0s autopkgtest: DBG: testbed init 0s autopkgtest [12:33:33]: starting date and time: 2025-02-19 12:33:33+0000 0s autopkgtest [12:33:33]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [12:33:33]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.by5by6hj/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:sphinx --apt-upgrade python-biopython --debug --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=sphinx/8.1.3-5 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-s390x-30.secgroup --name adt-plucky-s390x-python-biopython-20250219-123333-juju-7f2275-prod-proposed-migration-environment-15-5a58a9f7-96a4-41c9-917f-dd7024d665f5 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-s390x -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 0s autopkgtest: DBG: got reply from testbed: ok 0s autopkgtest: DBG: testbed open, scratch=None 0s autopkgtest: DBG: sending command to testbed: open 146s autopkgtest: DBG: got reply from testbed: ok /tmp/autopkgtest.IaIWjt 146s autopkgtest: DBG: sending command to testbed: print-execute-command 146s autopkgtest: DBG: got reply from testbed: ok /tmp/autopkgtest-ssh.qjiad5nu/runcmd 146s autopkgtest: DBG: sending command to testbed: capabilities 146s autopkgtest: DBG: got reply from testbed: ok revert-full-system reboot revert isolation-machine suggested-normal-user=ubuntu root-on-testbed 146s autopkgtest: DBG: testbed capabilities: ['revert-full-system', 'reboot', 'revert', 'isolation-machine', 'suggested-normal-user=ubuntu', 'root-on-testbed', 'has_internet'] 146s autopkgtest: DBG: testbed command ['mkdir', '-p', '/tmp/autopkgtest.IaIWjt'], kind short, sout raw, serr pipe, env [] 146s autopkgtest: DBG: testbed command exited with code 0 146s autopkgtest: DBG: sending command to testbed: copydown /home/ubuntu/autopkgtest/lib/in-testbed/wrapper.sh /tmp/autopkgtest.IaIWjt/wrapper.sh 146s autopkgtest: DBG: got reply from testbed: ok 146s autopkgtest: DBG: testbed command ['chmod', '-R', '0755', '--', '/tmp/autopkgtest.IaIWjt/wrapper.sh'], kind short, sout raw, serr pipe, env [] 147s autopkgtest: DBG: testbed command exited with code 0 147s autopkgtest: DBG: testbed command ['dpkg', '--print-architecture'], kind short, sout pipe, serr pipe, env [] 147s autopkgtest: DBG: testbed command exited with code 0 147s autopkgtest [12:36:00]: testbed dpkg architecture: s390x 147s autopkgtest: DBG: testbed command ['dpkg-query', '-W', '-f', '${Version}', 'apt'], kind short, sout pipe, serr pipe, env [] 147s autopkgtest: DBG: testbed command exited with code 0 147s autopkgtest [12:36:00]: testbed apt version: 2.9.30 147s autopkgtest: DBG: testbed command ['sh', '-ec', 'command -v eatmydata'], kind short, sout pipe, serr pipe, env [] 147s autopkgtest: DBG: testbed command exited with code 0 147s autopkgtest: DBG: testbed has eatmydata 147s autopkgtest: DBG: testbed command ['mkdir', '-p', '/etc/apt/preferences.d'], kind short, sout raw, serr pipe, env [] 147s autopkgtest: DBG: testbed command exited with code 0 147s autopkgtest [12:36:00]: @@@@@@@@@@@@@@@@@@@@ test bed setup 147s autopkgtest: DBG: testbed command ['sh', '-ec', '#!/bin/sh\n# Copyright © 2006-2018 Canonical Ltd.\n# Copyright © 2015-2017 Martin Pitt\n# Copyright © 2017 Steve Langasek\n# Copyright © 2017-2022 Paul Gevers\n# Copyright © 2018 Simon McVittie\n# SPDX-License-Identifier: GPL-2.0-or-later\n\n# This script returns the first suite found in apt sources. We can\'t just rely\n# on /etc/os-release because it doesn\'t allow to distinguish between Debian\n# unstable and testing.\n#\n# This release detection logic should be kept in sync with similar code in the\n# setup-testbed script.\n#\n# For more information on APT data sources see sources.list(5).\n\n# Usage $0\n\nset -eux\n\ndistro=UNKNOWN\nif [ -r /etc/os-release ]; then\n # shellcheck disable=SC1091\n distro=$(. /etc/os-release && echo "${ID:-$distro}")\nfi\n\n# Try guessing the default release from deb822-style format sources.\n#\n# While not mandatory, APT upstream expects distros to follow the\n# .sources naming pattern for the default deb822 sources.\napt_sources="/etc/apt/sources.list.d/$distro.sources"\nif [ -r "$apt_sources" ]; then\n release=$(sed -En \'s/^Suites:\\s*(\\w+).*/\\1/Ip\' "$apt_sources" | head -n1)\n [ -n "$release" ] && echo "$release" && exit\nfi\n\n# Try guessing the default release from one-line-style format sources.\napt_sources=/etc/apt/sources.list\nif [ -r "$apt_sources" ]; then\n release=$(sed -En \'/^(deb|deb-src) +(\\[.*\\] *)?(http|https|file):/ { s/\\[.*\\] +//; s/^[^ ]+ +[^ ]* +([^ ]+) +.*$/\\1/p }\' "$apt_sources" | head -n1)\n [ -n "$release" ] && echo "$release" && exit\nfi\n\n# Could not guess the default release\necho "Could not guess the default release from the APT sources." >&2\nexit 1\n'], kind short, sout pipe, serr pipe, env [] 147s autopkgtest: DBG: testbed command exited with code 0 147s autopkgtest [12:36:00]: testbed release detected to be: None 147s autopkgtest: DBG: testbed command ['sh', '-ec', '#!/bin/sh\n# SPDX-License-Identifier: GPL-2.0-or-later\n\n# This script returns the list of configured "deb" sources in one-line-style\n# source lists (/etc/apt/sources.list, /etc/apt/sources.list.d/*.list).\n# See sources.list(5) for more information on the APT source list formats.\n#\n# This script takes no arguments.\n\nset -eu\n\n# grep(1) returns 1 if no lines were selected from the input files, which\n# can happen if there are .list files, but they contain no "deb" entries.\n# We don\'t want to fail in this case, hence the "|| true", which we put\n# in a subshell because we want it to affect only the grep invocation.\n{\n if [ -f /etc/apt/sources.list ]; then\n printf \'%s\\0\' /etc/apt/sources.list\n fi\n if [ -d /etc/apt/sources.list.d ]; then\n find /etc/apt/sources.list.d -maxdepth 1 -type f -regex \'.*/[a-zA-Z0-9_.-]+\\.list\' -print0 \\\n | LC_ALL=C sort --zero-terminated\n fi\n} | xargs -0 --no-run-if-empty -- sh -c \'grep -h "^deb " "$@" || true\' "$(basename "$0")"\n'], kind short, sout pipe, serr pipe, env [] 148s autopkgtest: DBG: testbed command exited with code 0 148s autopkgtest: DBG: testbed command ['sh', '-ec', '#!/bin/sh\n# SPDX-License-Identifier: GPL-2.0-or-later\n\n# This script returns the list of configured sources in deb822-style source\n# lists (/etc/apt/sources.list.d/*.sources). Sources are not stripped out of\n# comments, extra blank lines or similar: the output of this script is meant to\n# be consumed by a deb822 parser that is able to correctly handle those.\n# See sources.list(5) for more information on the APT source list formats.\n#\n# This script takes no arguments.\n\nset -eu\n\n# Awk concatenates files making sure stanzas from separate files are separated\n# by a blank line, even if there are no newlines at EOF in the .sources files.\nif [ -d /etc/apt/sources.list.d ]; then\n find /etc/apt/sources.list.d -maxdepth 1 -type f -regex \'.*/[a-zA-Z0-9_.-]+\\.sources\' -print0 \\\n | LC_ALL=C sort --zero-terminated \\\n | xargs -0 --no-run-if-empty -- awk \'FNR == 1 && NR != 1 { print "" } { print }\'\nfi\n'], kind short, sout pipe, serr pipe, env [] 148s autopkgtest: DBG: testbed command exited with code 0 148s autopkgtest: DBG: adding APT source: Types: deb deb-src 148s URIs: http://ftpmaster.internal/ubuntu/ 148s Suites: plucky-proposed 148s Components: main restricted universe multiverse 148s Signed-By: /usr/share/keyrings/ubuntu-archive-keyring.gpg 148s autopkgtest: DBG: testbed command ['sh', '-ec', '"$@" >> "/etc/apt/sources.list.d/autopkgtest-add-apt-release-plucky-proposed.sources"', 'add_apt_source', 'printf', '%s\\n', 'Types: deb deb-src\nURIs: http://ftpmaster.internal/ubuntu/\nSuites: plucky-proposed\nComponents: main restricted universe multiverse\nSigned-By: /usr/share/keyrings/ubuntu-archive-keyring.gpg\n'], kind short, sout raw, serr pipe, env [] 148s autopkgtest: DBG: testbed command exited with code 0 148s autopkgtest: DBG: adding APT preference to autopkgtest-zz-plucky-proposed-baseline.pref: 148s Package: * 148s Pin: release plucky-proposed 148s Pin-Priority: 500 148s autopkgtest: DBG: testbed command ['sh', '-ec', '"$@" > "/etc/apt/preferences.d/autopkgtest-zz-plucky-proposed-baseline.pref"', 'add_apt_preference', 'printf', '%s\\n', 'Package: *\nPin: release plucky-proposed\nPin-Priority: 500'], kind short, sout raw, serr pipe, env [] 148s autopkgtest: DBG: testbed command exited with code 0 148s autopkgtest [12:36:01]: updating testbed package index (apt update) 148s autopkgtest: DBG: testbed command ['/bin/sh', '-ec', '"$@" 3>&2 2>&1', 'run_apt_command', '/usr/bin/eatmydata', 'apt-get', '--quiet', '--assume-yes', '-o=APT::Status-Fd=3', '-o=APT::Install-Recommends=false', '-o=Dpkg::Options::=--force-confnew', '-o=Debug::pkgProblemResolver=true', 'update'], kind install, sout raw, serr pipe, env ['DEBIAN_FRONTEND=noninteractive', 'APT_LISTBUGS_FRONTEND=none', 'APT_LISTCHANGES_FRONTEND=none'] 149s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 149s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 149s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 149s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 149s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.1 kB] 149s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [750 kB] 149s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.9 kB] 149s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 149s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [95.1 kB] 149s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x Packages [760 B] 149s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [646 kB] 149s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [4900 B] 149s Fetched 1700 kB in 1s (1673 kB/s) 150s Reading package lists... 150s autopkgtest: DBG: testbed command exited with code 0 150s autopkgtest: DBG: adding APT preference to autopkgtest-plucky-proposed.pref: 150s Package: * 150s Pin: release plucky-proposed 150s Pin-Priority: 100 150s 150s Package: src:sphinx:any 150s Pin: release plucky-proposed 150s Pin-Priority: 995 150s autopkgtest: DBG: testbed command ['sh', '-ec', '"$@" > "/etc/apt/preferences.d/autopkgtest-plucky-proposed.pref"', 'add_apt_preference', 'printf', '%s\\n', 'Package: *\nPin: release plucky-proposed\nPin-Priority: 100\n\nPackage: src:sphinx:any\nPin: release plucky-proposed\nPin-Priority: 995'], kind short, sout raw, serr pipe, env [] 150s autopkgtest: DBG: testbed command exited with code 0 150s autopkgtest: DBG: testbed command ['bash', '-ec', 'for d in /boot /boot/efi /boot/grub /etc/init /etc/init.d /etc/systemd/system /lib/systemd/system; do [ ! -d $d ] || touch -r $d /tmp/autopkgtest.IaIWjt/${d//\\//_}.stamp; done'], kind short, sout raw, serr pipe, env [] 151s autopkgtest: DBG: testbed command exited with code 0 151s autopkgtest: DBG: testbed command ['sh', '-ec', '#!/bin/sh\n# Canonical/Ubuntu specific testbed setup\n\nset -x\n\nRELEASE=$(lsb_release --codename --short 2>/dev/null)\n\n# Make the installed package versions match what is available from the configured\n# repositories, even if a downgrade is required.\n#\n# We may end up with images with packages newer than those available from the\n# repositories when opening a new release (images are created using the\n# previous release dailies as a base, which may include 0-day SRUs, or\n# Launchpad may fail to copy packages, see openssl 3.0.8-1ubuntu2), or when\n# package versions are pulled from the archive.\n#\n# Note: \'release a=\' matches the Suite field in the repository Release file.\ncat >/etc/apt/preferences.d/force-downgrade-to-release.pref <= Focal).\n#\n# Note: autoremove/--autoremove always runs on the entire set of installed\n# packages. Together with --autopurge/purge each removal becomes a purge.\n#\n# Removing \'?obsolete\' packages may remove the running kernel. This is not\n# expected to be an issue.\nif /usr/lib/apt/apt-helper analyze-pattern \'?true\' >/dev/null 2>&1; then\n # DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove \'?obsolete\'\n # Avoid removing the running kernel\n running_kernel_pattern="^linux-.*$(uname -r | sed \'s/\\./\\\\./g\').*"\n obsolete_pkgs="$(apt list \'?obsolete\' 2>/dev/null \\\n | tail -n+2 \\\n | cut -d\'/\' -f1 \\\n | grep -v "${running_kernel_pattern}" || true)"\n DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove ${obsolete_pkgs}\nelse\n # We\'re on an older release (analyze-pattern is not available).\n # Still do an autopurge to get rid of packages that got orphaned\n # by downgrades.\n eatmydata apt-get -y autoremove --purge\nfi\n\n# compatibility with old Jenkins testbeds for trusty\nif grep -q trusty /etc/lsb-release; then apt-get update || (sleep 10; apt-get update); apt-get install -y build-essential; fi\n\n# these packages really break tests, purge them if we use standard cloud images\n# (on lcy01)\nfor p in unattended-upgrades lxd lxd-client snapd; do\n [ ! -d /usr/share/doc/$p ] || $(which eatmydata || true) apt-get purge --auto-remove -y $p\ndone\n\nif type iptables >/dev/null 2>&1; then\n cat < /etc/rc.local\n#!