.11) ... 427s Removing python3-lib2to3 (3.12.2-3ubuntu2) ... 427s Processing triggers for libc-bin (2.39-0ubuntu6) ... 428s (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 ... 27121 files and directories currently installed.) 428s Purging configuration files for libblockdev3:armhf (3.1.0-1build1) ... 432s autopkgtest [03:23:59]: rebooting testbed after setup commands that affected boot 466s autopkgtest [03:24:33]: testbed running kernel: Linux 5.4.0-170-generic #188-Ubuntu SMP Wed Jan 10 09:51:10 UTC 2024 470s autopkgtest [03:24:37]: testbed dpkg architecture: armhf 486s autopkgtest [03:24:53]: @@@@@@@@@@@@@@@@@@@@ apt-source pdb2pqr 499s Get:1 http://ftpmaster.internal/ubuntu noble/universe pdb2pqr 3.6.1+dfsg-1 (dsc) [1860 B] 499s Get:2 http://ftpmaster.internal/ubuntu noble/universe pdb2pqr 3.6.1+dfsg-1 (tar) [7570 kB] 499s Get:3 http://ftpmaster.internal/ubuntu noble/universe pdb2pqr 3.6.1+dfsg-1 (diff) [9876 B] 499s gpgv: Signature made Mon Jun 12 17:36:50 2023 UTC 499s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 499s gpgv: Can't check signature: No public key 499s dpkg-source: warning: cannot verify inline signature for ./pdb2pqr_3.6.1+dfsg-1.dsc: no acceptable signature found 503s autopkgtest [03:25:09]: testing package pdb2pqr version 3.6.1+dfsg-1 503s autopkgtest [03:25:10]: build not needed 511s autopkgtest [03:25:18]: test installation-test: preparing testbed 526s Reading package lists... 526s Building dependency tree... 526s Reading state information... 527s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 528s Starting 2 pkgProblemResolver with broken count: 0 528s Done 529s Done 530s Starting pkgProblemResolver with broken count: 0 530s Starting 2 pkgProblemResolver with broken count: 0 530s Done 532s The following additional packages will be installed: 532s docutils-common libblas3 libgfortran5 liblapack3 pdb2pqr python3-docutils 532s python3-numpy python3-pdb2pqr python3-pdbx python3-propka python3-roman 532s sgml-base xml-core 532s Suggested packages: 532s apbs docutils-doc fonts-linuxlibertine | ttf-linux-libertine 532s texlive-lang-french texlive-latex-base texlive-latex-recommended gcc 532s gfortran python3-dev python3-pytest python-pdbx-doc python-propka-doc 532s sgml-base-doc debhelper 532s Recommended packages: 532s libpaper-utils python3-pil 532s The following NEW packages will be installed: 532s docutils-common libblas3 libgfortran5 liblapack3 pdb2pqr python3-docutils 532s python3-numpy python3-pdb2pqr python3-pdbx python3-propka python3-roman 532s sgml-base xml-core 533s 0 upgraded, 13 newly installed, 0 to remove and 1 not upgraded. 533s 1 not fully installed or removed. 533s Need to get 7753 kB of archives. 533s After this operation, 31.9 MB of additional disk space will be used. 533s Get:1 http://ftpmaster.internal/ubuntu noble/main armhf libblas3 armhf 3.12.0-3 [123 kB] 533s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgfortran5 armhf 14-20240315-1ubuntu1 [312 kB] 533s Get:3 http://ftpmaster.internal/ubuntu noble/main armhf liblapack3 armhf 3.12.0-3 [2085 kB] 534s Get:4 http://ftpmaster.internal/ubuntu noble/main armhf python3-numpy armhf 1:1.24.2-2 [4410 kB] 535s Get:5 http://ftpmaster.internal/ubuntu noble/main armhf sgml-base all 1.31 [11.4 kB] 535s Get:6 http://ftpmaster.internal/ubuntu noble/main armhf xml-core all 0.19 [20.3 kB] 535s Get:7 http://ftpmaster.internal/ubuntu noble/main armhf docutils-common all 0.20.1+dfsg-3 [132 kB] 535s Get:8 http://ftpmaster.internal/ubuntu noble/main armhf python3-roman all 3.3-3 [9632 B] 535s Get:9 http://ftpmaster.internal/ubuntu noble/main armhf python3-docutils all 0.20.1+dfsg-3 [393 kB] 535s Get:10 http://ftpmaster.internal/ubuntu noble/universe armhf python3-pdbx all 2.0.1-2 [16.5 kB] 535s Get:11 http://ftpmaster.internal/ubuntu noble/universe armhf python3-propka all 3.5.1-1 [85.5 kB] 535s Get:12 http://ftpmaster.internal/ubuntu noble/universe armhf python3-pdb2pqr all 3.6.1+dfsg-1 [145 kB] 535s Get:13 http://ftpmaster.internal/ubuntu noble/universe armhf pdb2pqr all 3.6.1+dfsg-1 [10.4 kB] 537s Fetched 7753 kB in 3s (2525 kB/s) 537s Selecting previously unselected package libblas3:armhf. 537s (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 ... 27117 files and directories currently installed.) 537s Preparing to unpack .../00-libblas3_3.12.0-3_armhf.deb ... 537s Unpacking libblas3:armhf (3.12.0-3) ... 537s Selecting previously unselected package libgfortran5:armhf. 537s Preparing to unpack .../01-libgfortran5_14-20240315-1ubuntu1_armhf.deb ... 537s Unpacking libgfortran5:armhf (14-20240315-1ubuntu1) ... 537s Selecting previously unselected package liblapack3:armhf. 537s Preparing to unpack .../02-liblapack3_3.12.0-3_armhf.deb ... 537s Unpacking liblapack3:armhf (3.12.0-3) ... 537s Selecting previously unselected package python3-numpy. 537s Preparing to unpack .../03-python3-numpy_1%3a1.24.2-2_armhf.deb ... 537s Unpacking python3-numpy (1:1.24.2-2) ... 539s Selecting previously unselected package sgml-base. 539s Preparing to unpack .../04-sgml-base_1.31_all.deb ... 539s Unpacking sgml-base (1.31) ... 539s Selecting previously unselected package xml-core. 539s Preparing to unpack .../05-xml-core_0.19_all.deb ... 539s Unpacking xml-core (0.19) ... 539s Selecting previously unselected package docutils-common. 539s Preparing to unpack .../06-docutils-common_0.20.1+dfsg-3_all.deb ... 539s Unpacking docutils-common (0.20.1+dfsg-3) ... 539s Selecting previously unselected package python3-roman. 539s Preparing to unpack .../07-python3-roman_3.3-3_all.deb ... 539s Unpacking python3-roman (3.3-3) ... 539s Selecting previously unselected package python3-docutils. 539s Preparing to unpack .../08-python3-docutils_0.20.1+dfsg-3_all.deb ... 539s Unpacking python3-docutils (0.20.1+dfsg-3) ... 539s Selecting previously unselected package python3-pdbx. 539s Preparing to unpack .../09-python3-pdbx_2.0.1-2_all.deb ... 539s Unpacking python3-pdbx (2.0.1-2) ... 539s Selecting previously unselected package python3-propka. 539s Preparing to unpack .../10-python3-propka_3.5.1-1_all.deb ... 539s Unpacking python3-propka (3.5.1-1) ... 540s Selecting previously unselected package python3-pdb2pqr. 540s Preparing to unpack .../11-python3-pdb2pqr_3.6.1+dfsg-1_all.deb ... 540s Unpacking python3-pdb2pqr (3.6.1+dfsg-1) ... 540s Selecting previously unselected package pdb2pqr. 540s Preparing to unpack .../12-pdb2pqr_3.6.1+dfsg-1_all.deb ... 540s Unpacking pdb2pqr (3.6.1+dfsg-1) ... 540s Setting up python3-propka (3.5.1-1) ... 541s Setting up python3-pdbx (2.0.1-2) ... 542s Setting up python3-roman (3.3-3) ... 542s Setting up libblas3:armhf (3.12.0-3) ... 542s 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 542s Setting up libgfortran5:armhf (14-20240315-1ubuntu1) ... 542s Setting up sgml-base (1.31) ... 542s Setting up liblapack3:armhf (3.12.0-3) ... 542s 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 542s Setting up python3-numpy (1:1.24.2-2) ... 551s Setting up xml-core (0.19) ... 552s Processing triggers for libc-bin (2.39-0ubuntu6) ... 552s Processing triggers for man-db (2.12.0-3build4) ... 553s Processing triggers for sgml-base (1.31) ... 553s Setting up docutils-common (0.20.1+dfsg-3) ... 553s Processing triggers for sgml-base (1.31) ... 553s Setting up python3-docutils (0.20.1+dfsg-3) ... 555s Setting up python3-pdb2pqr (3.6.1+dfsg-1) ... 556s Setting up pdb2pqr (3.6.1+dfsg-1) ... 556s Setting up autopkgtest-satdep (0) ... 578s (Reading database ... 28631 files and directories currently installed.) 578s Removing autopkgtest-satdep (0) ... 590s autopkgtest [03:26:37]: test installation-test: [----------------------- 593s Run pdb2pqr... 594s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 594s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 594s 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). 594s INFO:Checking and transforming input arguments. 594s INFO:Loading topology files. 594s INFO:Loading molecule: examples/1a1p/1a1p.pdb 594s INFO:Setting up molecule. 594s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 594s INFO:Created biomolecule object with 14 residues and 208 atoms. 594s INFO:Setting termini states for biomolecule chains. 594s INFO:Loading forcefield. 594s INFO:Loading hydrogen topology definitions. 594s INFO:This biomolecule is clean. No repair needed. 594s INFO:Updating disulfide bridges. 594s INFO:Debumping biomolecule. 594s INFO:Adding hydrogens to biomolecule. 594s INFO:Debumping biomolecule (again). 594s INFO:Optimizing hydrogen bonds 595s INFO:Applying force field to biomolecule states. 595s INFO:Regenerating headers. 595s INFO:Regenerating PDB lines. 595s WARNING:Ignoring 852 header lines in output. 595s WARNING:Ignoring 3 missing lines in output. 595s autopkgtest [03:26:42]: test installation-test: -----------------------] 600s autopkgtest [03:26:47]: test installation-test: - - - - - - - - - - results - - - - - - - - - - 600s installation-test PASS 605s autopkgtest [03:26:52]: test pdb2pka-test: preparing testbed 621s Reading package lists... 622s Building dependency tree... 622s Reading state information... 623s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 623s Starting 2 pkgProblemResolver with broken count: 0 623s Done 624s Done 625s Starting pkgProblemResolver with broken count: 0 625s Starting 2 pkgProblemResolver with broken count: 0 626s Done 628s The following additional packages will be installed: 628s fonts-font-awesome fonts-lato libjs-jquery libjs-sphinxdoc libjs-underscore 628s pdb2pqr-doc sphinx-rtd-theme-common 628s Recommended packages: 628s javascript-common 628s The following NEW packages will be installed: 628s fonts-font-awesome fonts-lato libjs-jquery libjs-sphinxdoc libjs-underscore 628s pdb2pqr-doc sphinx-rtd-theme-common 628s 0 upgraded, 7 newly installed, 0 to remove and 1 not upgraded. 628s 1 not fully installed or removed. 628s Need to get 5162 kB of archives. 628s After this operation, 20.1 MB of additional disk space will be used. 628s Get:1 http://ftpmaster.internal/ubuntu noble/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 629s Get:2 http://ftpmaster.internal/ubuntu noble/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 629s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjs-sphinxdoc all 7.2.6-5 [149 kB] 629s Get:4 http://ftpmaster.internal/ubuntu noble/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 629s Get:5 http://ftpmaster.internal/ubuntu noble/main armhf fonts-lato all 2.015-1 [2781 kB] 630s Get:6 http://ftpmaster.internal/ubuntu noble/main armhf sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1012 kB] 630s Get:7 http://ftpmaster.internal/ubuntu noble/universe armhf pdb2pqr-doc all 3.6.1+dfsg-1 [258 kB] 633s Fetched 5162 kB in 2s (2121 kB/s) 633s Selecting previously unselected package libjs-jquery. 633s (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 ... 28631 files and directories currently installed.) 633s Preparing to unpack .../0-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 633s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 633s Selecting previously unselected package libjs-underscore. 633s Preparing to unpack .../1-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 633s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 634s Selecting previously unselected package libjs-sphinxdoc. 634s Preparing to unpack .../2-libjs-sphinxdoc_7.2.6-5_all.deb ... 634s Unpacking libjs-sphinxdoc (7.2.6-5) ... 634s Selecting previously unselected package fonts-font-awesome. 634s Preparing to unpack .../3-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 634s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 634s Selecting previously unselected package fonts-lato. 634s Preparing to unpack .../4-fonts-lato_2.015-1_all.deb ... 634s Unpacking fonts-lato (2.015-1) ... 635s Selecting previously unselected package sphinx-rtd-theme-common. 635s Preparing to unpack .../5-sphinx-rtd-theme-common_2.0.0+dfsg-1_all.deb ... 635s Unpacking sphinx-rtd-theme-common (2.0.0+dfsg-1) ... 635s Selecting previously unselected package pdb2pqr-doc. 635s Preparing to unpack .../6-pdb2pqr-doc_3.6.1+dfsg-1_all.deb ... 636s Unpacking pdb2pqr-doc (3.6.1+dfsg-1) ... 636s Setting up fonts-lato (2.015-1) ... 636s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 636s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 636s Setting up sphinx-rtd-theme-common (2.0.0+dfsg-1) ... 636s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 636s Setting up libjs-sphinxdoc (7.2.6-5) ... 636s Setting up pdb2pqr-doc (3.6.1+dfsg-1) ... 636s Setting up autopkgtest-satdep (0) ... 660s (Reading database ... 28965 files and directories currently installed.) 660s Removing autopkgtest-satdep (0) ... 673s autopkgtest [03:28:00]: test pdb2pka-test: [----------------------- 676s Run pdb2pqr... 677s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 677s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 677s 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). 677s INFO:Checking and transforming input arguments. 677s INFO:Loading topology files. 677s INFO:Loading molecule: 1a1p/1a1p.pdb 677s INFO:Setting up molecule. 677s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 677s INFO:Created biomolecule object with 14 residues and 208 atoms. 677s INFO:Setting termini states for biomolecule chains. 677s INFO:Loading forcefield. 677s INFO:Loading hydrogen topology definitions. 677s INFO:This biomolecule is clean. No repair needed. 677s INFO:Updating disulfide bridges. 677s INFO:Debumping biomolecule. 677s INFO:Adding hydrogens to biomolecule. 677s INFO:Debumping biomolecule (again). 677s INFO:Optimizing hydrogen bonds 678s INFO:Applying force field to biomolecule states. 678s INFO:Regenerating headers. 678s INFO:Regenerating PDB lines. 678s WARNING:Ignoring 852 header lines in output. 678s WARNING:Ignoring 3 missing lines in output. 678s autopkgtest [03:28:05]: test pdb2pka-test: -----------------------] 683s pdb2pka-test PASSautopkgtest [03:28:10]: test pdb2pka-test: - - - - - - - - - - results - - - - - - - - - - 683s 688s autopkgtest [03:28:15]: test command1: preparing testbed 701s Reading package lists... 702s Building dependency tree... 702s Reading state information... 703s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 704s Starting 2 pkgProblemResolver with broken count: 0 704s Done 705s Done 705s Starting pkgProblemResolver with broken count: 0 706s Starting 2 pkgProblemResolver with broken count: 0 706s Done 708s The following additional packages will be installed: 708s python3-dateutil python3-iniconfig python3-packaging python3-pandas 708s python3-pandas-lib python3-pluggy python3-pytest python3-testfixtures 708s Suggested packages: 708s python-pandas-doc python3-statsmodels python-testfixtures-doc 708s Recommended packages: 708s python3-scipy python3-matplotlib python3-bottleneck python3-numexpr 708s python3-odf python3-openpyxl python3-bs4 python3-html5lib python3-lxml 708s python3-tables 708s The following NEW packages will be installed: 708s python3-dateutil python3-iniconfig python3-packaging python3-pandas 708s python3-pandas-lib python3-pluggy python3-pytest python3-testfixtures 708s 0 upgraded, 8 newly installed, 0 to remove and 1 not upgraded. 708s 1 not fully installed or removed. 708s Need to get 11.7 MB of archives. 708s After this operation, 51.0 MB of additional disk space will be used. 708s Get:1 http://ftpmaster.internal/ubuntu noble/main armhf python3-dateutil all 2.8.2-3 [79.2 kB] 708s Get:2 http://ftpmaster.internal/ubuntu noble/universe armhf python3-pandas-lib armhf 2.1.4+dfsg-4ubuntu2 [8219 kB] 711s Get:3 http://ftpmaster.internal/ubuntu noble/universe armhf python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 712s Get:4 http://ftpmaster.internal/ubuntu noble/universe armhf python3-iniconfig all 1.1.1-2 [6024 B] 712s Get:5 http://ftpmaster.internal/ubuntu noble/main armhf python3-packaging all 23.2-1 [40.6 kB] 712s Get:6 http://ftpmaster.internal/ubuntu noble/universe armhf python3-pluggy all 1.4.0-1 [20.4 kB] 712s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf python3-pytest all 8.0.2-1 [248 kB] 712s Get:8 http://ftpmaster.internal/ubuntu noble/universe armhf python3-testfixtures all 8.1.0-1 [73.5 kB] 713s Fetched 11.7 MB in 4s (2830 kB/s) 714s Selecting previously unselected package python3-dateutil. 714s (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 ... 28965 files and directories currently installed.) 714s Preparing to unpack .../0-python3-dateutil_2.8.2-3_all.deb ... 714s Unpacking python3-dateutil (2.8.2-3) ... 714s Selecting previously unselected package python3-pandas-lib:armhf. 714s Preparing to unpack .../1-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_armhf.deb ... 714s Unpacking python3-pandas-lib:armhf (2.1.4+dfsg-4ubuntu2) ... 715s Selecting previously unselected package python3-pandas. 715s Preparing to unpack .../2-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 715s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 717s Selecting previously unselected package python3-iniconfig. 717s Preparing to unpack .../3-python3-iniconfig_1.1.1-2_all.deb ... 717s Unpacking python3-iniconfig (1.1.1-2) ... 717s Selecting previously unselected package python3-packaging. 717s Preparing to unpack .../4-python3-packaging_23.2-1_all.deb ... 717s Unpacking python3-packaging (23.2-1) ... 717s Selecting previously unselected package python3-pluggy. 717s Preparing to unpack .../5-python3-pluggy_1.4.0-1_all.deb ... 717s Unpacking python3-pluggy (1.4.0-1) ... 717s Selecting previously unselected package python3-pytest. 717s Preparing to unpack .../6-python3-pytest_8.0.2-1_all.deb ... 717s Unpacking python3-pytest (8.0.2-1) ... 717s Selecting previously unselected package python3-testfixtures. 718s Preparing to unpack .../7-python3-testfixtures_8.1.0-1_all.deb ... 718s Unpacking python3-testfixtures (8.1.0-1) ... 718s Setting up python3-iniconfig (1.1.1-2) ... 718s Setting up python3-pandas-lib:armhf (2.1.4+dfsg-4ubuntu2) ... 718s Setting up python3-testfixtures (8.1.0-1) ... 719s Setting up python3-packaging (23.2-1) ... 720s Setting up python3-pluggy (1.4.0-1) ... 720s Setting up python3-dateutil (2.8.2-3) ... 721s Setting up python3-pytest (8.0.2-1) ... 722s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... 743s Setting up autopkgtest-satdep (0) ... 743s Processing triggers for man-db (2.12.0-3build4) ... 770s (Reading database ... 30979 files and directories currently installed.) 770s Removing autopkgtest-satdep (0) ... 782s autopkgtest [03:29:49]: test command1: pytest-3 782s autopkgtest [03:29:49]: test command1: [----------------------- 790s ============================= test session starts ============================== 790s platform linux -- Python 3.12.2, pytest-8.0.2, pluggy-1.4.0 790s rootdir: /tmp/autopkgtest.bHaQls/build.yWb/src 790s configfile: pytest.ini 790s 790s ----------------------------- live log collection ------------------------------ 790s WARNING py.warnings:warnings.py:110 /tmp/autopkgtest.bHaQls/build.yWb/src/tests/core_test.py:81: PytestUnknownMarkWarning: Unknown pytest.mark.long_test - is this a typo? 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[ 65%] 792s tests/core_test.py::test_long_pdb[2FRG] SKIPPED (not running tests r...) [ 65%] 792s tests/core_test.py::test_long_pdb[2FWG] SKIPPED (not running tests r...) [ 65%] 792s tests/core_test.py::test_long_pdb[1IS5] SKIPPED (not running tests r...) [ 66%] 792s tests/core_test.py::test_broken_backbone[1EJG] 792s -------------------------------- live log call --------------------------------- 792s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_1EJG_0/1EJG.log 792s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 792s 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). 792s 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). 792s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 792s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 793s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 1EJG 794s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 794s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 794s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 46 residues and 650 atoms. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in THR A 1. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in THR A 1. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 1. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 1. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 1. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H1 in THR A 1. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H2 in THR A 1. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H3 in THR A 1. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in THR A 1. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 1. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG1 in THR A 1. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 1. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 1. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 1. 794s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 1. At least one of the instances is being ignored. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in THR A 2. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 2. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 2. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 2. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in THR A 2. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 2. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG1 in THR A 2. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 2. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 2. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 2. 794s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 2. At least one of the instances is being ignored. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ILE A 7. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in ILE A 7. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in ILE A 7. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 7. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 7. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 7. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 7. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ILE A 7. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 7. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 7. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 7. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 7. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 7. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 7. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 7. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 7. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 7. 794s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 7. At least one of the instances is being ignored. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in VAL A 8. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in VAL A 8. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in VAL A 8. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in VAL A 8. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in VAL A 8. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in VAL A 8. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in VAL A 8. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in VAL A 8. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG11 in VAL A 8. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in VAL A 8. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in VAL A 8. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in VAL A 8. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in VAL A 8. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in VAL A 8. 794s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in VAL A 8. At least one of the instances is being ignored. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NE in ARG A 10. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in ARG A 10. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NH1 in ARG A 10. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NH2 in ARG A 10. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE in ARG A 10. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH11 in ARG A 10. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH12 in ARG A 10. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH21 in ARG A 10. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH22 in ARG A 10. 794s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ARG A 10. At least one of the instances is being ignored. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ASN A 12. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ASN A 12. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASN A 12. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASN A 12. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: ND2 in ASN A 12. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ASN A 12. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ASN A 12. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ASN A 12. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ASN A 12. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ASN A 12. 794s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASN A 12. At least one of the instances is being ignored. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PHE A 13. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in PHE A 13. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in PHE A 13. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE1 in PHE A 13. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE2 in PHE A 13. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in PHE A 13. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD1 in PHE A 13. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PHE A 13. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE1 in PHE A 13. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE2 in PHE A 13. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HZ in PHE A 13. 794s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PHE A 13. At least one of the instances is being ignored. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 19. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 19. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 19. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 19. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 19. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PRO A 19. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in PRO A 19. 794s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 19. At least one of the instances is being ignored. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in SER A 22. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in SER A 22. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in SER A 22. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in SER A 22. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in SER A 22. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in SER A 22. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in SER A 22. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in SER A 22. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in SER A 22. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in SER A 22. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in SER A 22. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in SER A 22. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in SER A 22. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG in SER A 22. 794s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in SER A 22. At least one of the instances is being ignored. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in GLU A 23. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in GLU A 23. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OE1 in GLU A 23. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OE2 in GLU A 23. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in GLU A 23. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in GLU A 23. 794s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in GLU A 23. At least one of the instances is being ignored. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in ILE A 25. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ILE A 25. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in ILE A 25. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in ILE A 25. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 25. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ILE A 25. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 25. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in ILE A 25. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in ILE A 25. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ILE A 25. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ILE A 25. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ILE A 25. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in ILE A 25. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 25. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 25. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 25. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ILE A 25. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ILE A 25. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD23 in ILE A 25. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 25. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 25. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 25. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 25. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 25. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 25. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 25. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 25. 794s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 25. At least one of the instances is being ignored. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in TYR A 29. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in TYR A 29. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in TYR A 29. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE1 in TYR A 29. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE2 in TYR A 29. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in TYR A 29. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OH in TYR A 29. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD1 in TYR A 29. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in TYR A 29. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE1 in TYR A 29. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE2 in TYR A 29. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH in TYR A 29. 794s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in TYR A 29. At least one of the instances is being ignored. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 34. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 34. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 34. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 34. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 34. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 34. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 34. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 34. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 34. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 34. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 34. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 34. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 34. 794s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 34. At least one of the instances is being ignored. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in PRO A 36. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 36. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 36. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 36. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 36. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 36. 794s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 36. At least one of the instances is being ignored. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 39. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 39. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 39. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 39. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 39. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 39. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 39. 794s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 39. At least one of the instances is being ignored. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ASP A 43. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASP A 43. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASP A 43. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD2 in ASP A 43. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ASP A 43. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ASP A 43. 794s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASP A 43. At least one of the instances is being ignored. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASN A 46. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASN A 46. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: ND2 in ASN A 46. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ASN A 46. 794s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ASN A 46. 794s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASN A 46. At least one of the instances is being ignored. 794s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 795s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 795s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 795s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 795s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 795s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 795s 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 795s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 796s XFAIL [ 66%] 796s tests/core_test.py::test_broken_backbone[3U7T] 796s -------------------------------- live log call --------------------------------- 796s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_3U7T_0/3U7T.log 796s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 796s 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). 796s 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). 796s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 796s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 796s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 3U7T 797s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 797s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 797s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 46 residues and 652 atoms. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in PRO A 22. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in PRO A 22. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in PRO A 22. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in PRO A 22. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in PRO A 22. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG in PRO A 22. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in PRO A 22. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 22. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 22. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in PRO A 22. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 22. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in PRO A 22. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 22. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 22. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PRO A 22. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in PRO A 22. 797s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 22. At least one of the instances is being ignored. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in LEU A 25. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in LEU A 25. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in LEU A 25. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in LEU A 25. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in LEU A 25. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in LEU A 25. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in LEU A 25. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in LEU A 25. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in LEU A 25. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in LEU A 25. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in LEU A 25. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in LEU A 25. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in LEU A 25. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in LEU A 25. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in LEU A 25. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in LEU A 25. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in LEU A 25. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in LEU A 25. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in LEU A 25. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in LEU A 25. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in LEU A 25. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in LEU A 25. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in LEU A 25. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in LEU A 25. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in LEU A 25. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in LEU A 25. 797s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD23 in LEU A 25. 797s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in LEU A 25. At least one of the instances is being ignored. 797s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 797s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 797s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 797s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 797s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 797s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 798s 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 798s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 798s XFAIL [ 66%] 798s tests/core_test.py::test_broken_backbone[4MGP] 798s -------------------------------- live log call --------------------------------- 798s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_4MGP_0/4MGP.log 798s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 798s 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). 798s 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). 798s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 798s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 798s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 4MGP 799s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 799s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 799s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 23 residues and 163 atoms. 799s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in MET A 21. 799s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in MET A 21. 799s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in MET A 21. 799s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: SD in MET A 21. 799s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE in MET A 21. 799s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in MET A 21. At least one of the instances is being ignored. 799s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 799s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 799s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 799s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 12 missing atoms in biomolecule. 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 799s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 799s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 11 at coordinates 1.430, -1.683, -11.529 799s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 11 at coordinates 1.940, -0.315, -11.800 799s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CG to residue LYS A 14 at coordinates -1.600, -8.819, -6.913 799s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CD to residue LYS A 14 at coordinates -2.056, -8.844, -8.361 799s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 14 at coordinates -3.548, -9.031, -8.498 799s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 14 at coordinates -3.947, -9.048, -9.928 799s 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 799s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 799s XFAIL [ 67%] 799s tests/core_test.py::test_broken_backbone[2V75] 799s -------------------------------- live log call --------------------------------- 799s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_2V75_0/2V75.log 799s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 799s 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). 799s 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). 799s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 799s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 799s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 2V75 800s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 800s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 800s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 90 residues and 687 atoms. 800s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 801s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 801s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 801s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 801s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 801s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 801s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 801s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 801s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 801s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 801s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 801s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 801s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 801s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 801s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 801s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 801s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 801s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 801s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 801s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 8 missing atoms in biomolecule. 801s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 801s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 801s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 801s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 801s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 801s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 801s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 801s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 801s 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 801s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 801s XFAIL [ 67%] 801s tests/core_test.py::test_protonated_terminals[C-terminal HID] 801s -------------------------------- live log call --------------------------------- 801s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_protonated_terminals_C_te0/cterm_hid.log 801s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 801s 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). 801s 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). 801s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 801s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 801s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/cterm_hid.pdb 801s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 801s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 115 atoms. 801s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 801s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 801s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 801s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 801s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 801s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 1 missing atoms in biomolecule. 801s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 801s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue HIS B 209 at coordinates -25.652, 1.939, 26.402 801s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 801s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 801s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 801s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 801s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 802s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 802s INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). 802s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 802s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 802s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. 802s INFO common:common.py:198 0 atoms have position differences > 0 802s INFO common:common.py:198 0 atoms have position differences > 0.01 802s INFO common:common.py:198 0 atoms have charge differences > 0 802s INFO common:common.py:198 0 atoms have charge differences > 0.01 802s INFO common:common.py:198 0 atoms have radius differences > 0 802s INFO common:common.py:198 0 atoms have radius differences > 0.01 802s PASSED [ 67%] 802s tests/core_test.py::test_cyclic_peptide[Cyclic peptide] 802s -------------------------------- live log call --------------------------------- 802s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_cyclic_peptide_Cyclic_pep0/5vav_cyclic_peptide.log 802s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 802s 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). 802s 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). 802s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 802s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 802s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/5vav_cyclic_peptide.pdb 802s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 802s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 209 atoms. 802s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 802s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 802s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 802s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 802s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 802s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 803s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 803s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 803s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 803s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 803s INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). 803s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 803s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 803s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. 