/bin/sh\n\n# work around broken PTMU; LP: #1572026, RT#90771\niptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu || true\n\n# These addresses are used at least by rust-reqwest and should not be reachable\n# See https://bugs.launchpad.net/ubuntu/+source/rust-reqwest/+bug/2080346\niptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP || true\niptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP || true\nEOF\n chmod 755 /etc/rc.local\n # shellcheck disable=SC1091\n . /etc/rc.local\nfi\n\n# work around broken tty on ppc64el instances (LP: #1607075)\nif [ "$(uname -m)" = ppc64le ] && [ "$(systemctl is-active keyboard-setup.service 2>/dev/null|| true)" = failed ]; then\n systemctl reset-failed keyboard-setup.service\n systemctl mask keyboard-setup.service\nfi\n\n# work around late urandom pool initialization (LP: #1622893)\nif [ -d /run/systemd/system ] && systemd-detect-virt --quiet --vm; then\n mkdir -p /etc/systemd/system/systemd-random-seed.service.d/\n cat < /etc/systemd/system/systemd-random-seed.service.d/fakeentropy.conf\n[Service]\nExecStart=/usr/bin/perl -E \'open \\$\\$f, "/bin/bash" or die; open \\$\\$rnd, ">/dev/random" or die; for (\\$\\$i = 0; \\$\\$i < 10; ++\\$\\$i) {read \\$\\$f, \\$\\$d, 64; ioctl \\$\\$rnd, 0x40085203, pack("ii", 64*8, 64) . \\$\\$d}\'\nEOF\nfi\n\n# set compressor to lz4 where supported, we care about compression speed\nif grep -q lz4 /etc/initramfs-tools/initramfs.conf; then\n echo COMPRESS=lz4 > /etc/initramfs-tools/conf.d/lz4\nfi'], kind install, sout raw, serr raw, env ['AUTOPKGTEST_IS_SETUP_COMMAND=1', 'AUTOPKGTEST_NORMAL_USER=ubuntu', 'ADT_NORMAL_USER=ubuntu'] 151s + lsb_release --codename --short 151s + RELEASE=plucky 151s + cat 151s + [ plucky != trusty ] 151s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 151s Reading package lists... 151s Building dependency tree... 151s Reading state information... 151s Calculating upgrade... 151s The following packages were automatically installed and are no longer required: 151s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 151s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 151s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 151s linux-tools-6.11.0-8-generic 151s Use 'sudo apt autoremove' to remove them. 151s The following packages will be upgraded: 151s iproute2 liblsof0 libp11-kit0 lsof 153s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 153s Need to get 1791 kB of archives. 153s After this operation, 17.4 kB of additional disk space will be used. 153s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x iproute2 s390x 6.13.0-1ubuntu1 [1174 kB] 153s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libp11-kit0 s390x 0.25.5-2ubuntu3 [316 kB] 153s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x lsof s390x 4.99.4+dfsg-1 [243 kB] 153s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x liblsof0 s390x 4.99.4+dfsg-1 [58.5 kB] 153s Preconfiguring packages ... 153s Fetched 1791 kB in 1s (2473 kB/s) 153s (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 ... 81030 files and directories currently installed.) 153s Preparing to unpack .../iproute2_6.13.0-1ubuntu1_s390x.deb ... 153s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 153s Preparing to unpack .../libp11-kit0_0.25.5-2ubuntu3_s390x.deb ... 153s Unpacking libp11-kit0:s390x (0.25.5-2ubuntu3) over (0.25.5-2ubuntu2) ... 153s Preparing to unpack .../lsof_4.99.4+dfsg-1_s390x.deb ... 153s Unpacking lsof (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 153s Preparing to unpack .../liblsof0_4.99.4+dfsg-1_s390x.deb ... 153s Unpacking liblsof0 (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 153s Setting up liblsof0 (4.99.4+dfsg-1) ... 153s Setting up iproute2 (6.13.0-1ubuntu1) ... 153s Setting up libp11-kit0:s390x (0.25.5-2ubuntu3) ... 153s Setting up lsof (4.99.4+dfsg-1) ... 153s Processing triggers for man-db (2.13.0-1) ... 154s Processing triggers for libc-bin (2.40-4ubuntu1) ... 154s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 154s + /usr/lib/apt/apt-helper analyze-pattern ?true 154s + uname+ sed -r s/\./\\./g 154s 154s + running_kernel_pattern=^linux-.*6\.12\.0-15-generic.* 154s + apt list ?obsolete 154s + tail -n+2 154s + cut -d/ -f1 154s + grep -v ^linux-.*6\.12\.0-15-generic.* 154s + true 154s + obsolete_pkgs= 154s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove 154s Reading package lists... 154s Building dependency tree... 154s Reading state information... 154s The following packages will be REMOVED: 154s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 154s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 154s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 154s linux-tools-6.11.0-8-generic* 155s 0 upgraded, 0 newly installed, 9 to remove and 0 not upgraded. 155s After this operation, 167 MB disk space will be freed. 155s (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 ... 81031 files and directories currently installed.) 155s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 155s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 155s Removing libpython3.12t64:s390x (3.12.9-1) ... 155s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 155s Removing libnsl2:s390x (1.3.0-3build3) ... 155s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 155s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 155s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 156s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 156s Processing triggers for libc-bin (2.40-4ubuntu1) ... 156s (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 ... 55931 files and directories currently installed.) 156s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 156s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 157s + grep -q trusty /etc/lsb-release 157s + [ ! -d /usr/share/doc/unattended-upgrades ] 157s + [ ! -d /usr/share/doc/lxd ] 157s + [ ! -d /usr/share/doc/lxd-client ] 157s + [ ! -d /usr/share/doc/snapd ] 157s + type iptables 157s + cat 157s + chmod 755 /etc/rc.local 157s + . /etc/rc.local 157s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 157s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 157s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 157s + uname -m 157s + [ s390x = ppc64le ] 157s + [ -d /run/systemd/system ] 157s + systemd-detect-virt --quiet --vm 157s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 157s + cat 157s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 157s + echo COMPRESS=lz4 157s autopkgtest: DBG: testbed command exited with code 0 157s autopkgtest [12:36:10]: upgrading testbed (apt dist-upgrade and autopurge) 157s autopkgtest: DBG: testbed command ['/bin/sh', '-ec', '"$@" 3>&2 2>&1', 'run_apt_command', '/usr/bin/eatmydata', 'apt-get', '--quiet', '--assume-yes', '-o=APT::Status-Fd=3', '-o=APT::Install-Recommends=false', '-o=Dpkg::Options::=--force-confnew', '-o=Debug::pkgProblemResolver=true', 'dist-upgrade'], kind install, sout raw, serr pipe, env ['DEBIAN_FRONTEND=noninteractive', 'APT_LISTBUGS_FRONTEND=none', 'APT_LISTCHANGES_FRONTEND=none'] 157s Reading package lists... 157s Building dependency tree... 157s Reading state information... 157s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 157s Starting 2 pkgProblemResolver with broken count: 0 157s Done 157s Entering ResolveByKeep 157s 158s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 158s autopkgtest: DBG: testbed command exited with code 0 158s autopkgtest: DBG: testbed command ['/bin/sh', '-ec', '"$@" 3>&2 2>&1', 'run_apt_command', '/usr/bin/eatmydata', 'apt-get', '--quiet', '--assume-yes', '-o=APT::Status-Fd=3', '-o=APT::Install-Recommends=false', '-o=Dpkg::Options::=--force-confnew', '-o=Debug::pkgProblemResolver=true', '--purge', 'autoremove'], kind install, sout raw, serr pipe, env ['DEBIAN_FRONTEND=noninteractive', 'APT_LISTBUGS_FRONTEND=none', 'APT_LISTCHANGES_FRONTEND=none'] 158s Reading package lists... 158s Building dependency tree... 158s Reading state information... 158s Starting pkgProblemResolver with broken count: 0 158s Starting 2 pkgProblemResolver with broken count: 0 158s Done 158s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 158s autopkgtest: DBG: testbed command exited with code 0 158s autopkgtest: DBG: testbed command ['bash', '-ec', '[ ! -e /run/autopkgtest_no_reboot.stamp ] || exit 0;for d in /boot /boot/efi /boot/grub /etc/init /etc/init.d /etc/systemd/system /lib/systemd/system; do s=/tmp/autopkgtest.IaIWjt/${d//\\//_}.stamp; [ ! -d $d ] || [ `stat -c %Y $d` = `stat -c %Y $s` ]; done'], kind short, sout raw, serr raw, env [] 158s autopkgtest: DBG: testbed command exited with code 1 158s autopkgtest [12:36:11]: rebooting testbed after setup commands that affected boot 158s autopkgtest: DBG: sending command to testbed: reboot 179s autopkgtest: DBG: got reply from testbed: ok 179s autopkgtest: DBG: testbed supports reboot, creating /tmp/autopkgtest-reboot 179s autopkgtest: DBG: testbed command ['mkdir', '-p', '/tmp/autopkgtest.IaIWjt'], kind short, sout raw, serr pipe, env [] 179s autopkgtest: DBG: testbed command exited with code 0 179s autopkgtest: DBG: sending command to testbed: copydown /home/ubuntu/autopkgtest/lib/in-testbed/reboot.sh /tmp/autopkgtest.IaIWjt/autopkgtest-reboot 179s autopkgtest: DBG: got reply from testbed: ok 179s autopkgtest: DBG: testbed command ['chmod', '-R', '0755', '--', '/tmp/autopkgtest.IaIWjt/autopkgtest-reboot'], kind short, sout raw, serr pipe, env [] 180s autopkgtest: DBG: testbed command exited with code 0 180s autopkgtest: DBG: testbed command ['ln', '-fns', '/tmp/autopkgtest.IaIWjt/autopkgtest-reboot', '/tmp/autopkgtest-reboot'], kind short, sout raw, serr pipe, env [] 180s autopkgtest: DBG: testbed command exited with code 0 180s autopkgtest: DBG: testbed command ['ln', '-fns', '/tmp/autopkgtest.IaIWjt/autopkgtest-reboot', '/sbin/autopkgtest-reboot'], kind short, sout raw, serr pipe, env [] 180s autopkgtest: DBG: testbed command exited with code 0 180s autopkgtest: DBG: testbed command ['mkdir', '-p', '/tmp/autopkgtest.IaIWjt'], kind short, sout raw, serr pipe, env [] 180s autopkgtest: DBG: testbed command exited with code 0 180s autopkgtest: DBG: sending command to testbed: copydown /home/ubuntu/autopkgtest/lib/in-testbed/reboot-prepare.sh /tmp/autopkgtest.IaIWjt/autopkgtest-reboot-prepare 180s autopkgtest: DBG: got reply from testbed: ok 180s autopkgtest: DBG: testbed command ['chmod', '-R', '0755', '--', '/tmp/autopkgtest.IaIWjt/autopkgtest-reboot-prepare'], kind short, sout raw, serr pipe, env [] 181s autopkgtest: DBG: testbed command exited with code 0 181s autopkgtest: DBG: testbed command ['ln', '-fns', '/tmp/autopkgtest.IaIWjt/autopkgtest-reboot-prepare', '/tmp/autopkgtest-reboot-prepare'], kind short, sout raw, serr pipe, env [] 181s autopkgtest: DBG: testbed command exited with code 0 181s autopkgtest: DBG: testbed command ['uname', '-srv'], kind short, sout pipe, serr pipe, env [] 181s autopkgtest: DBG: testbed command exited with code 0 181s autopkgtest [12:36:34]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP Tue Feb 4 15:05:57 UTC 2025 181s autopkgtest: DBG: testbed command ['sh', '-c', 'nproc; cat /proc/cpuinfo 2>/dev/null || true'], kind short, sout pipe, serr pipe, env [] 181s autopkgtest: DBG: testbed command exited with code 0 181s autopkgtest: DBG: testbed command ['sh', '-ec', "dpkg-query --show -f '${Package}\\t${Version}\\n' > /tmp/autopkgtest.IaIWjt/testbed-packages"], kind short, sout raw, serr pipe, env [] 181s autopkgtest: DBG: testbed command exited with code 0 181s autopkgtest: DBG: sending command to testbed: copyup /tmp/autopkgtest.IaIWjt/testbed-packages /tmp/autopkgtest-work.by5by6hj/out/testbed-packages 182s autopkgtest: DBG: got reply from testbed: ok 182s autopkgtest: DBG: testbed supports reboot, creating /tmp/autopkgtest-reboot 182s autopkgtest: DBG: testbed command ['mkdir', '-p', '/tmp/autopkgtest.IaIWjt'], kind short, sout raw, serr pipe, env [] 182s autopkgtest: DBG: testbed command exited with code 0 182s autopkgtest: DBG: sending command to testbed: copydown /home/ubuntu/autopkgtest/lib/in-testbed/reboot.sh /tmp/autopkgtest.IaIWjt/autopkgtest-reboot 182s autopkgtest: DBG: got reply from testbed: ok 182s autopkgtest: DBG: testbed command ['chmod', '-R', '0755', '--', '/tmp/autopkgtest.IaIWjt/autopkgtest-reboot'], kind short, sout raw, serr pipe, env [] 182s autopkgtest: DBG: testbed command exited with code 0 182s autopkgtest: DBG: testbed command ['ln', '-fns', '/tmp/autopkgtest.IaIWjt/autopkgtest-reboot', '/tmp/autopkgtest-reboot'], kind short, sout raw, serr pipe, env [] 182s autopkgtest: DBG: testbed command exited with code 0 182s autopkgtest: DBG: testbed command ['ln', '-fns', '/tmp/autopkgtest.IaIWjt/autopkgtest-reboot', '/sbin/autopkgtest-reboot'], kind short, sout raw, serr pipe, env [] 183s autopkgtest: DBG: testbed command exited with code 0 183s autopkgtest: DBG: testbed command ['mkdir', '-p', '/tmp/autopkgtest.IaIWjt'], kind short, sout raw, serr pipe, env [] 183s autopkgtest: DBG: testbed command exited with code 0 183s autopkgtest: DBG: sending command to testbed: copydown /home/ubuntu/autopkgtest/lib/in-testbed/reboot-prepare.sh /tmp/autopkgtest.IaIWjt/autopkgtest-reboot-prepare 183s autopkgtest: DBG: got reply from testbed: ok 183s autopkgtest: DBG: testbed command ['chmod', '-R', '0755', '--', '/tmp/autopkgtest.IaIWjt/autopkgtest-reboot-prepare'], kind short, sout raw, serr pipe, env [] 183s autopkgtest: DBG: testbed command exited with code 0 183s autopkgtest: DBG: testbed command ['ln', '-fns', '/tmp/autopkgtest.IaIWjt/autopkgtest-reboot-prepare', '/tmp/autopkgtest-reboot-prepare'], kind short, sout raw, serr pipe, env [] 183s autopkgtest: DBG: testbed command exited with code 0 183s autopkgtest: DBG: testbed command ['uname', '-srv'], kind short, sout pipe, serr pipe, env [] 183s autopkgtest: DBG: testbed command exited with code 0 183s autopkgtest: DBG: Binaries: initialising 183s autopkgtest [12:36:36]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biopython 183s autopkgtest: DBG: blame += python-biopython 183s autopkgtest: DBG: testbed reset: modified=False, deps_installed=[], deps_new=[] 183s autopkgtest: DBG: testbed command ['apt-cache', 'showsrc', '--only-source', 'python-biopython'], kind short, sout pipe, serr pipe, env [] 184s autopkgtest: DBG: testbed command exited with code 0 184s autopkgtest: DBG: testbed command ['apt-cache', 'policy', '^python-biopython-doc$'], kind short, sout pipe, serr raw, env [] 184s autopkgtest: DBG: testbed command exited with code 0 184s autopkgtest: DBG: testbed command ['apt-cache', 'show', 'python-biopython-doc=1.85+dfsg-2'], kind short, sout pipe, serr raw, env [] 184s autopkgtest: DBG: testbed command exited with code 0 184s autopkgtest: DBG: testbed command ['apt-cache', 'policy', '^python3-biopython$'], kind short, sout pipe, serr raw, env [] 185s autopkgtest: DBG: testbed command exited with code 0 185s autopkgtest: DBG: testbed command ['apt-cache', 'show', 'python3-biopython=1.85+dfsg-2'], kind short, sout pipe, serr raw, env [] 185s autopkgtest: DBG: testbed command exited with code 0 185s autopkgtest: DBG: testbed command ['apt-cache', 'policy', '^python3-biopython-sql$'], kind short, sout pipe, serr raw, env [] 185s autopkgtest: DBG: testbed command exited with code 0 185s autopkgtest: DBG: testbed command ['apt-cache', 'show', 'python3-biopython-sql=1.85+dfsg-2'], kind short, sout pipe, serr raw, env [] 185s autopkgtest: DBG: testbed command exited with code 0 185s autopkgtest: DBG: install_deps: deps_new=[] 185s autopkgtest: DBG: testbed command ['sh', '-ec', 'command -v dpkg-source'], kind short, sout pipe, serr pipe, env [] 185s autopkgtest: DBG: testbed command exited with code 0 185s autopkgtest: DBG: testbed command ['sh', '-ec', 'su --shell=/bin/sh ubuntu -c \'set -e; exec 3>&1 >&2; set -x; cd /; builddir=$(mktemp -d /tmp/autopkgtest.IaIWjt/build.XXX); cd $builddir; OUT=$(apt-get source -d -q --only-source python-biopython=1.85+dfsg-2 2>&1) || RC=$?;if [ -n "$RC" ]; then if echo "$OUT" | grep -q "Unable to find a source package"; then exit 1; else exit $RC; fi;fi;echo "$OUT" | grep ^Get: || true;dpkg-source -x python-biopython_*.dsc src >/dev/null; chmod -R a+rX .; cd [a-z0-9]*/.; pwd >&3; sed -n "1 {s/).*//; s/ (/\\n/; p}" debian/changelog >&3\''], kind build, sout pipe, serr raw, env ['ADT_TEST_TRIGGERS=sphinx/8.1.3-5'] 186s + cd / 186s + mktemp -d /tmp/autopkgtest.IaIWjt/build.XXX 186s + builddir=/tmp/autopkgtest.IaIWjt/build.Jxz 186s + cd /tmp/autopkgtest.IaIWjt/build.Jxz 186s + apt-get source -d -q --only-source python-biopython=1.85+dfsg-2 187s + OUT=Reading package lists... 187s NOTICE: 'python-biopython' packaging is maintained in the 'Git' version control system at: 187s https://salsa.debian.org/med-team/python-biopython.git 187s Please use: 187s git clone https://salsa.debian.org/med-team/python-biopython.git 187s to retrieve the latest (possibly unreleased) updates to the package. 187s Need to get 14.7 MB of source archives. 187s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.85+dfsg-2 (dsc) [3439 B] 187s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.85+dfsg-2 (tar) [14.6 MB] 187s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.85+dfsg-2 (diff) [42.9 kB] 187s Fetched 14.7 MB in 2s (8442 kB/s) 187s Download complete and in download only mode 187s + [ -n ] 187s + echo Reading package lists... 187s NOTICE: 'python-biopython' packaging is maintained in the 'Git' version control system at: 187s https://salsa.debian.org/med-team/python-biopython.git 187s Please use: 187s git clone https://salsa.debian.org/med-team/python-biopython.git 187s to retrieve the latest (possibly unreleased) updates to the package. 187s Need to get 14.7 MB of source archives. 187s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.85+dfsg-2 (dsc) [3439 B] 187s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.85+dfsg-2 (tar) [14.6 MB] 187s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.85+dfsg-2 (diff) [42.9 kB] 187s Fetched 14.7 MB in 2s (8442 kB/s) 187s Download complete and in download only mode 187s + grep ^Get: 187s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.85+dfsg-2 (dsc) [3439 B] 187s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.85+dfsg-2 (tar) [14.6 MB] 187s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.85+dfsg-2 (diff) [42.9 kB] 187s + dpkg-source -x python-biopython_1.85+dfsg-2.dsc src 188s gpgv: Signature made Thu Feb 6 14:44:48 2025 UTC 188s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 188s gpgv: issuer "crusoe@debian.org" 188s gpgv: Can't check signature: No public key 188s dpkg-source: warning: cannot verify inline signature for ./python-biopython_1.85+dfsg-2.dsc: no acceptable signature found 189s + chmod -R a+rX . 189s + cd src/. 189s + pwd 189s + sed -n 1 {s/).*//; s/ (/\n/; p} debian/changelog 189s autopkgtest: DBG: testbed command exited with code 0 189s autopkgtest [12:36:42]: testing package python-biopython version 1.85+dfsg-2 189s autopkgtest: DBG: sending command to testbed: copyup /tmp/autopkgtest.IaIWjt/build.Jxz/src/debian/ /tmp/autopkgtest-work.by5by6hj/out/pkg/debian/ 189s autopkgtest: DBG: got reply from testbed: ok 189s autopkgtest: DBG: processing dependency @ 189s autopkgtest: DBG: synthesised dependency python3-biopython 189s autopkgtest: DBG: synthesised dependency python-biopython-doc 189s autopkgtest: DBG: synthesised dependency python3-biopython-sql 189s autopkgtest: DBG: processing dependency python3-setuptools 189s autopkgtest: DBG: processing dependency python3-all 189s autopkgtest: DBG: Test defined: name dependencies path None command "sh debian/tests/run-unit-test" restrictions ['allow-stderr'] features ['test-name=dependencies'] depends ['python3-biopython', 'python-biopython-doc', 'python3-biopython-sql', 'python3-setuptools', 'python3-all'] 189s autopkgtest: DBG: processing dependency @ 189s autopkgtest: DBG: synthesised dependency python3-biopython 189s autopkgtest: DBG: synthesised dependency python-biopython-doc 189s autopkgtest: DBG: synthesised dependency python3-biopython-sql 189s autopkgtest: DBG: processing dependency @builddeps@ 189s autopkgtest: DBG: synthesised dependency debhelper-compat (= 13) 189s autopkgtest: DBG: synthesised dependency dh-sequence-python3 189s autopkgtest: DBG: synthesised dependency python3-all-dev:native 189s autopkgtest: DBG: synthesised dependency libpython3-all-dev 189s autopkgtest: DBG: synthesised dependency python3-numpy 189s autopkgtest: DBG: synthesised dependency flex 189s autopkgtest: DBG: synthesised dependency python3-reportlab (>= 4.0.4-1~) 189s autopkgtest: DBG: synthesised dependency hevea 189s autopkgtest: DBG: synthesised dependency texlive-latex-base 189s autopkgtest: DBG: synthesised dependency texlive-latex-extra 189s autopkgtest: DBG: synthesised dependency texlive-fonts-recommended 189s autopkgtest: DBG: synthesised dependency bwa 189s autopkgtest: DBG: synthesised dependency clustalo 189s autopkgtest: DBG: synthesised dependency clustalw [any-amd64] 189s autopkgtest: DBG: synthesised dependency dialign 189s autopkgtest: DBG: synthesised dependency dssp 189s autopkgtest: DBG: synthesised dependency emboss [!armel !armhf !i386 !hppa !m68k !powerpc !s390x !sh4] 189s autopkgtest: DBG: synthesised dependency fasttree 189s autopkgtest: DBG: synthesised dependency mafft 189s autopkgtest: DBG: synthesised dependency muscle3 [i386 amd64 x32] 189s autopkgtest: DBG: synthesised dependency ncbi-blast+ 189s autopkgtest: DBG: synthesised dependency phylip 189s autopkgtest: DBG: synthesised dependency phyml [any-amd64] 189s autopkgtest: DBG: synthesised dependency prank 189s autopkgtest: DBG: synthesised dependency probcons 189s autopkgtest: DBG: synthesised dependency python3-networkx 189s autopkgtest: DBG: synthesised dependency python3-numpydoc 189s autopkgtest: DBG: synthesised dependency python3-mysqldb 189s autopkgtest: DBG: synthesised dependency python3-matplotlib 189s autopkgtest: DBG: synthesised dependency python3-mmtf 189s autopkgtest: DBG: synthesised dependency python3-pil 189s autopkgtest: DBG: synthesised dependency python3-rdflib 189s autopkgtest: DBG: synthesised dependency python3-psycopg2 [any-amd64] 189s autopkgtest: DBG: synthesised dependency python3-pygments 189s autopkgtest: DBG: synthesised dependency python3-igraph 189s autopkgtest: DBG: synthesised dependency python3-scipy 189s autopkgtest: DBG: synthesised dependency python3-setuptools 189s autopkgtest: DBG: synthesised dependency python3-sphinx 189s autopkgtest: DBG: synthesised dependency python3-sphinx-rtd-theme 189s autopkgtest: DBG: synthesised dependency raxml [any-amd64 any-i386] 189s autopkgtest: DBG: synthesised dependency samtools [any-amd64] 189s autopkgtest: DBG: synthesised dependency t-coffee 189s autopkgtest: DBG: synthesised dependency wise 189s autopkgtest: DBG: synthesised dependency build-essential 189s autopkgtest: DBG: Test defined: name full_suite path None command "sh debian/tests/run-unit-test" restrictions ['allow-stderr', 'skip-not-installable'] features ['test-name=full_suite'] depends ['python3-biopython', 'python-biopython-doc', 'python3-biopython-sql', 'debhelper-compat (= 13)', 'dh-sequence-python3', 'python3-all-dev:native', 'libpython3-all-dev', 'python3-numpy', 'flex', 'python3-reportlab (>= 4.0.4-1~) ', 'hevea', 'texlive-latex-base', 'texlive-latex-extra', 'texlive-fonts-recommended', 'bwa ', 'clustalo ', 'clustalw [any-amd64] ', 'dialign ', 'dssp ', 'emboss [!armel !armhf !i386 !hppa !m68k !powerpc !s390x !sh4] ', 'fasttree ', 'mafft ', 'muscle3 [i386 amd64 x32] ', 'ncbi-blast+ ', 'phylip ', 'phyml [any-amd64] ', 'prank ', 'probcons ', 'python3-networkx ', 'python3-numpydoc ', 'python3-mysqldb ', 'python3-matplotlib ', 'python3-mmtf ', 'python3-pil ', 'python3-rdflib ', 'python3-psycopg2 [any-amd64] ', 'python3-pygments ', 'python3-igraph ', 'python3-scipy ', 'python3-setuptools', 'python3-sphinx ', 'python3-sphinx-rtd-theme ', 'raxml [any-amd64 any-i386] ', 'samtools [any-amd64] ', 't-coffee ', 'wise ', 'build-essential'] 189s autopkgtest [12:36:42]: build not needed 189s autopkgtest: DBG: sending command to testbed: copyup /tmp/autopkgtest.IaIWjt/build.Jxz/src/ /tmp/autopkgtest-work.by5by6hj/out/tests-tree/ 194s autopkgtest: DBG: got reply from testbed: ok 194s autopkgtest: DBG: processing dependency @ 194s autopkgtest: DBG: synthesised dependency python3-biopython 194s autopkgtest: DBG: synthesised dependency python-biopython-doc 194s autopkgtest: DBG: synthesised dependency python3-biopython-sql 194s autopkgtest: DBG: processing dependency python3-setuptools 194s autopkgtest: DBG: processing dependency python3-all 194s autopkgtest: DBG: Test defined: name dependencies path None command "sh debian/tests/run-unit-test" restrictions ['allow-stderr'] features ['test-name=dependencies'] depends ['python3-biopython', 'python-biopython-doc', 'python3-biopython-sql', 'python3-setuptools', 'python3-all'] 194s autopkgtest: DBG: processing dependency @ 194s autopkgtest: DBG: synthesised dependency python3-biopython 194s autopkgtest: DBG: synthesised dependency python-biopython-doc 194s autopkgtest: DBG: synthesised dependency python3-biopython-sql 194s autopkgtest: DBG: processing dependency @builddeps@ 194s autopkgtest: DBG: synthesised dependency debhelper-compat (= 13) 194s autopkgtest: DBG: synthesised dependency dh-sequence-python3 194s autopkgtest: DBG: synthesised dependency python3-all-dev:native 194s autopkgtest: DBG: synthesised dependency libpython3-all-dev 194s autopkgtest: DBG: synthesised dependency python3-numpy 194s autopkgtest: DBG: synthesised dependency flex 194s autopkgtest: DBG: synthesised dependency python3-reportlab (>= 4.0.4-1~) 194s autopkgtest: DBG: synthesised dependency hevea 194s autopkgtest: DBG: synthesised dependency texlive-latex-base 194s autopkgtest: DBG: synthesised dependency texlive-latex-extra 194s autopkgtest: DBG: synthesised dependency texlive-fonts-recommended 194s autopkgtest: DBG: synthesised dependency bwa 194s autopkgtest: DBG: synthesised dependency clustalo 194s autopkgtest: DBG: synthesised dependency clustalw [any-amd64] 194s autopkgtest: DBG: synthesised dependency dialign 194s autopkgtest: DBG: synthesised dependency dssp 194s autopkgtest: DBG: synthesised dependency emboss [!armel !armhf !i386 !hppa !m68k !powerpc !s390x !sh4] 194s autopkgtest: DBG: synthesised dependency fasttree 194s autopkgtest: DBG: synthesised dependency mafft 194s autopkgtest: DBG: synthesised dependency muscle3 [i386 amd64 x32] 194s autopkgtest: DBG: synthesised dependency ncbi-blast+ 194s autopkgtest: DBG: synthesised dependency phylip 194s autopkgtest: DBG: synthesised dependency phyml [any-amd64] 194s autopkgtest: DBG: synthesised dependency prank 194s autopkgtest: DBG: synthesised dependency probcons 194s autopkgtest: DBG: synthesised dependency python3-networkx 194s autopkgtest: DBG: synthesised dependency python3-numpydoc 194s autopkgtest: DBG: synthesised dependency python3-mysqldb 194s autopkgtest: DBG: synthesised dependency python3-matplotlib 194s autopkgtest: DBG: synthesised dependency python3-mmtf 194s autopkgtest: DBG: synthesised