803s INFO common:common.py:198 0 atoms have position differences > 0 803s INFO common:common.py:198 0 atoms have position differences > 0.01 803s INFO common:common.py:198 0 atoms have charge differences > 0 803s INFO common:common.py:198 0 atoms have charge differences > 0.01 803s INFO common:common.py:198 0 atoms have radius differences > 0 803s INFO common:common.py:198 0 atoms have radius differences > 0.01 803s PASSED [ 68%] 803s tests/io_test.py::test_read_pqr[tests/data/dx2cube.pqr] PASSED [ 68%] 803s tests/io_test.py::test_read_pqr[tests/data/cterm_hid_out.pqr] PASSED [ 68%] 803s tests/io_test.py::test_read_pqr[tests/data/5vav_cyclic_peptide_out.pqr] PASSED [ 68%] 803s 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%] 803s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=TYL06.pqr] PASSED [ 69%] 803s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=SWANSON.pqr] PASSED [ 69%] 804s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PEOEPB.pqr] PASSED [ 70%] 804s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PARSE.pqr] PASSED [ 70%] 804s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=CHARMM.pqr] PASSED [ 70%] 804s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=AMBER.pqr] PASSED [ 71%] 804s tests/io_test.py::test_read_pqr[tests/data/1AFS_userff_usernames_whitespace.pqr] PASSED [ 71%] 805s tests/io_test.py::test_read_pqr[tests/data/1AFS_nodebump_noopt_whitespace_ff=AMBER.pqr] PASSED [ 71%] 805s tests/io_test.py::test_read_pqr[tests/data/1AFS_neutralc_neutraln_whitespace_ff=PARSE.pqr] PASSED [ 72%] 805s tests/io_test.py::test_read_pqr[tests/data/1AFS_ff=AMBER.pqr] PASSED [ 72%] 805s tests/io_test.py::test_read_pqr[tests/data/1AFS_drop-water_ff=AMBER.pqr] PASSED [ 72%] 805s tests/io_test.py::test_read_pqr[tests/data/1AFS_clean_whitespace.pqr] PASSED [ 73%] 805s tests/io_test.py::test_read_pqr[tests/data/1AFS_chain_whitespace_ff=AMBER.pqr] PASSED [ 73%] 806s tests/io_test.py::test_read_pqr[tests/data/1AFS_apbs-input_include-header_whitespace_ff=AMBER.pqr] PASSED [ 73%] 806s tests/io_test.py::test_read_pqr[tests/data/1A1P_assign-only_whitespace_ff=AMBER.pqr] PASSED [ 74%] 806s tests/io_test.py::test_read_qcd PASSED [ 74%] 806s tests/io_test.py::test_dx2cube 806s -------------------------------- live log call --------------------------------- 806s INFO io_test:io_test.py:44 Reading PQR from tests/data/dx2cube.pqr... 806s INFO io_test:io_test.py:47 Reading DX from tests/data/dx2cube.dx... 808s INFO io_test:io_test.py:50 Writing Cube to /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 811s INFO io_test:io_test.py:53 Reading this cube from /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 811s INFO io_test:io_test.py:55 Reading test cube from tests/data/dx2cube.cube... 813s INFO io_test:io_test.py:68 No differences found in output 813s PASSED [ 74%] 815s tests/ligand_test.py::test_peoe_charges 815s -------------------------------- live log call --------------------------------- 815s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 815s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 815s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 815s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 815s PASSED [ 75%] 818s tests/ligand_test.py::test_assign_parameters[1HPX-ligand.mol2] 818s -------------------------------- live log call --------------------------------- 818s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 818s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 818s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 818s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 818s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 818s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 818s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 818s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 818s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 818s PASSED [ 75%] 820s tests/ligand_test.py::test_assign_parameters[1QBS-ligand.mol2] 820s -------------------------------- live log call --------------------------------- 820s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 820s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 820s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 820s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 820s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 820s PASSED [ 75%] 820s tests/ligand_test.py::test_assign_parameters[1US0-ligand.mol2] 820s -------------------------------- live log call --------------------------------- 820s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 820s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 820s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 820s PASSED [ 75%] 820s tests/ligand_test.py::test_assign_parameters[acetate.mol2] 820s -------------------------------- live log call --------------------------------- 820s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 820s PASSED [ 76%] 820s tests/ligand_test.py::test_assign_parameters[acetonitrile.mol2] 820s -------------------------------- live log call --------------------------------- 820s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 820s PASSED [ 76%] 820s tests/ligand_test.py::test_assign_parameters[acetylcholine.mol2] 820s -------------------------------- live log call --------------------------------- 820s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 820s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 820s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 820s PASSED [ 76%] 821s tests/ligand_test.py::test_assign_parameters[adp.mol2] 821s -------------------------------- live log call --------------------------------- 821s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 821s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 821s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 821s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 821s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 821s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 821s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 821s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 821s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 821s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 821s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 821s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 821s INFO ligand_test:ligand_test.py:73 Total charge: -2.00 -> -2.00 821s PASSED [ 77%] 821s tests/ligand_test.py::test_assign_parameters[anthracene.mol2] 821s -------------------------------- live log call --------------------------------- 821s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 821s PASSED [ 77%] 821s tests/ligand_test.py::test_assign_parameters[cyclohexane.mol2] 821s -------------------------------- live log call --------------------------------- 821s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 821s PASSED [ 77%] 821s tests/ligand_test.py::test_assign_parameters[ethanol.mol2] 821s -------------------------------- live log call --------------------------------- 821s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 821s PASSED [ 78%] 821s tests/ligand_test.py::test_assign_parameters[fatty-acid.mol2] 821s -------------------------------- live log call --------------------------------- 821s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 821s PASSED [ 78%] 821s tests/ligand_test.py::test_assign_parameters[glycerol.mol2] 821s -------------------------------- live log call --------------------------------- 821s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 821s PASSED [ 78%] 821s tests/ligand_test.py::test_assign_parameters[naphthalene.mol2] 821s -------------------------------- live log call --------------------------------- 821s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 821s PASSED [ 79%] 821s tests/ligand_test.py::test_assign_parameters[pyrrole.mol2] 821s -------------------------------- live log call --------------------------------- 821s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 821s PASSED [ 79%] 821s tests/ligand_test.py::test_assign_parameters[tetramethylammonium.mol2] 821s -------------------------------- live log call --------------------------------- 821s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 821s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 821s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 821s PASSED [ 79%] 823s tests/ligand_test.py::test_formal_charge[1HPX-ligand.mol2] 823s -------------------------------- live log call --------------------------------- 823s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 823s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 823s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 823s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 823s PASSED [ 80%] 826s tests/ligand_test.py::test_formal_charge[1QBS-ligand.mol2] 826s -------------------------------- live log call --------------------------------- 826s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 826s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 826s PASSED [ 80%] 826s tests/ligand_test.py::test_formal_charge[1US0-ligand.mol2] 826s -------------------------------- live log call --------------------------------- 826s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 826s PASSED [ 80%] 826s tests/ligand_test.py::test_formal_charge[acetate.mol2] PASSED [ 81%] 826s tests/ligand_test.py::test_formal_charge[acetonitrile.mol2] PASSED [ 81%] 826s tests/ligand_test.py::test_formal_charge[acetylcholine.mol2] 826s -------------------------------- live log call --------------------------------- 826s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 826s PASSED [ 81%] 826s tests/ligand_test.py::test_formal_charge[adp.mol2] 826s -------------------------------- live log call --------------------------------- 826s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 826s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 826s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 826s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 826s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 826s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 826s PASSED [ 81%] 826s tests/ligand_test.py::test_formal_charge[anthracene.mol2] PASSED [ 82%] 826s tests/ligand_test.py::test_formal_charge[cyclohexane.mol2] PASSED [ 82%] 826s tests/ligand_test.py::test_formal_charge[ethanol.mol2] PASSED [ 82%] 827s tests/ligand_test.py::test_formal_charge[fatty-acid.mol2] PASSED [ 83%] 827s tests/ligand_test.py::test_formal_charge[glycerol.mol2] PASSED [ 83%] 827s tests/ligand_test.py::test_formal_charge[naphthalene.mol2] PASSED [ 83%] 827s tests/ligand_test.py::test_formal_charge[pyrrole.mol2] PASSED [ 84%] 827s tests/ligand_test.py::test_formal_charge[tetramethylammonium.mol2] 827s -------------------------------- live log call --------------------------------- 827s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 827s PASSED [ 84%] 827s tests/ligand_test.py::test_torsions[acetylcholine.mol2] PASSED [ 84%] 827s tests/ligand_test.py::test_torsions[ethanol.mol2] PASSED [ 85%] 827s tests/ligand_test.py::test_torsions[pyrrole.mol2] PASSED [ 85%] 827s tests/ligand_test.py::test_torsions[tetramethylammonium.mol2] PASSED [ 85%] 827s tests/ligand_test.py::test_torsions[glycerol.mol2] PASSED [ 86%] 827s tests/ligand_test.py::test_torsions[cyclohexane.mol2] PASSED [ 86%] 829s tests/ligand_test.py::test_rings[1HPX-ligand.mol2] PASSED [ 86%] 833s tests/ligand_test.py::test_rings[1QBS-ligand.mol2] PASSED [ 87%] 833s tests/ligand_test.py::test_rings[1US0-ligand.mol2] PASSED [ 87%] 833s tests/ligand_test.py::test_rings[acetate.mol2] PASSED [ 87%] 833s tests/ligand_test.py::test_rings[acetonitrile.mol2] PASSED [ 87%] 833s tests/ligand_test.py::test_rings[acetylcholine.mol2] PASSED [ 88%] 833s