dependency python3-pil 194s autopkgtest: DBG: synthesised dependency python3-rdflib 194s autopkgtest: DBG: synthesised dependency python3-psycopg2 [any-amd64] 194s autopkgtest: DBG: synthesised dependency python3-pygments 194s autopkgtest: DBG: synthesised dependency python3-igraph 194s autopkgtest: DBG: synthesised dependency python3-scipy 194s autopkgtest: DBG: synthesised dependency python3-setuptools 194s autopkgtest: DBG: synthesised dependency python3-sphinx 194s autopkgtest: DBG: synthesised dependency python3-sphinx-rtd-theme 194s autopkgtest: DBG: synthesised dependency raxml [any-amd64 any-i386] 194s autopkgtest: DBG: synthesised dependency samtools [any-amd64] 194s autopkgtest: DBG: synthesised dependency t-coffee 194s autopkgtest: DBG: synthesised dependency wise 194s autopkgtest: DBG: synthesised dependency build-essential 194s autopkgtest: DBG: Test defined: name full_suite path None command "sh debian/tests/run-unit-test" restrictions ['allow-stderr', 'skip-not-installable'] features ['test-name=full_suite'] depends ['python3-biopython', 'python-biopython-doc', 'python3-biopython-sql', 'debhelper-compat (= 13)', 'dh-sequence-python3', 'python3-all-dev:native', 'libpython3-all-dev', 'python3-numpy', 'flex', 'python3-reportlab (>= 4.0.4-1~) ', 'hevea', 'texlive-latex-base', 'texlive-latex-extra', 'texlive-fonts-recommended', 'bwa ', 'clustalo ', 'clustalw [any-amd64] ', 'dialign ', 'dssp ', 'emboss [!armel !armhf !i386 !hppa !m68k !powerpc !s390x !sh4] ', 'fasttree ', 'mafft ', 'muscle3 [i386 amd64 x32] ', 'ncbi-blast+ ', 'phylip ', 'phyml [any-amd64] ', 'prank ', 'probcons ', 'python3-networkx ', 'python3-numpydoc ', 'python3-mysqldb ', 'python3-matplotlib ', 'python3-mmtf ', 'python3-pil ', 'python3-rdflib ', 'python3-psycopg2 [any-amd64] ', 'python3-pygments ', 'python3-igraph ', 'python3-scipy ', 'python3-setuptools', 'python3-sphinx ', 'python3-sphinx-rtd-theme ', 'raxml [any-amd64 any-i386] ', 'samtools [any-amd64] ', 't-coffee ', 'wise ', 'build-essential'] 194s autopkgtest [12:36:47]: test dependencies: preparing testbed 194s autopkgtest: DBG: testbed reset: modified=False, deps_installed=[], deps_new=['python3-biopython', 'python-biopython-doc', 'python3-biopython-sql', 'python3-setuptools', 'python3-all'] 194s autopkgtest: DBG: Binaries: no registered binaries, not publishing anything 194s autopkgtest: DBG: install_deps: deps_new=['python3-biopython', 'python-biopython-doc', 'python3-biopython-sql', 'python3-setuptools', 'python3-all'] 194s autopkgtest: DBG: install-deps: satisfying python3-biopython, python-biopython-doc, python3-biopython-sql, python3-setuptools, python3-all 194s autopkgtest: DBG: can use apt-get on testbed: True 194s autopkgtest: DBG: testbed command ['/bin/sh', '-ec', '"$@" 3>&2 2>&1', 'run_apt_command', '/usr/bin/eatmydata', 'apt-get', '--quiet', '--assume-yes', '-o=APT::Status-Fd=3', '-o=APT::Install-Recommends=false', '-o=Dpkg::Options::=--force-confnew', '-o=Debug::pkgProblemResolver=true', 'satisfy', 'python3-biopython, python-biopython-doc, python3-biopython-sql, python3-setuptools, python3-all'], kind install, sout raw, serr pipe, env ['DEBIAN_FRONTEND=noninteractive', 'APT_LISTBUGS_FRONTEND=none', 'APT_LISTCHANGES_FRONTEND=none'] 194s Reading package lists... 194s Building dependency tree... 194s Reading state information... 195s Starting pkgProblemResolver with broken count: 0 195s Starting 2 pkgProblemResolver with broken count: 0 195s Done 195s The following NEW packages will be installed: 195s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 195s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libfreetype6 195s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 195s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore 195s liblapack3 liblcms2-2 libnsl2 libopenjp2-7 libpixman-1-0 195s libpython3.12-minimal libpython3.12-stdlib libraqm0 libsharpyuv0 libtiff6 195s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 195s python-biopython-doc python3-all python3-biopython python3-biopython-sql 195s python3-cairo python3-freetype python3-numpy python3-pil python3-reportlab 195s python3-rlpycairo python3.12 python3.12-minimal sgml-base w3c-sgml-lib 195s x11-common xfonts-encodings xfonts-utils xml-core 195s 0 upgraded, 55 newly installed, 0 to remove and 0 not upgraded. 195s Need to get 53.6 MB of archives. 195s After this operation, 161 MB of additional disk space will be used. 195s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.12-minimal s390x 3.12.9-1 [836 kB] 195s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x python3.12-minimal s390x 3.12.9-1 [2403 kB] 196s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x sgml-base all 1.31 [11.4 kB] 196s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libnsl2 s390x 1.3.0-3build3 [44.1 kB] 196s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.12-stdlib s390x 3.12.9-1 [2071 kB] 196s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x python3.12 s390x 3.12.9-1 [671 kB] 196s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 196s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 196s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libfontenc1 s390x 1:1.1.8-1build1 [14.8 kB] 196s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB] 196s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x x11-common all 1:7.7+23ubuntu3 [21.7 kB] 196s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 196s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x xfonts-utils s390x 1:7.7+7 [101 kB] 196s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-urw-base35 all 20200910-8 [11.0 MB] 197s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig-config s390x 2.15.0-2ubuntu1 [37.5 kB] 197s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.1-2 [252 kB] 197s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x libfontconfig1 s390x 2.15.0-2ubuntu1 [150 kB] 197s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x libpixman-1-0 s390x 0.44.0-3 [201 kB] 197s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-render0 s390x 1.17.0-2 [17.0 kB] 197s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-shm0 s390x 1.17.0-2 [5862 B] 197s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB] 197s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x libcairo2 s390x 1.18.2-2 [580 kB] 197s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.23-1 [46.1 kB] 197s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 15-20250213-1ubuntu1 [620 kB] 197s Get:25 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 15-20250213-1ubuntu1 [151 kB] 197s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB] 197s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x libharfbuzz0b s390x 10.2.0-1 [538 kB] 197s Get:28 http://ftpmaster.internal/ubuntu plucky/main s390x libimagequant0 s390x 2.18.0-1build1 [43.3 kB] 197s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8 s390x 2.1.5-3ubuntu2 [147 kB] 197s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 197s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 197s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 197s Get:33 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 197s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.1-2 [2971 kB] 197s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x liblcms2-2 s390x 2.16-2 [175 kB] 197s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x libraqm0 s390x 0.10.2-1 [15.8 kB] 197s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x libsharpyuv0 s390x 1.5.0-0.1 [16.7 kB] 197s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] 197s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x libwebp7 s390x 1.5.0-0.1 [210 kB] 197s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu4 [217 kB] 197s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x libwebpdemux2 s390x 1.5.0-0.1 [12.6 kB] 197s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x libwebpmux3 s390x 1.5.0-0.1 [25.8 kB] 197s Get:43 http://ftpmaster.internal/ubuntu plucky/universe s390x python-biopython-doc all 1.85+dfsg-2 [18.2 MB] 198s Get:44 http://ftpmaster.internal/ubuntu plucky/main s390x python3-all s390x 3.13.1-1~exp2 [898 B] 198s Get:45 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:1.26.4+ds-13 [4601 kB] 198s Get:46 http://ftpmaster.internal/ubuntu plucky/main s390x libopenjp2-7 s390x 2.5.0-2ubuntu3 [208 kB] 198s Get:47 http://ftpmaster.internal/ubuntu plucky/main s390x python3-pil s390x 11.1.0-5 [527 kB] 198s Get:48 http://ftpmaster.internal/ubuntu plucky/main s390x python3-cairo s390x 1.26.1-2build1 [138 kB] 198s Get:49 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-freetype all 2.5.1-1 [92.3 kB] 198s Get:50 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-rlpycairo all 0.3.0-3 [9130 B] 198s Get:51 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-reportlab all 4.3.0-1 [1137 kB] 198s Get:52 http://ftpmaster.internal/ubuntu plucky/main s390x xml-core all 0.19 [20.3 kB] 198s Get:53 http://ftpmaster.internal/ubuntu plucky/universe s390x w3c-sgml-lib all 1.3-3 [280 kB] 198s Get:54 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-biopython s390x 1.85+dfsg-2 [1756 kB] 198s Get:55 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-biopython-sql all 1.85+dfsg-2 [26.4 kB] 198s Fetched 53.6 MB in 3s (17.1 MB/s) 198s Selecting previously unselected package libpython3.12-minimal:s390x. 198s (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 ... 55929 files and directories currently installed.) 198s Preparing to unpack .../00-libpython3.12-minimal_3.12.9-1_s390x.deb ... 198s Unpacking libpython3.12-minimal:s390x (3.12.9-1) ... 199s Selecting previously unselected package python3.12-minimal. 199s Preparing to unpack .../01-python3.12-minimal_3.12.9-1_s390x.deb ... 199s Unpacking python3.12-minimal (3.12.9-1) ... 199s Selecting previously unselected package sgml-base. 199s Preparing to unpack .../02-sgml-base_1.31_all.deb ... 199s Unpacking sgml-base (1.31) ... 199s Selecting previously unselected package libnsl2:s390x. 199s Preparing to unpack .../03-libnsl2_1.3.0-3build3_s390x.deb ... 199s Unpacking libnsl2:s390x (1.3.0-3build3) ... 199s Selecting previously unselected package libpython3.12-stdlib:s390x. 199s Preparing to unpack .../04-libpython3.12-stdlib_3.12.9-1_s390x.deb ... 199s Unpacking libpython3.12-stdlib:s390x (3.12.9-1) ... 199s Selecting previously unselected package python3.12. 199s Preparing to unpack .../05-python3.12_3.12.9-1_s390x.deb ... 199s Unpacking python3.12 (3.12.9-1) ... 199s Selecting previously unselected package fonts-dejavu-mono. 199s Preparing to unpack .../06-fonts-dejavu-mono_2.37-8_all.deb ... 199s Unpacking fonts-dejavu-mono (2.37-8) ... 199s Selecting previously unselected package fonts-dejavu-core. 199s Preparing to unpack .../07-fonts-dejavu-core_2.37-8_all.deb ... 199s Unpacking fonts-dejavu-core (2.37-8) ... 199s Selecting previously unselected package libfontenc1:s390x. 199s Preparing to unpack .../08-libfontenc1_1%3a1.1.8-1build1_s390x.deb ... 199s Unpacking libfontenc1:s390x (1:1.1.8-1build1) ... 199s Selecting previously unselected package libfreetype6:s390x. 199s Preparing to unpack .../09-libfreetype6_2.13.3+dfsg-1_s390x.deb ... 199s Unpacking libfreetype6:s390x (2.13.3+dfsg-1) ... 199s Selecting previously unselected package x11-common. 199s Preparing to unpack .../10-x11-common_1%3a7.7+23ubuntu3_all.deb ... 199s Unpacking x11-common (1:7.7+23ubuntu3) ... 199s Selecting previously unselected package xfonts-encodings. 199s Preparing to unpack .../11-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 199s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 199s Selecting previously unselected package xfonts-utils. 199s Preparing to unpack .../12-xfonts-utils_1%3a7.7+7_s390x.deb ... 199s Unpacking xfonts-utils (1:7.7+7) ... 199s Selecting previously unselected package fonts-urw-base35. 199s Preparing to unpack .../13-fonts-urw-base35_20200910-8_all.deb ... 199s Unpacking fonts-urw-base35 (20200910-8) ... 199s Selecting previously unselected package fontconfig-config. 199s Preparing to unpack .../14-fontconfig-config_2.15.0-2ubuntu1_s390x.deb ... 199s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 199s Selecting previously unselected package libblas3:s390x. 199s Preparing to unpack .../15-libblas3_3.12.1-2_s390x.deb ... 199s Unpacking libblas3:s390x (3.12.1-2) ... 199s Selecting previously unselected package libfontconfig1:s390x. 199s Preparing to unpack .../16-libfontconfig1_2.15.0-2ubuntu1_s390x.deb ... 199s Unpacking libfontconfig1:s390x (2.15.0-2ubuntu1) ... 199s Selecting previously unselected package libpixman-1-0:s390x. 199s Preparing to unpack .../17-libpixman-1-0_0.44.0-3_s390x.deb ... 199s Unpacking libpixman-1-0:s390x (0.44.0-3) ... 199s Selecting previously unselected package libxcb-render0:s390x. 199s Preparing to unpack .../18-libxcb-render0_1.17.0-2_s390x.deb ... 199s Unpacking libxcb-render0:s390x (1.17.0-2) ... 199s Selecting previously unselected package libxcb-shm0:s390x. 199s Preparing to unpack .../19-libxcb-shm0_1.17.0-2_s390x.deb ... 199s Unpacking libxcb-shm0:s390x (1.17.0-2) ... 199s Selecting previously unselected package libxrender1:s390x. 199s Preparing to unpack .../20-libxrender1_1%3a0.9.10-1.1build1_s390x.deb ... 199s Unpacking libxrender1:s390x (1:0.9.10-1.1build1) ... 199s Selecting previously unselected package libcairo2:s390x. 199s Preparing to unpack .../21-libcairo2_1.18.2-2_s390x.deb ... 199s Unpacking libcairo2:s390x (1.18.2-2) ... 199s Selecting previously unselected package libdeflate0:s390x. 199s Preparing to unpack .../22-libdeflate0_1.23-1_s390x.deb ... 199s Unpacking libdeflate0:s390x (1.23-1) ... 199s Selecting previously unselected package libgfortran5:s390x. 199s Preparing to unpack .../23-libgfortran5_15-20250213-1ubuntu1_s390x.deb ... 199s Unpacking libgfortran5:s390x (15-20250213-1ubuntu1) ... 199s Selecting previously unselected package libgomp1:s390x. 199s Preparing to unpack .../24-libgomp1_15-20250213-1ubuntu1_s390x.deb ... 199s Unpacking libgomp1:s390x (15-20250213-1ubuntu1) ... 199s Selecting previously unselected package libgraphite2-3:s390x. 199s Preparing to unpack .../25-libgraphite2-3_1.3.14-2ubuntu1_s390x.deb ... 199s Unpacking libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 199s Selecting previously unselected package libharfbuzz0b:s390x. 199s Preparing to unpack .../26-libharfbuzz0b_10.2.0-1_s390x.deb ... 199s Unpacking libharfbuzz0b:s390x (10.2.0-1) ... 199s Selecting previously unselected package libimagequant0:s390x. 199s Preparing to unpack .../27-libimagequant0_2.18.0-1build1_s390x.deb ... 199s Unpacking libimagequant0:s390x (2.18.0-1build1) ... 199s Selecting previously unselected package libjpeg-turbo8:s390x. 199s Preparing to unpack .../28-libjpeg-turbo8_2.1.5-3ubuntu2_s390x.deb ... 199s Unpacking libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 199s Selecting previously unselected package libjpeg8:s390x. 199s Preparing to unpack .../29-libjpeg8_8c-2ubuntu11_s390x.deb ... 199s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 199s Selecting previously unselected package libjs-jquery. 199s Preparing to unpack .../30-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 199s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 199s Selecting previously unselected package libjs-underscore. 199s Preparing to unpack .../31-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 199s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 199s Selecting previously unselected package libjs-sphinxdoc. 199s Preparing to unpack .../32-libjs-sphinxdoc_8.1.3-5_all.deb ... 199s Unpacking libjs-sphinxdoc (8.1.3-5) ... 199s Selecting previously unselected package liblapack3:s390x. 199s Preparing to unpack .../33-liblapack3_3.12.1-2_s390x.deb ... 199s Unpacking liblapack3:s390x (3.12.1-2) ... 199s Selecting previously unselected package liblcms2-2:s390x. 199s Preparing to unpack .../34-liblcms2-2_2.16-2_s390x.deb ... 199s Unpacking liblcms2-2:s390x (2.16-2) ... 199s Selecting previously unselected package libraqm0:s390x. 199s Preparing to unpack .../35-libraqm0_0.10.2-1_s390x.deb ... 199s Unpacking libraqm0:s390x (0.10.2-1) ... 199s Selecting previously unselected package libsharpyuv0:s390x. 199s Preparing to unpack .../36-libsharpyuv0_1.5.0-0.1_s390x.deb ... 199s Unpacking libsharpyuv0:s390x (1.5.0-0.1) ... 199s Selecting previously unselected package libjbig0:s390x. 199s Preparing to unpack .../37-libjbig0_2.1-6.1ubuntu2_s390x.deb ... 199s Unpacking libjbig0:s390x (2.1-6.1ubuntu2) ... 199s Selecting previously unselected package libwebp7:s390x. 199s Preparing to unpack .../38-libwebp7_1.5.0-0.1_s390x.deb ... 199s Unpacking libwebp7:s390x (1.5.0-0.1) ... 199s Selecting previously unselected package libtiff6:s390x. 199s Preparing to unpack .../39-libtiff6_4.5.1+git230720-4ubuntu4_s390x.deb ... 199s Unpacking libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 199s Selecting previously unselected package libwebpdemux2:s390x. 199s Preparing to unpack .../40-libwebpdemux2_1.5.0-0.1_s390x.deb ... 199s Unpacking libwebpdemux2:s390x (1.5.0-0.1) ... 199s Selecting previously unselected package libwebpmux3:s390x. 199s Preparing to unpack .../41-libwebpmux3_1.5.0-0.1_s390x.deb ... 199s Unpacking libwebpmux3:s390x (1.5.0-0.1) ... 199s Selecting previously unselected package python-biopython-doc. 199s Preparing to unpack .../42-python-biopython-doc_1.85+dfsg-2_all.deb ... 199s Unpacking python-biopython-doc (1.85+dfsg-2) ... 200s Selecting previously unselected package python3-all. 200s Preparing to unpack .../43-python3-all_3.13.1-1~exp2_s390x.deb ... 200s Unpacking python3-all (3.13.1-1~exp2) ... 200s Selecting previously unselected package python3-numpy. 200s Preparing to unpack .../44-python3-numpy_1%3a1.26.4+ds-13_s390x.deb ... 200s Unpacking python3-numpy (1:1.26.4+ds-13) ... 200s Selecting previously unselected package libopenjp2-7:s390x. 200s Preparing to unpack .../45-libopenjp2-7_2.5.0-2ubuntu3_s390x.deb ... 200s Unpacking libopenjp2-7:s390x (2.5.0-2ubuntu3) ... 200s Selecting previously unselected package python3-pil:s390x. 200s Preparing to unpack .../46-python3-pil_11.1.0-5_s390x.deb ... 200s Unpacking python3-pil:s390x (11.1.0-5) ... 200s Selecting previously unselected package python3-cairo. 200s Preparing to unpack .../47-python3-cairo_1.26.1-2build1_s390x.deb ... 200s Unpacking python3-cairo (1.26.1-2build1) ... 200s Selecting previously unselected package python3-freetype. 200s Preparing to unpack .../48-python3-freetype_2.5.1-1_all.deb ... 200s Unpacking python3-freetype (2.5.1-1) ... 200s Selecting previously unselected package python3-rlpycairo. 200s Preparing to unpack .../49-python3-rlpycairo_0.3.0-3_all.deb ... 200s Unpacking python3-rlpycairo (0.3.0-3) ... 200s Selecting previously unselected package python3-reportlab. 200s Preparing to unpack .../50-python3-reportlab_4.3.0-1_all.deb ... 200s Unpacking python3-reportlab (4.3.0-1) ... 200s Selecting previously unselected package xml-core. 200s Preparing to unpack .../51-xml-core_0.19_all.deb ... 200s Unpacking xml-core (0.19) ... 200s Selecting previously unselected package w3c-sgml-lib. 200s Preparing to unpack .../52-w3c-sgml-lib_1.3-3_all.deb ... 200s Unpacking w3c-sgml-lib (1.3-3) ... 200s Selecting previously unselected package python3-biopython. 200s Preparing to unpack .../53-python3-biopython_1.85+dfsg-2_s390x.deb ... 200s Unpacking python3-biopython (1.85+dfsg-2) ... 200s Selecting previously unselected package python3-biopython-sql. 200s Preparing to unpack .../54-python3-biopython-sql_1.85+dfsg-2_all.deb ... 200s Unpacking python3-biopython-sql (1.85+dfsg-2) ... 200s Setting up libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 200s Setting up liblcms2-2:s390x (2.16-2) ... 200s Setting up libpixman-1-0:s390x (0.44.0-3) ... 200s Setting up libsharpyuv0:s390x (1.5.0-0.1) ... 200s Setting up libxrender1:s390x (1:0.9.10-1.1build1) ... 200s Setting up libxcb-render0:s390x (1.17.0-2) ... 200s Setting up libpython3.12-minimal:s390x (3.12.9-1) ... 200s Setting up x11-common (1:7.7+23ubuntu3) ... 200s Setting up libdeflate0:s390x (1.23-1) ... 200s Setting up libxcb-shm0:s390x (1.17.0-2) ... 200s Setting up libgomp1:s390x (15-20250213-1ubuntu1) ... 200s Setting up libjbig0:s390x (2.1-6.1ubuntu2) ... 200s Setting up libfontenc1:s390x (1:1.1.8-1build1) ... 200s Setting up libblas3:s390x (3.12.1-2) ... 200s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 200s Setting up libfreetype6:s390x (2.13.3+dfsg-1) ... 200s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 200s Setting up libimagequant0:s390x (2.18.0-1build1) ... 200s Setting up fonts-dejavu-mono (2.37-8) ... 200s Setting up fonts-dejavu-core (2.37-8) ... 200s Setting up libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 200s Setting up libgfortran5:s390x (15-20250213-1ubuntu1) ... 200s Setting up libwebp7:s390x (1.5.0-0.1) ... 200s Setting up libnsl2:s390x (1.3.0-3build3) ... 200s Setting up libopenjp2-7:s390x (2.5.0-2ubuntu3) ... 200s Setting up libharfbuzz0b:s390x (10.2.0-1) ... 200s Setting up sgml-base (1.31) ... 201s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 201s Setting up libwebpmux3:s390x (1.5.0-0.1) ... 201s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 201s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 201s Setting up python3.12-minimal (3.12.9-1) ... 201s Setting up liblapack3:s390x (3.12.1-2) ... 201s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 201s Setting up libpython3.12-stdlib:s390x (3.12.9-1) ... 201s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 202s Setting up libwebpdemux2:s390x (1.5.0-0.1) ... 202s Setting up python3.12 (3.12.9-1) ... 203s Setting up python3-all (3.13.1-1~exp2) ... 203s Setting up python3-freetype (2.5.1-1) ... 203s Setting up xfonts-utils (1:7.7+7) ... 203s Setting up libraqm0:s390x (0.10.2-1) ... 203s Setting up python3-numpy (1:1.26.4+ds-13) ... 206s Setting up libjs-sphinxdoc (8.1.3-5) ... 206s Setting up python-biopython-doc (1.85+dfsg-2) ... 206s Setting up libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 207s Setting up xml-core (0.19) ... 207s Setting up libfontconfig1:s390x (2.15.0-2ubuntu1) ... 207s Setting up fonts-urw-base35 (20200910-8) ... 207s Setting up libcairo2:s390x (1.18.2-2) ... 207s Setting up python3-pil:s390x (11.1.0-5) ... 207s Setting up python3-cairo (1.26.1-2build1) ... 207s Setting up python3-rlpycairo (0.3.0-3) ... 208s Setting up python3-reportlab (4.3.0-1) ... 209s Processing triggers for libc-bin (2.40-4ubuntu1) ... 209s Processing triggers for systemd (257.2-3ubuntu1) ... 209s Processing triggers for man-db (2.13.0-1) ... 210s Processing triggers for sgml-base (1.31) ... 210s Setting up w3c-sgml-lib (1.3-3) ... 234s Setting up python3-biopython (1.85+dfsg-2) ... 236s Setting up python3-biopython-sql (1.85+dfsg-2) ... 237s autopkgtest: DBG: testbed command exited with code 0 237s autopkgtest: DBG: testbed command ['dpkg-query', '--show', '-f', '${Status}', 'python3-biopython'], kind short, sout pipe, serr pipe, env [] 237s autopkgtest: DBG: testbed command exited with code 0 237s autopkgtest: DBG: testbed command ['dpkg-query', '--show', '-f', '${Status}', 'python-biopython-doc'], kind short, sout pipe, serr pipe, env [] 237s autopkgtest: DBG: testbed command exited with code 0 237s autopkgtest: DBG: testbed command ['dpkg-query', '--show', '-f', '${Status}', 'python3-biopython-sql'], kind short, sout pipe, serr pipe, env [] 237s autopkgtest: DBG: testbed command exited with code 0 237s autopkgtest: DBG: testbed command ['sh', '-ec', "dpkg-query --show -f '${Package}\\t${Version}\\n' > /tmp/autopkgtest.IaIWjt/dependencies-packages.all"], kind short, sout raw, serr pipe, env [] 238s autopkgtest: DBG: testbed command exited with code 0 238s autopkgtest: DBG: sending command to testbed: copyup /tmp/autopkgtest.IaIWjt/dependencies-packages.all /tmp/autopkgtest-work.by5by6hj/out/dependencies-packages.all 238s autopkgtest: DBG: got reply from testbed: ok 238s autopkgtest: DBG: testbed command ['test', '-e', '/tmp/autopkgtest.IaIWjt/build.Jxz/src'], kind short, sout raw, serr raw, env [] 238s autopkgtest: DBG: testbed command exited with code 0 238s autopkgtest: DBG: copydown: tb path /tmp/autopkgtest.IaIWjt/build.Jxz/src already exists 238s autopkgtest [12:37:31]: test dependencies: sh debian/tests/run-unit-test 238s autopkgtest [12:37:31]: test dependencies: [----------------------- 238s autopkgtest: DBG: testbed command ['su', '-s', '/bin/bash', 'ubuntu', '-c', "set -e; exec /tmp/autopkgtest.IaIWjt/wrapper.sh --debug --artifacts=/tmp/autopkgtest.IaIWjt/dependencies-artifacts --chdir=/tmp/autopkgtest.IaIWjt/build.Jxz/src --env=AUTOPKGTEST_TESTBED_ARCH=s390x --env=AUTOPKGTEST_TEST_ARCH=s390x --env=DEB_BUILD_OPTIONS=parallel=2 --env=DEBIAN_FRONTEND=noninteractive --env=LANG=C.UTF-8 --unset-env=LANGUAGE --unset-env=LC_ADDRESS --unset-env=LC_ALL --unset-env=LC_COLLATE --unset-env=LC_CTYPE --unset-env=LC_IDENTIFICATION --unset-env=LC_MEASUREMENT --unset-env=LC_MESSAGES --unset-env=LC_MONETARY --unset-env=LC_NAME --unset-env=LC_NUMERIC --unset-env=LC_PAPER --unset-env=LC_TELEPHONE --unset-env=LC_TIME --script-pid-file=/tmp/autopkgtest_script_pid --source-profile --stderr=/tmp/autopkgtest.IaIWjt/dependencies-stderr --stdout=/tmp/autopkgtest.IaIWjt/dependencies-stdout --tmp=/tmp/autopkgtest.IaIWjt/autopkgtest_tmp --env=ADT_TEST_TRIGGERS=sphinx/8.1.3-5 -- bash -ec 'sh debian/tests/run-unit-test'"], kind test, sout raw, serr raw, env [] 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: creating AUTOPKGTEST_ARTIFACTS: /tmp/autopkgtest.IaIWjt/dependencies-artifacts 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: changing to directory: /tmp/autopkgtest.IaIWjt/build.Jxz/src 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: setting environment: AUTOPKGTEST_TESTBED_ARCH=s390x 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: setting environment: AUTOPKGTEST_TEST_ARCH=s390x 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: setting environment: DEB_BUILD_OPTIONS=parallel=2 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: setting environment: DEBIAN_FRONTEND=noninteractive 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: setting environment: LANG=C.UTF-8 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: unsetting environment: LANGUAGE 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: unsetting environment: LC_ADDRESS 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: unsetting environment: LC_ALL 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: unsetting environment: LC_COLLATE 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: unsetting environment: LC_CTYPE 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: unsetting environment: LC_IDENTIFICATION 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: unsetting environment: LC_MEASUREMENT 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: unsetting environment: LC_MESSAGES 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: unsetting environment: LC_MONETARY 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: unsetting environment: LC_NAME 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: unsetting environment: LC_NUMERIC 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: unsetting environment: LC_PAPER 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: unsetting environment: LC_TELEPHONE 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: unsetting environment: LC_TIME 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: will create pid file: /tmp/autopkgtest_script_pid 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: pretending to be a login shell 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: will write standard error to /tmp/autopkgtest.IaIWjt/dependencies-stderr 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: will write stdout to /tmp/autopkgtest.IaIWjt/dependencies-stdout 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: creating AUTOPKGTEST_TMP: /tmp/autopkgtest.IaIWjt/autopkgtest_tmp 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: setting environment: ADT_TEST_TRIGGERS=sphinx/8.1.3-5 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: command to run: bash -ec sh debian/tests/run-unit-test 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: copying /tmp/tmp.Aujpxgl42T/out to stdout and file: /tmp/autopkgtest.IaIWjt/dependencies-stdout 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: copying /tmp/tmp.Aujpxgl42T/err to standard error and file: /tmp/autopkgtest.IaIWjt/dependencies-stdout 238s /tmp/autopkgtest.IaIWjt/wrapper.sh: writing script pid 3720 to /tmp/autopkgtest_script_pid 238s cp: cannot stat '/usr/share/libcifpp/mmcif_pdbx.dic': No such file or directory 238s cp: cannot stat '/usr/share/libcifpp/mmcif_ma.dic': No such file or directory 239s mkdir: created directory 'Bio' 239s mkdir: created directory 'Bio/Align' 239s mkdir: created directory 'Bio/Align/substitution_matrices' 239s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 239s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 240s test_Ace ... ok 240s test_Affy ... ok 242s test_AlignIO ... ok 242s test_AlignIO_ClustalIO ... ok 242s test_AlignIO_EmbossIO ... ok 242s test_AlignIO_FastaIO ... ok 242s test_AlignIO_MauveIO ... ok 242s test_AlignIO_PhylipIO ... ok 242s test_AlignIO_convert ... ok 242s test_AlignInfo ... ok 243s test_Align_Alignment ... ok 243s test_Align_a2m ... ok 243s test_Align_bed ... ok 243s test_Align_bigbed ... ok 244s test_Align_bigmaf ... ok 244s test_Align_bigpsl ... ok 244s test_Align_chain ... ok 244s test_Align_clustal ... ok 249s test_Align_codonalign ... ok 249s test_Align_emboss ... ok 249s test_Align_exonerate ... ok 249s test_Align_fasta ... ok 249s test_Align_hhr ... ok 250s test_Align_maf ... ok 250s test_Align_mauve ... ok 250s test_Align_msf ... ok 250s test_Align_nexus ... ok 250s test_Align_phylip ... ok 250s test_Align_psl ... ok 251s test_Align_sam ... ok 252s test_Align_stockholm ... ok 253s test_Align_tabular ... ok 253s test_Application ... ok 253s test_BioSQL_MySQLdb_online ... skipping. internet not available 253s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 253s test_BioSQL_mysql_connector_online ... skipping. internet not available 253s test_BioSQL_psycopg2_online ... skipping. internet not available 256s test_BioSQL_sqlite3 ... ok 256s test_BioSQL_sqlite3_online ... skipping. internet not available 256s test_Blast_Record ... ok 256s test_Blast_parser ... ok 256s test_CAPS ... ok 256s test_Chi2 ... ok 256s test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. 257s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 257s test_Cluster ... ok 257s test_CodonTable ... ok 257s test_ColorSpiral ... ok 257s test_Compass ... ok 258s test_Consensus ... ok 258s test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. 258s test_EMBL_unittest ... ok 258s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 258s test_EmbossPrimer ... ok 262s test_Entrez ... ok 262s test_Entrez_online ... skipping. internet not available 263s test_Entrez_parser ... ok 263s test_Enzyme ... ok 263s test_ExPASy ... skipping. internet not available 263s test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. 263s test_File ... ok 263s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 263s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 263s ok 265s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 267s ok 268s test_GraphicsChromosome ... ok 268s test_GraphicsDistribution ... ok 268s test_GraphicsGeneral ... ok 269s test_HMMCasino ... ok 269s test_HMMGeneral ... ok 269s test_KEGG ... ok 269s test_KEGG_online ... skipping. internet not available 274s test_KGML_graphics ... ok 275s test_KGML_graphics_online ... skipping. internet not available 275s test_KGML_nographics ... ok 276s test_KeyWList ... ok 276s test_LogisticRegression ... ok 276s test_MafIO_index ... ok 276s test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper. 277s test_MarkovModel ... ok 277s test_Medline ... ok 277s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 277s test_NCBIXML ... Exception ignored in: 277s Traceback (most recent call last): 277s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 277s expat_parser.Parse(NULL, True) 277s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 277s ok 277s test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper. 277s test_NCBI_qblast ... ok 277s test_NMR ... ok 277s test_NaiveBayes ... ok 278s test_Nexus ... ok 278s test_PAML_baseml ... ok 279s test_PAML_codeml ... ok 279s test_PAML_yn00 ... ok 285s test_PDB_CEAligner ... ok 285s test_PDB_DSSP ... ok 285s test_PDB_Dice ... ok 285s test_PDB_Disordered ... ok 285s test_PDB_Exposure ... ok 285s test_PDB_FragmentMapper ... ok 287s test_PDB_KDTree ... ok 287s test_PDB_MMCIF2Dict ... ok 288s test_PDB_MMCIFIO ... ok 289s test_PDB_MMCIFParser ... ok 289s test_PDB_NACCESS ... ok 289s test_PDB_PDBIO ... ok 289s test_PDB_PDBList ... skipping. internet not available 301s test_PDB_PDBMLParser ... ok 301s test_PDB_PDBParser ... ok 301s test_PDB_PSEA ... skipping. Download and install psea from ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/. Make sure that psea is on path 301s test_PDB_Polypeptide ... ok 301s test_PDB_QCPSuperimposer ... ok 305s test_PDB_SASA ... ok 306s test_PDB_SMCRA ... ok 306s test_PDB_Selection ... ok 306s test_PDB_StructureAlignment ... ok 306s test_PDB_Superimposer ... ok 306s test_PDB_alphafold_db ... skipping. internet not available 306s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 306s 306s test_PDB_parse_pdb_header ... ok 306s test_PDB_vectors ... ok 306s test_PQR ... ok 306s test_Pathway ... ok 306s test_Phd ... ok 307s test_Phylo ... ok 307s test_PhyloXML ... ok 307s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 307s test_Phylo_NeXML ... ok 307s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 307s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 307s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 308s test_PopGen_GenePop_nodepend ... ok 308s test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. 308s test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper. 308s test_ProtParam ... ok 308s test_RCSBFormats ... ok 308s test_Restriction ... ok 308s test_SCOP_Astral ... ok 308s test_SCOP_Cla ... ok 308s test_SCOP_Des ... ok 308s test_SCOP_Dom ... ok 308s test_SCOP_Hie ... ok 308s test_SCOP_Raf ... ok 308s test_SCOP_Residues ... ok 309s test_SCOP_Scop ... ok 309s test_SVDSuperimposer ... ok 309s test_SearchIO_blast_tab ... ok 309s test_SearchIO_blast_tab_index ... ok 309s test_SearchIO_blast_xml ... ok 310s test_SearchIO_blast_xml_index ... ok 310s test_SearchIO_blat_psl ... ok 311s test_SearchIO_blat_psl_index ... ok 311s test_SearchIO_exonerate ... ok 311s test_SearchIO_exonerate_text_index ... ok 311s test_SearchIO_exonerate_vulgar_index ... ok 311s test_SearchIO_fasta_m10 ... ok 311s test_SearchIO_fasta_m10_index ... ok 311s test_SearchIO_hhsuite2_text ... ok 311s test_SearchIO_hmmer2_text ... ok 312s test_SearchIO_hmmer2_text_index ... ok 312s test_SearchIO_hmmer3_domtab ... ok 312s test_SearchIO_hmmer3_domtab_index ... ok 312s test_SearchIO_hmmer3_tab ... ok 312s test_SearchIO_hmmer3_tab_index ... ok 312s test_SearchIO_hmmer3_text ... ok 312s test_SearchIO_hmmer3_text_index ... ok 312s test_SearchIO_interproscan_xml ... ok 312s test_SearchIO_model ... ok 313s test_SearchIO_write ... ok 313s test_SeqFeature ... ok 331s test_SeqIO ... ok 331s test_SeqIO_AbiIO ... ok 331s test_SeqIO_FastaIO ... ok 331s test_SeqIO_Gck ... ok 331s test_SeqIO_Gfa ... ok 331s test_SeqIO_Insdc ... ok 331s test_SeqIO_NibIO ... ok 334s test_SeqIO_PdbIO ... ok 334s test_SeqIO_QualityIO ... ok 334s test_SeqIO_SeqXML ... ok 335s test_SeqIO_SffIO ... ok 335s test_SeqIO_SnapGene ... ok 335s test_SeqIO_TwoBitIO ... ok 336s test_SeqIO_UniprotIO ... ok 336s test_SeqIO_Xdna ... ok 336s test_SeqIO_features ... ok 351s test_SeqIO_index ... ok 351s test_SeqIO_online ... skipping. internet not available 351s test_SeqIO_write ... ok 351s test_SeqRecord ... ok 351s test_SeqUtils ... ok 353s test_Seq_objs ... ok 353s test_SwissProt ... ok 353s test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper. 353s test_TogoWS ... skipping. internet not available 353s test_TreeConstruction ... ok 353s test_UniGene ... ok 353s test_UniProt ... skipping. internet not available 353s test_UniProt_GOA ... ok 354s test_align ... ok 354s test_align_substitution_matrices ... ok 356s test_bgzf ... ok 356s test_cellosaurus ... ok 361s test_codonalign ... ok 361s test_geo ... ok 362s test_kNN ... ok 362s test_motifs ... ok 362s test_motifs_online ... skipping. internet not available 362s test_pairwise2 ... /usr/lib/python3/dist-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module. 362s warnings.warn( 362s ok 362s test_pairwise2_no_C ... ok 363s test_pairwise_aligner ... ok 363s test_pairwise_alignment_map ... ok 370s test_phenotype ... ok 371s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 371s test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper. 371s test_prodoc ... ok 371s test_prosite ... ok 371s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 371s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 371s test_seq ... ok 371s test_translate ... ok 371s ---------------------------------------------------------------------- 371s Ran 216 tests in 131.661 seconds 371s 371s Skipping any tests requiring internet access 371s Python version: 3.12.9 (main, Feb 5 2025, 01:31:18) [GCC 14.2.0] 371s Operating system: posix linux 371s sys:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 371s sys:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 372s test_Ace ... ok 372s test_Affy ... ok 374s test_AlignIO ... ok 374s test_AlignIO_ClustalIO ... ok 374s test_AlignIO_EmbossIO ... ok 374s test_AlignIO_FastaIO ... ok 374s test_AlignIO_MauveIO ... ok 374s test_AlignIO_PhylipIO ... ok 374s test_AlignIO_convert ... ok 374s test_AlignInfo ... ok 374s test_Align_Alignment ... ok 374s test_Align_a2m ... ok 375s test_Align_bed ... ok 375s test_Align_bigbed ... ok 375s test_Align_bigmaf ... ok 376s test_Align_bigpsl ... ok 376s test_Align_chain ... ok 376s test_Align_clustal ... ok 381s test_Align_codonalign ... ok 381s test_Align_emboss ... ok 381s test_Align_exonerate ... ok 381s test_Align_fasta ... ok 381s test_Align_hhr ... ok 382s test_Align_maf ... ok 382s test_Align_mauve ... ok 382s test_Align_msf ... ok 382s test_Align_nexus ... ok 382s test_Align_phylip ... ok 383s test_Align_psl ... ok 383s test_Align_sam ... ok 385s test_Align_stockholm ... ok 385s test_Align_tabular ... ok 385s test_Application ... ok 386s test_BioSQL_MySQLdb_online ... skipping. internet not available 386s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 386s test_BioSQL_mysql_connector_online ... skipping. internet not available 386s test_BioSQL_psycopg2_online ... skipping. internet not available 390s test_BioSQL_sqlite3 ... ok 390s test_BioSQL_sqlite3_online ... skipping. internet not available 390s test_Blast_Record ... ok 390s test_Blast_parser ... ok 390s test_CAPS ... ok 390s test_Chi2 ... ok 390s test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. 390s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 390s test_Cluster ... ok 390s test_CodonTable ... ok 391s test_ColorSpiral ... ok 391s test_Compass ... ok 392s test_Consensus ... ok 392s test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. 392s test_EMBL_unittest ... ok 392s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 392s test_EmbossPrimer ... ok 396s test_Entrez ... ok 396s test_Entrez_online ... skipping. internet not available 396s test_Entrez_parser ... ok 396s test_Enzyme ... ok 396s test_ExPASy ... skipping. internet not available 396s test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. 