tests/ligand_test.py::test_rings[adp.mol2] PASSED [ 88%] 833s tests/ligand_test.py::test_rings[anthracene.mol2] PASSED [ 88%] 833s tests/ligand_test.py::test_rings[cyclohexane.mol2] PASSED [ 89%] 833s tests/ligand_test.py::test_rings[ethanol.mol2] PASSED [ 89%] 833s tests/ligand_test.py::test_rings[fatty-acid.mol2] PASSED [ 89%] 833s tests/ligand_test.py::test_rings[glycerol.mol2] PASSED [ 90%] 833s tests/ligand_test.py::test_rings[naphthalene.mol2] PASSED [ 90%] 833s tests/ligand_test.py::test_rings[pyrrole.mol2] PASSED [ 90%] 833s tests/ligand_test.py::test_rings[tetramethylammonium.mol2] PASSED [ 91%] 833s tests/ligand_test.py::test_ligand_biomolecule[1HPX] SKIPPED (not run...) [ 91%] 834s tests/logging_test.py::test_log_output_in_pqr_location[1A1P.pdb-1A1P_assign-only_whitespace_ff=AMBER_log.pqr] PASSED [ 91%] 834s tests/propka_test.py::test_propka_apo[1K1I] SKIPPED (not running tes...) [ 92%] 834s tests/propka_test.py::test_propka_apo[1AFS] SKIPPED (not running tes...) [ 92%] 834s tests/propka_test.py::test_propka_apo[1FAS] SKIPPED (not running tes...) [ 92%] 834s tests/propka_test.py::test_propka_apo[5DV8] SKIPPED (not running tes...) [ 93%] 834s tests/propka_test.py::test_propka_apo[5D8V] SKIPPED (not running tes...) [ 93%] 834s tests/propka_test.py::test_propka_pka[1K1I] SKIPPED (not running tes...) [ 93%] 834s tests/propka_test.py::test_propka_pka[1AFS] SKIPPED (not running tes...) [ 93%] 834s tests/propka_test.py::test_propka_pka[1FAS] SKIPPED (not running tes...) [ 94%] 834s tests/propka_test.py::test_propka_pka[5DV8] SKIPPED (not running tes...) [ 94%] 834s tests/propka_test.py::test_propka_pka[5D8V] SKIPPED (not running tes...) [ 94%] 834s tests/regression_test.py::test_basic[1AFS basic local] 834s -------------------------------- live log call --------------------------------- 834s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_basic_1AFS_basic_local_0/output.log 834s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 834s 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). 834s 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). 834s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 834s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 835s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 835s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 835s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 835s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 835s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 835s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 835s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 835s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 835s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 835s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 835s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 835s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 835s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 835s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 835s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 835s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 835s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 835s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 835s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 835s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 835s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 836s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 838s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 843s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 847s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 847s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 847s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 847s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 847s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 847s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 847s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 848s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 848s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 848s WARNING pdb2pqr.io:io.py:40 Suppressing further "Skipped atom during water optimization" messages 860s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 860s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 860s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 861s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 861s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 861s WARNING common:common.py:186 6 atoms have position differences > 0 861s INFO common:common.py:198 0 atoms have position differences > 0.01 861s INFO common:common.py:198 0 atoms have charge differences > 0 861s INFO common:common.py:198 0 atoms have charge differences > 0.01 861s INFO common:common.py:198 0 atoms have radius differences > 0 861s INFO common:common.py:198 0 atoms have radius differences > 0.01 861s PASSED [ 95%] 861s tests/regression_test.py::test_forcefields[1AFS whitespace AMBER] 861s -------------------------------- live log call --------------------------------- 861s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa0/output.log 861s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 861s 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). 861s 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). 861s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 861s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 862s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 862s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 862s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 862s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 862s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 862s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 862s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 862s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 862s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 862s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 862s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 862s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 862s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 862s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 862s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 862s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 862s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 862s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 862s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 862s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 862s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 863s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 865s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 869s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 882s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 882s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 882s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 882s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 882s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 883s WARNING common:common.py:186 6 atoms have position differences > 0 883s INFO common:common.py:198 0 atoms have position differences > 0.01 883s INFO common:common.py:198 0 atoms have charge differences > 0 883s INFO common:common.py:198 0 atoms have charge differences > 0.01 883s INFO common:common.py:198 0 atoms have radius differences > 0 883s INFO common:common.py:198 0 atoms have radius differences > 0.01 883s PASSED [ 95%] 883s tests/regression_test.py::test_forcefields[1AFS whitespace CHARMM] 883s -------------------------------- live log call --------------------------------- 883s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa1/output.log 883s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 883s 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). 883s 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). 883s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 883s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 883s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 884s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 884s WARNING pdb2pqr.io:io.py:40 Suppressing further "Unable to find amino or nucleic acid definition for" messages 884s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 884s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 884s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 884s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 884s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 884s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 884s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 884s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 884s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 884s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 884s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 884s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 884s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 884s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 884s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 885s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 887s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 891s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 906s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 906s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 906s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 906s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. 906s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 907s WARNING common:common.py:186 5 atoms have position differences > 0 907s INFO common:common.py:198 0 atoms have position differences > 0.01 907s INFO common:common.py:198 0 atoms have charge differences > 0 907s INFO common:common.py:198 0 atoms have charge differences > 0.01 907s INFO common:common.py:198 0 atoms have radius differences > 0 907s INFO common:common.py:198 0 atoms have radius differences > 0.01 907s PASSED [ 95%] 907s tests/regression_test.py::test_forcefields[1AFS whitespace PARSE] 907s -------------------------------- live log call --------------------------------- 907s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa2/output.log 907s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 907s 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). 907s 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). 907s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 907s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 907s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 907s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 907s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 907s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 907s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 907s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 907s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 907s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 907s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 907s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 907s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 907s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 907s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 907s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 907s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 907s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 907s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 908s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 910s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 916s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 933s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 933s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 933s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 933s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 933s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 934s WARNING common:common.py:186 6 atoms have position differences > 0 934s INFO common:common.py:198 0 atoms have position differences > 0.01 934s INFO common:common.py:198 0 atoms have charge differences > 0 934s INFO common:common.py:198 0 atoms have charge differences > 0.01 934s INFO common:common.py:198 0 atoms have radius differences > 0 934s INFO common:common.py:198 0 atoms have radius differences > 0.01 934s PASSED [ 96%] 934s tests/regression_test.py::test_forcefields[1AFS whitespace PEOEPB] 934s -------------------------------- live log call --------------------------------- 934s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa3/output.log 934s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 934s 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). 934s 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). 934s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 934s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 934s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 934s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 934s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 934s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 935s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 935s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 935s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 935s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 935s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 935s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 935s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 935s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 935s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 935s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 935s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 935s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 935s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 936s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 938s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 943s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 959s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 959s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 959s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 959s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. 959s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 960s WARNING common:common.py:186 6 atoms have position differences > 0 960s INFO common:common.py:198 0 atoms have position differences > 0.01 960s INFO common:common.py:198 0 atoms have charge differences > 0 960s INFO common:common.py:198 0 atoms have charge differences > 0.01 960s INFO common:common.py:198 0 atoms have radius differences > 0 960s INFO common:common.py:198 0 atoms have radius differences > 0.01 960s PASSED [ 96%] 960s tests/regression_test.py::test_forcefields[1AFS whitespace SWANSON] 960s -------------------------------- live log call --------------------------------- 960s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa4/output.log 960s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 960s 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). 960s 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). 960s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 960s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 961s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 961s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 961s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 961s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 961s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 961s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 961s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 961s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 961s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 961s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 961s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 961s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 961s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 961s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 961s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 961s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 961s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 962s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 964s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 969s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 983s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 983s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 983s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 984s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5428 header lines in output. 984s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 985s WARNING common:common.py:186 6 atoms have position differences > 0 985s INFO common:common.py:198 0 atoms have position differences > 0.01 985s INFO common:common.py:198 0 atoms have charge differences > 0 985s INFO common:common.py:198 0 atoms have charge differences > 0.01 985s INFO common:common.py:198 0 atoms have radius differences > 0 985s INFO common:common.py:198 0 atoms have radius differences > 0.01 985s PASSED [ 96%] 985s tests/regression_test.py::test_forcefields[1AFS whitespace TYL06] 985s -------------------------------- live log call --------------------------------- 985s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa5/output.log 985s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 985s 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). 985s 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). 985s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 985s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 985s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 985s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 986s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 986s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 986s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 986s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 986s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 986s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 986s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 986s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 986s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 986s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 986s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 986s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 986s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 986s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 986s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 987s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 989s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 993s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 1008s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 1008s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 1008s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 1008s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 1008s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 1009s WARNING common:common.py:186 6 atoms have position differences > 0 1009s INFO common:common.py:198 0 atoms have position differences > 0.01 1009s INFO common:common.py:198 0 atoms have charge differences > 0 1009s INFO common:common.py:198 0 atoms have charge differences > 0.01 1009s INFO common:common.py:198 0 atoms have radius differences > 0 1009s INFO common:common.py:198 0 atoms have radius differences > 0.01 1009s PASSED [ 97%] 1009s tests/regression_test.py::test_other_options[1AFS whitespace clean] 1009s -------------------------------- live log call --------------------------------- 1009s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_whites0/output.log 1009s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 1009s 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). 1009s 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). 1009s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 1009s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 1010s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 1010s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 1010s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 1010s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 1010s INFO PDB2PQR3.6.1:main.py:778 Arguments specified cleaning only; skipping remaining steps. 1011s INFO common:common.py:198 0 atoms have position differences > 0 1011s INFO common:common.py:198 0 atoms have position differences > 0.01 1011s INFO common:common.py:198 0 atoms have charge differences > 0 1011s INFO common:common.py:198 0 atoms have charge differences > 0.01 1011s INFO common:common.py:198 0 atoms have radius differences > 0 1011s INFO common:common.py:198 0 atoms have radius differences > 0.01 1011s PASSED [ 97%] 1011s tests/regression_test.py::test_other_options[1A1P assign-only whitespace AMBER] 1011s -------------------------------- live log call --------------------------------- 1011s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_assign0/output.log 1011s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 1011s 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). 1011s 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). 1011s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 1011s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 1011s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb 1011s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 1011s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. 1011s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 1011s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 1011s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 1011s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 1011s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 1011s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 1011s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. 1011s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 1011s INFO common:common.py:198 0 atoms have position differences > 0 1011s INFO common:common.py:198 0 atoms have position differences > 0.01 1011s INFO common:common.py:198 0 atoms have charge differences > 0 1011s INFO common:common.py:198 0 atoms have charge differences > 0.01 1011s INFO common:common.py:198 0 atoms have radius differences > 0 1011s INFO common:common.py:198 0 atoms have radius differences > 0.01 1011s PASSED [ 97%] 1011s tests/regression_test.py::test_other_options[1A1P nodebump noopt whitespace AMBER] 1011s -------------------------------- live log call --------------------------------- 1011s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_nodebu0/output.log 1011s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 1011s 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). 1011s 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). 1011s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 1011s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 1012s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb 1012s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 1012s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. 