396s test_File ... ok 396s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 396s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 397s ok 398s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 400s ok 401s test_GraphicsChromosome ... ok 401s test_GraphicsDistribution ... ok 402s test_GraphicsGeneral ... ok 402s test_HMMCasino ... ok 402s test_HMMGeneral ... ok 402s test_KEGG ... ok 402s test_KEGG_online ... skipping. internet not available 408s test_KGML_graphics ... ok 408s test_KGML_graphics_online ... skipping. internet not available 408s test_KGML_nographics ... ok 409s test_KeyWList ... ok 409s test_LogisticRegression ... ok 409s test_MafIO_index ... ok 409s test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper. 410s test_MarkovModel ... ok 410s test_Medline ... ok 410s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 410s test_NCBIXML ... Exception ignored in: 410s Traceback (most recent call last): 410s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 410s expat_parser.Parse(NULL, True) 410s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 410s ok 410s test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper. 410s test_NCBI_qblast ... ok 410s test_NMR ... ok 410s test_NaiveBayes ... ok 411s test_Nexus ... ok 411s test_PAML_baseml ... ok 411s test_PAML_codeml ... ok 411s test_PAML_yn00 ... ok 418s test_PDB_CEAligner ... ok 418s test_PDB_DSSP ... ok 418s test_PDB_Dice ... ok 418s test_PDB_Disordered ... ok 418s test_PDB_Exposure ... ok 419s test_PDB_FragmentMapper ... ok 420s test_PDB_KDTree ... ok 420s test_PDB_MMCIF2Dict ... ok 421s test_PDB_MMCIFIO ... ok 422s test_PDB_MMCIFParser ... ok 422s test_PDB_NACCESS ... ok 422s test_PDB_PDBIO ... ok 422s test_PDB_PDBList ... skipping. internet not available 433s test_PDB_PDBMLParser ... ok 433s test_PDB_PDBParser ... ok 433s test_PDB_PSEA ... skipping. Download and install psea from ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/. Make sure that psea is on path 433s test_PDB_Polypeptide ... ok 433s test_PDB_QCPSuperimposer ... ok 437s test_PDB_SASA ... ok 438s test_PDB_SMCRA ... ok 438s test_PDB_Selection ... ok 438s test_PDB_StructureAlignment ... ok 438s test_PDB_Superimposer ... ok 438s test_PDB_alphafold_db ... skipping. internet not available 439s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 439s 439s test_PDB_parse_pdb_header ... ok 439s test_PDB_vectors ... ok 439s test_PQR ... ok 439s test_Pathway ... ok 439s test_Phd ... ok 439s test_Phylo ... ok 439s test_PhyloXML ... ok 440s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 440s test_Phylo_NeXML ... ok 440s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 440s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 440s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 440s test_PopGen_GenePop_nodepend ... ok 440s test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. 440s test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper. 440s test_ProtParam ... ok 440s test_RCSBFormats ... ok 440s test_Restriction ... ok 440s test_SCOP_Astral ... ok 441s test_SCOP_Cla ... ok 441s test_SCOP_Des ... ok 441s test_SCOP_Dom ... ok 441s test_SCOP_Hie ... ok 441s test_SCOP_Raf ... ok 441s test_SCOP_Residues ... ok 441s test_SCOP_Scop ... ok 441s test_SVDSuperimposer ... ok 441s test_SearchIO_blast_tab ... ok 441s test_SearchIO_blast_tab_index ... ok 441s test_SearchIO_blast_xml ... ok 442s test_SearchIO_blast_xml_index ... ok 443s test_SearchIO_blat_psl ... ok 443s test_SearchIO_blat_psl_index ... ok 443s test_SearchIO_exonerate ... ok 443s test_SearchIO_exonerate_text_index ... ok 443s test_SearchIO_exonerate_vulgar_index ... ok 443s test_SearchIO_fasta_m10 ... ok 443s test_SearchIO_fasta_m10_index ... ok 443s test_SearchIO_hhsuite2_text ... ok 443s test_SearchIO_hmmer2_text ... ok 443s test_SearchIO_hmmer2_text_index ... ok 443s test_SearchIO_hmmer3_domtab ... ok 443s test_SearchIO_hmmer3_domtab_index ... ok 444s test_SearchIO_hmmer3_tab ... ok 444s test_SearchIO_hmmer3_tab_index ... ok 444s test_SearchIO_hmmer3_text ... ok 444s test_SearchIO_hmmer3_text_index ... ok 444s test_SearchIO_interproscan_xml ... ok 444s test_SearchIO_model ... ok 444s test_SearchIO_write ... ok 444s test_SeqFeature ... ok 460s test_SeqIO ... ok 461s test_SeqIO_AbiIO ... ok 461s test_SeqIO_FastaIO ... ok 461s test_SeqIO_Gck ... ok 461s test_SeqIO_Gfa ... ok 461s test_SeqIO_Insdc ... ok 461s test_SeqIO_NibIO ... ok 463s test_SeqIO_PdbIO ... ok 463s test_SeqIO_QualityIO ... ok 463s test_SeqIO_SeqXML ... ok 463s test_SeqIO_SffIO ... ok 463s test_SeqIO_SnapGene ... ok 464s test_SeqIO_TwoBitIO ... ok 464s test_SeqIO_UniprotIO ... ok 464s test_SeqIO_Xdna ... ok 465s test_SeqIO_features ... ok 477s test_SeqIO_index ... ok 477s test_SeqIO_online ... skipping. internet not available 477s test_SeqIO_write ... ok 477s test_SeqRecord ... ok 477s test_SeqUtils ... ok 479s test_Seq_objs ... ok 479s test_SwissProt ... ok 479s test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper. 479s test_TogoWS ... skipping. internet not available 479s test_TreeConstruction ... ok 479s test_UniGene ... ok 479s test_UniProt ... skipping. internet not available 480s test_UniProt_GOA ... ok 480s test_align ... ok 480s test_align_substitution_matrices ... ok 483s test_bgzf ... ok 483s test_cellosaurus ... ok 487s test_codonalign ... ok 488s test_geo ... ok 488s test_kNN ... ok 488s test_motifs ... ok 488s test_motifs_online ... skipping. internet not available 488s test_pairwise2 ... /usr/lib/python3/dist-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module. 488s warnings.warn( 488s ok 488s test_pairwise2_no_C ... ok 488s test_pairwise_aligner ... ok 489s test_pairwise_alignment_map ... ok 496s test_phenotype ... ok 496s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 496s test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper. 496s test_prodoc ... ok 496s test_prosite ... ok 496s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 496s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 496s test_seq ... ok 496s test_translate ... ok 496s ---------------------------------------------------------------------- 496s Ran 216 tests in 124.721 seconds 496s 496s Skipping any tests requiring internet access 496s Python version: 3.13.2 (main, Feb 5 2025, 01:23:35) [GCC 14.2.0] 496s Operating system: posix linux 497s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 497s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 497s /tmp/autopkgtest.IaIWjt/wrapper.sh: checking for leaked background processes... 497s /tmp/autopkgtest.IaIWjt/wrapper.sh: waiting for tee/cat subprocesses... 497s /tmp/autopkgtest.IaIWjt/wrapper.sh: cleaning up... 497s /tmp/autopkgtest.IaIWjt/wrapper.sh: Exit status: 0 497s autopkgtest: DBG: testbed command exited with code 0 497s autopkgtest [12:41:50]: test dependencies: -----------------------] 497s autopkgtest: DBG: testbed executing test finished with exit status 0 497s autopkgtest: DBG: sending command to testbed: copyup /tmp/autopkgtest.IaIWjt/dependencies-stdout /tmp/autopkgtest-work.by5by6hj/out/dependencies-stdout 497s autopkgtest: DBG: got reply from testbed: ok 497s autopkgtest: DBG: sending command to testbed: copyup /tmp/autopkgtest.IaIWjt/dependencies-stderr /tmp/autopkgtest-work.by5by6hj/out/dependencies-stderr 497s autopkgtest: DBG: got reply from testbed: ok 497s autopkgtest [12:41:50]: test dependencies: - - - - - - - - - - results - - - - - - - - - - 497s autopkgtest: DBG: sending command to testbed: copyup /tmp/autopkgtest.IaIWjt/dependencies-artifacts/ /tmp/autopkgtest-work.by5by6hj/out/artifacts/ 497s dependencies PASS 498s autopkgtest: DBG: got reply from testbed: ok 498s autopkgtest: DBG: testbed command ['rm', '-rf', '/tmp/autopkgtest.IaIWjt/dependencies-artifacts', '/tmp/autopkgtest.IaIWjt/autopkgtest_tmp'], kind short, sout raw, serr pipe, env [] 498s autopkgtest: DBG: testbed command exited with code 0 498s autopkgtest [12:41:51]: test full_suite: preparing testbed 498s autopkgtest: DBG: testbed reset: modified=False, deps_installed=['python3-biopython', 'python-biopython-doc', 'python3-biopython-sql', 'python3-setuptools', 'python3-all'], deps_new=['python3-biopython', 'python-biopython-doc', 'python3-biopython-sql', 'debhelper-compat (= 13)', 'dh-sequence-python3', 'python3-all-dev:native', 'libpython3-all-dev', 'python3-numpy', 'flex', 'python3-reportlab (>= 4.0.4-1~) ', 'hevea', 'texlive-latex-base', 'texlive-latex-extra', 'texlive-fonts-recommended', 'bwa ', 'clustalo ', 'clustalw [any-amd64] ', 'dialign ', 'dssp ', 'emboss [!armel !armhf !i386 !hppa !m68k !powerpc !s390x !sh4] ', 'fasttree ', 'mafft ', 'muscle3 [i386 amd64 x32] ', 'ncbi-blast+ ', 'phylip ', 'phyml [any-amd64] ', 'prank ', 'probcons ', 'python3-networkx ', 'python3-numpydoc ', 'python3-mysqldb ', 'python3-matplotlib ', 'python3-mmtf ', 'python3-pil ', 'python3-rdflib ', 'python3-psycopg2 [any-amd64] ', 'python3-pygments ', 'python3-igraph ', 'python3-scipy ', 'python3-setuptools', 'python3-sphinx ', 'python3-sphinx-rtd-theme ', 'raxml [any-amd64 any-i386] ', 'samtools [any-amd64] ', 't-coffee ', 'wise ', 'build-essential'] 498s autopkgtest: DBG: testbed reset 498s autopkgtest: DBG: sending command to testbed: revert 631s autopkgtest: DBG: got reply from testbed: ok /tmp/autopkgtest.IaIWjt 631s autopkgtest: DBG: sending command to testbed: print-execute-command 631s autopkgtest: DBG: got reply from testbed: ok /tmp/autopkgtest-ssh.qjiad5nu/runcmd 631s autopkgtest: DBG: sending command to testbed: capabilities 631s autopkgtest: DBG: got reply from testbed: ok revert-full-system reboot root-on-testbed revert isolation-machine ok suggested-normal-user=ubuntu 631s autopkgtest: DBG: testbed capabilities: ['revert-full-system', 'reboot', 'root-on-testbed', 'revert', 'isolation-machine', 'ok', 'suggested-normal-user=ubuntu', 'has_internet'] 631s autopkgtest: DBG: testbed command ['mkdir', '-p', '/tmp/autopkgtest.IaIWjt'], kind short, sout raw, serr pipe, env [] 632s autopkgtest: DBG: testbed command exited with code 0 632s autopkgtest: DBG: sending command to testbed: copydown /home/ubuntu/autopkgtest/lib/in-testbed/wrapper.sh /tmp/autopkgtest.IaIWjt/wrapper.sh 632s autopkgtest: DBG: got reply from testbed: ok 632s autopkgtest: DBG: testbed command ['chmod', '-R', '0755', '--', '/tmp/autopkgtest.IaIWjt/wrapper.sh'], kind short, sout raw, serr pipe, env [] 632s autopkgtest: DBG: testbed command exited with code 0 632s autopkgtest: DBG: testbed command ['dpkg', '--print-architecture'], kind short, sout pipe, serr pipe, env [] 632s autopkgtest: DBG: testbed command exited with code 0 632s autopkgtest [12:44:05]: testbed dpkg architecture: s390x 632s autopkgtest: DBG: testbed command ['dpkg-query', '-W', '-f', '${Version}', 'apt'], kind short, sout pipe, serr pipe, env [] 632s autopkgtest: DBG: testbed command exited with code 0 632s autopkgtest [12:44:05]: testbed apt version: 2.9.30 632s autopkgtest: DBG: testbed command ['sh', '-ec', 'command -v eatmydata'], kind short, sout pipe, serr pipe, env [] 633s autopkgtest: DBG: testbed command exited with code 0 633s autopkgtest: DBG: testbed has eatmydata 633s autopkgtest: DBG: testbed command ['mkdir', '-p', '/etc/apt/preferences.d'], kind short, sout raw, serr pipe, env [] 633s autopkgtest: DBG: testbed command exited with code 0 633s autopkgtest [12:44:06]: @@@@@@@@@@@@@@@@@@@@ test bed setup 633s autopkgtest: DBG: testbed command ['sh', '-ec', '#!/bin/sh\n# Copyright © 2006-2018 Canonical Ltd.\n# Copyright © 2015-2017 Martin Pitt\n# Copyright © 2017 Steve Langasek\n# Copyright © 2017-2022 Paul Gevers\n# Copyright © 2018 Simon McVittie\n# SPDX-License-Identifier: GPL-2.0-or-later\n\n# This script returns the first suite found in apt sources. We can\'t just rely\n# on /etc/os-release because it doesn\'t allow to distinguish between Debian\n# unstable and testing.\n#\n# This release detection logic should be kept in sync with similar code in the\n# setup-testbed script.\n#\n# For more information on APT data sources see sources.list(5).\n\n# Usage $0\n\nset -eux\n\ndistro=UNKNOWN\nif [ -r /etc/os-release ]; then\n # shellcheck disable=SC1091\n distro=$(. /etc/os-release && echo "${ID:-$distro}")\nfi\n\n# Try guessing the default release from deb822-style format sources.\n#\n# While not mandatory, APT upstream expects distros to follow the\n# .sources naming pattern for the default deb822 sources.\napt_sources="/etc/apt/sources.list.d/$distro.sources"\nif [ -r "$apt_sources" ]; then\n release=$(sed -En \'s/^Suites:\\s*(\\w+).*/\\1/Ip\' "$apt_sources" | head -n1)\n [ -n "$release" ] && echo "$release" && exit\nfi\n\n# Try guessing the default release from one-line-style format sources.\napt_sources=/etc/apt/sources.list\nif [ -r "$apt_sources" ]; then\n release=$(sed -En \'/^(deb|deb-src) +(\\[.*\\] *)?(http|https|file):/ { s/\\[.*\\] +//; s/^[^ ]+ +[^ ]* +([^ ]+) +.*$/\\1/p }\' "$apt_sources" | head -n1)\n [ -n "$release" ] && echo "$release" && exit\nfi\n\n# Could not guess the default release\necho "Could not guess the default release from the APT sources." >&2\nexit 1\n'], kind short, sout pipe, serr pipe, env [] 633s autopkgtest: DBG: testbed command exited with code 0 633s autopkgtest [12:44:06]: testbed release detected to be: plucky 633s autopkgtest: DBG: testbed command ['sh', '-ec', '#!/bin/sh\n# SPDX-License-Identifier: GPL-2.0-or-later\n\n# This script returns the list of configured "deb" sources in one-line-style\n# source lists (/etc/apt/sources.list, /etc/apt/sources.list.d/*.list).\n# See sources.list(5) for more information on the APT source list formats.\n#\n# This script takes no arguments.\n\nset -eu\n\n# grep(1) returns 1 if no lines were selected from the input files, which\n# can happen if there are .list files, but they contain no "deb" entries.