1012s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 1012s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 1012s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 1012s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 1012s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 1012s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 1012s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 1012s INFO pdb2pqr.hydrogens:__init__.py:370 Initializing water bonding optimization... 1012s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 1012s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 1012s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 1012s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. 1012s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 1012s INFO common:common.py:198 0 atoms have position differences > 0 1012s INFO common:common.py:198 0 atoms have position differences > 0.01 1012s INFO common:common.py:198 0 atoms have charge differences > 0 1012s INFO common:common.py:198 0 atoms have charge differences > 0.01 1012s INFO common:common.py:198 0 atoms have radius differences > 0 1012s INFO common:common.py:198 0 atoms have radius differences > 0.01 1012s PASSED [ 98%] 1012s tests/regression_test.py::test_other_options[1AFS chain whitespace AMBER] 1012s -------------------------------- live log call --------------------------------- 1012s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_chain_0/output.log 1012s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 1012s 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). 1012s 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). 1012s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 1012s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 1013s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 1013s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 1013s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 1013s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 1013s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 1013s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 1013s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 1013s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 1013s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 1013s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 1013s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 1013s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 1013s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 1013s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 1013s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 1013s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 1013s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 1014s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 1016s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 1020s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 1036s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 1036s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 1036s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 1038s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 1038s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 1038s WARNING common:common.py:186 6 atoms have position differences > 0 1038s INFO common:common.py:198 0 atoms have position differences > 0.01 1038s INFO common:common.py:198 0 atoms have charge differences > 0 1038s INFO common:common.py:198 0 atoms have charge differences > 0.01 1038s INFO common:common.py:198 0 atoms have radius differences > 0 1038s INFO common:common.py:198 0 atoms have radius differences > 0.01 1038s PASSED [ 98%] 1038s tests/regression_test.py::test_other_options[1AFS neutralc neutraln PARSE] 1038s -------------------------------- live log call --------------------------------- 1038s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_neutra0/output.log 1038s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 1038s 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). 1038s 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). 1038s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 1038s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 1038s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 1038s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 1038s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 1038s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 1038s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 1038s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 1038s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 1038s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 1038s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 1038s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 1038s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 1038s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 1038s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 1038s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 1038s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 1038s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 1038s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 1039s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 1040s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 1044s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 1057s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 1057s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 1057s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 1057s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 1057s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 1058s WARNING common:common.py:186 6 atoms have position differences > 0 1058s INFO common:common.py:198 0 atoms have position differences > 0.01 1058s INFO common:common.py:198 0 atoms have charge differences > 0 1058s INFO common:common.py:198 0 atoms have charge differences > 0.01 1058s INFO common:common.py:198 0 atoms have radius differences > 0 1058s INFO common:common.py:198 0 atoms have radius differences > 0.01 1058s PASSED [ 98%] 1058s tests/regression_test.py::test_other_options[1AFS drop-water AMBER] 1058s -------------------------------- live log call --------------------------------- 1058s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_drop_w0/output.log 1058s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 1058s 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). 1058s 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). 1058s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 1058s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 1059s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 1059s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 1059s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 1059s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 642 residues and 5300 atoms. 1059s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 1059s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 1059s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 1059s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 1059s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 1059s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 1059s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 1059s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 1059s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 1059s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 1059s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 1059s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 1059s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 1059s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 1060s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 1062s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 1067s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 1074s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 1075s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 1075s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 1075s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 1075s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 1076s WARNING common:common.py:186 6 atoms have position differences > 0 1076s INFO common:common.py:198 0 atoms have position differences > 0.01 1076s INFO common:common.py:198 0 atoms have charge differences > 0 1076s INFO common:common.py:198 0 atoms have charge differences > 0.01 1076s INFO common:common.py:198 0 atoms have radius differences > 0 1076s INFO common:common.py:198 0 atoms have radius differences > 0.01 1076s PASSED [ 99%] 1076s tests/regression_test.py::test_other_options[1AFS userff usernames whitespace] 1076s -------------------------------- live log call --------------------------------- 1076s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_userff0/output.log 1076s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 1076s 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). 1076s 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). 1076s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 1076s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 1076s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 1076s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 1076s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 1076s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 1076s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 1076s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 1076s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 1076s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 1076s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 1076s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 1076s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 1076s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 1076s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 1076s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 1076s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 1076s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 1076s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 1077s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 1079s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 1082s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 1096s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 1097s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 1097s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 1097s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 1097s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 1098s WARNING common:common.py:186 6 atoms have position differences > 0 1098s INFO common:common.py:198 0 atoms have position differences > 0.01 1098s INFO common:common.py:198 0 atoms have charge differences > 0 1098s INFO common:common.py:198 0 atoms have charge differences > 0.01 1098s INFO common:common.py:198 0 atoms have radius differences > 0 1098s INFO common:common.py:198 0 atoms have radius differences > 0.01 1098s PASSED [ 99%] 1098s tests/test_version.py::test_version_exists PASSED [ 99%] 1098s tests/test_version.py::test_version PASSED [100%] 1098s 1098s =============================== warnings summary =============================== 1098s ../../../../usr/lib/python3/dist-packages/dateutil/tz/tz.py:37 1098s /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). 1098s EPOCH = datetime.datetime.utcfromtimestamp(0) 1098s 1098s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 1098s ====== 92 passed, 220 skipped, 4 xfailed, 1 warning in 311.30s (0:05:11) ======= 1099s autopkgtest [03:35:06]: test command1: -----------------------] 1104s autopkgtest [03:35:11]: test command1: - - - - - - - - - - results - - - - - - - - - - 1104s command1 PASS 1109s autopkgtest [03:35:16]: @@@@@@@@@@@@@@@@@@@@ summary 1109s installation-test PASS 1109s pdb2pka-test PASS 1109s command1 PASS