\n# We don\'t want to fail in this case, hence the "|| true", which we put\n# in a subshell because we want it to affect only the grep invocation.\n{\n if [ -f /etc/apt/sources.list ]; then\n printf \'%s\\0\' /etc/apt/sources.list\n fi\n if [ -d /etc/apt/sources.list.d ]; then\n find /etc/apt/sources.list.d -maxdepth 1 -type f -regex \'.*/[a-zA-Z0-9_.-]+\\.list\' -print0 \\\n | LC_ALL=C sort --zero-terminated\n fi\n} | xargs -0 --no-run-if-empty -- sh -c \'grep -h "^deb " "$@" || true\' "$(basename "$0")"\n'], kind short, sout pipe, serr pipe, env [] 633s autopkgtest: DBG: testbed command exited with code 0 633s autopkgtest: DBG: testbed command ['sh', '-ec', '#!/bin/sh\n# SPDX-License-Identifier: GPL-2.0-or-later\n\n# This script returns the list of configured sources in deb822-style source\n# lists (/etc/apt/sources.list.d/*.sources). Sources are not stripped out of\n# comments, extra blank lines or similar: the output of this script is meant to\n# be consumed by a deb822 parser that is able to correctly handle those.\n# See sources.list(5) for more information on the APT source list formats.\n#\n# This script takes no arguments.\n\nset -eu\n\n# Awk concatenates files making sure stanzas from separate files are separated\n# by a blank line, even if there are no newlines at EOF in the .sources files.\nif [ -d /etc/apt/sources.list.d ]; then\n find /etc/apt/sources.list.d -maxdepth 1 -type f -regex \'.*/[a-zA-Z0-9_.-]+\\.sources\' -print0 \\\n | LC_ALL=C sort --zero-terminated \\\n | xargs -0 --no-run-if-empty -- awk \'FNR == 1 && NR != 1 { print "" } { print }\'\nfi\n'], kind short, sout pipe, serr pipe, env [] 633s autopkgtest: DBG: testbed command exited with code 0 633s autopkgtest: DBG: adding APT source: Types: deb deb-src 633s URIs: http://ftpmaster.internal/ubuntu/ 633s Suites: plucky-proposed 633s Components: main restricted universe multiverse 633s Signed-By: /usr/share/keyrings/ubuntu-archive-keyring.gpg 633s autopkgtest: DBG: testbed command ['sh', '-ec', '"$@" >> "/etc/apt/sources.list.d/autopkgtest-add-apt-release-plucky-proposed.sources"', 'add_apt_source', 'printf', '%s\\n', 'Types: deb deb-src\nURIs: http://ftpmaster.internal/ubuntu/\nSuites: plucky-proposed\nComponents: main restricted universe multiverse\nSigned-By: /usr/share/keyrings/ubuntu-archive-keyring.gpg\n'], kind short, sout raw, serr pipe, env [] 633s autopkgtest: DBG: testbed command exited with code 0 633s autopkgtest: DBG: adding APT preference to autopkgtest-zz-plucky-proposed-baseline.pref: 633s Package: * 633s Pin: release plucky-proposed 633s Pin-Priority: 500 633s autopkgtest: DBG: testbed command ['sh', '-ec', '"$@" > "/etc/apt/preferences.d/autopkgtest-zz-plucky-proposed-baseline.pref"', 'add_apt_preference', 'printf', '%s\\n', 'Package: *\nPin: release plucky-proposed\nPin-Priority: 500'], kind short, sout raw, serr pipe, env [] 634s autopkgtest: DBG: testbed command exited with code 0 634s autopkgtest [12:44:07]: updating testbed package index (apt update) 634s autopkgtest: DBG: testbed command ['/bin/sh', '-ec', '"$@" 3>&2 2>&1', 'run_apt_command', '/usr/bin/eatmydata', 'apt-get', '--quiet', '--assume-yes', '-o=APT::Status-Fd=3', '-o=APT::Install-Recommends=false', '-o=Dpkg::Options::=--force-confnew', '-o=Debug::pkgProblemResolver=true', 'update'], kind install, sout raw, serr pipe, env ['DEBIAN_FRONTEND=noninteractive', 'APT_LISTBUGS_FRONTEND=none', 'APT_LISTCHANGES_FRONTEND=none'] 634s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 634s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 634s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 634s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 634s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [750 kB] 635s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.1 kB] 635s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 635s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.9 kB] 635s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [95.1 kB] 635s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x Packages [760 B] 635s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [646 kB] 635s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [4900 B] 635s Fetched 1700 kB in 1s (1889 kB/s) 635s Reading package lists... 635s autopkgtest: DBG: testbed command exited with code 0 635s autopkgtest: DBG: adding APT preference to autopkgtest-plucky-proposed.pref: 635s Package: * 635s Pin: release plucky-proposed 635s Pin-Priority: 100 635s 635s Package: src:sphinx:any 635s Pin: release plucky-proposed 635s Pin-Priority: 995 635s autopkgtest: DBG: testbed command ['sh', '-ec', '"$@" > "/etc/apt/preferences.d/autopkgtest-plucky-proposed.pref"', 'add_apt_preference', 'printf', '%s\\n', 'Package: *\nPin: release plucky-proposed\nPin-Priority: 100\n\nPackage: src:sphinx:any\nPin: release plucky-proposed\nPin-Priority: 995'], kind short, sout raw, serr pipe, env [] 636s autopkgtest: DBG: testbed command exited with code 0 636s autopkgtest: DBG: testbed command ['bash', '-ec', 'for d in /boot /boot/efi /boot/grub /etc/init /etc/init.d /etc/systemd/system /lib/systemd/system; do [ ! -d $d ] || touch -r $d /tmp/autopkgtest.IaIWjt/${d//\\//_}.stamp; done'], kind short, sout raw, serr pipe, env [] 636s autopkgtest: DBG: testbed command exited with code 0 636s autopkgtest: DBG: testbed command ['sh', '-ec', '#!/bin/sh\n# Canonical/Ubuntu specific testbed setup\n\nset -x\n\nRELEASE=$(lsb_release --codename --short 2>/dev/null)\n\n# Make the installed package versions match what is available from the configured\n# repositories, even if a downgrade is required.\n#\n# We may end up with images with packages newer than those available from the\n# repositories when opening a new release (images are created using the\n# previous release dailies as a base, which may include 0-day SRUs, or\n# Launchpad may fail to copy packages, see openssl 3.0.8-1ubuntu2), or when\n# package versions are pulled from the archive.\n#\n# Note: \'release a=\' matches the Suite field in the repository Release file.\ncat >/etc/apt/preferences.d/force-downgrade-to-release.pref <= Focal).\n#\n# Note: autoremove/--autoremove always runs on the entire set of installed\n# packages. Together with --autopurge/purge each removal becomes a purge.\n#\n# Removing \'?obsolete\' packages may remove the running kernel. This is not\n# expected to be an issue.\nif /usr/lib/apt/apt-helper analyze-pattern \'?true\' >/dev/null 2>&1; then\n # DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove \'?obsolete\'\n # Avoid removing the running kernel\n running_kernel_pattern="^linux-.*$(uname -r | sed \'s/\\./\\\\./g\').*"\n obsolete_pkgs="$(apt list \'?obsolete\' 2>/dev/null \\\n | tail -n+2 \\\n | cut -d\'/\' -f1 \\\n | grep -v "${running_kernel_pattern}" || true)"\n DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove ${obsolete_pkgs}\nelse\n # We\'re on an older release (analyze-pattern is not available).\n # Still do an autopurge to get rid of packages that got orphaned\n # by downgrades.\n eatmydata apt-get -y autoremove --purge\nfi\n\n# compatibility with old Jenkins testbeds for trusty\nif grep -q trusty /etc/lsb-release; then apt-get update || (sleep 10; apt-get update); apt-get install -y build-essential; fi\n\n# these packages really break tests, purge them if we use standard cloud images\n# (on lcy01)\nfor p in unattended-upgrades lxd lxd-client snapd; do\n [ ! -d /usr/share/doc/$p ] || $(which eatmydata || true) apt-get purge --auto-remove -y $p\ndone\n\nif type iptables >/dev/null 2>&1; then\n cat < /etc/rc.local\n#!/bin/sh\n\n# work around broken PTMU; LP: #1572026, RT#90771\niptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu || true\n\n# These addresses are used at least by rust-reqwest and should not be reachable\n# See https://bugs.launchpad.net/ubuntu/+source/rust-reqwest/+bug/2080346\niptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP || true\niptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP || true\nEOF\n chmod 755 /etc/rc.local\n # shellcheck disable=SC1091\n . /etc/rc.local\nfi\n\n# work around broken tty on ppc64el instances (LP: #1607075)\nif [ "$(uname -m)" = ppc64le ] && [ "$(systemctl is-active keyboard-setup.service 2>/dev/null|| true)" = failed ]; then\n systemctl reset-failed keyboard-setup.service\n systemctl mask keyboard-setup.service\nfi\n\n# work around late urandom pool initialization (LP: #1622893)\nif [ -d /run/systemd/system ] && systemd-detect-virt --quiet --vm; then\n mkdir -p /etc/systemd/system/systemd-random-seed.service.d/\n cat < /etc/systemd/system/systemd-random-seed.service.d/fakeentropy.conf\n[Service]\nExecStart=/usr/bin/perl -E \'open \\$\\$f, "/bin/bash" or die; open \\$\\$rnd, ">/dev/random" or die; for (\\$\\$i = 0; \\$\\$i < 10; ++\\$\\$i) {read \\$\\$f, \\$\\$d, 64; ioctl \\$\\$rnd, 0x40085203, pack("ii", 64*8, 64) . \\$\\$d}\'\nEOF\nfi\n\n# set compressor to lz4 where supported, we care about compression speed\nif grep -q lz4 /etc/initramfs-tools/initramfs.conf; then\n echo COMPRESS=lz4 > /etc/initramfs-tools/conf.d/lz4\nfi'], kind install, sout raw, serr raw, env ['AUTOPKGTEST_IS_SETUP_COMMAND=1', 'AUTOPKGTEST_NORMAL_USER=ubuntu', 'ADT_NORMAL_USER=ubuntu'] 636s + lsb_release --codename --short 636s + RELEASE=plucky 636s + cat 636s + [ plucky != trusty ] 636s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 636s Reading package lists... 636s Building dependency tree... 636s Reading state information... 636s Calculating upgrade... 636s The following packages were automatically installed and are no longer required: 636s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 636s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 636s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 636s linux-tools-6.11.0-8-generic 636s Use 'sudo apt autoremove' to remove them. 636s The following packages will be upgraded: 636s iproute2 liblsof0 libp11-kit0 lsof 637s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 637s Need to get 1791 kB of archives. 637s After this operation, 17.4 kB of additional disk space will be used. 637s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x iproute2 s390x 6.13.0-1ubuntu1 [1174 kB] 637s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libp11-kit0 s390x 0.25.5-2ubuntu3 [316 kB] 637s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x lsof s390x 4.99.4+dfsg-1 [243 kB] 637s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x liblsof0 s390x 4.99.4+dfsg-1 [58.5 kB] 637s Preconfiguring packages ... 637s Fetched 1791 kB in 1s (2855 kB/s) 637s (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 ... 81030 files and directories currently installed.) 637s Preparing to unpack .../iproute2_6.13.0-1ubuntu1_s390x.deb ... 638s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 638s Preparing to unpack .../libp11-kit0_0.25.5-2ubuntu3_s390x.deb ... 638s Unpacking libp11-kit0:s390x (0.25.5-2ubuntu3) over (0.25.5-2ubuntu2) ... 638s Preparing to unpack .../lsof_4.99.4+dfsg-1_s390x.deb ... 638s Unpacking lsof (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 638s Preparing to unpack .../liblsof0_4.99.4+dfsg-1_s390x.deb ... 638s Unpacking liblsof0 (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 638s Setting up liblsof0 (4.99.4+dfsg-1) ... 638s Setting up iproute2 (6.13.0-1ubuntu1) ... 638s Setting up libp11-kit0:s390x (0.25.5-2ubuntu3) ... 638s Setting up lsof (4.99.4+dfsg-1) ... 638s Processing triggers for man-db (2.13.0-1) ... 638s Processing triggers for libc-bin (2.40-4ubuntu1) ... 639s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 639s + /usr/lib/apt/apt-helper analyze-pattern ?true 639s + uname -r 639s + sed s/\./\\./g 639s + running_kernel_pattern=^linux-.*6\.12\.0-15-generic.* 639s + apt list ?obsolete 639s + tail -n+2 639s + cut -d/ -f1 639s + grep -v ^linux-.*6\.12\.0-15-generic.* 639s + true 639s + obsolete_pkgs= 639s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove 639s Reading package lists... 639s Building dependency tree... 639s Reading state information... 639s The following packages will be REMOVED: 639s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 639s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 639s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 639s linux-tools-6.11.0-8-generic* 639s 0 upgraded, 0 newly installed, 9 to remove and 0 not upgraded. 639s After this operation, 167 MB disk space will be freed. 639s (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 ... 81031 files and directories currently installed.) 639s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 639s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 639s Removing libpython3.12t64:s390x (3.12.9-1) ... 639s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 639s Removing libnsl2:s390x (1.3.0-3build3) ... 639s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 639s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 640s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 641s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 641s Processing triggers for libc-bin (2.40-4ubuntu1) ... 641s (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 ... 55931 files and directories currently installed.) 641s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 641s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 641s + grep -q trusty /etc/lsb-release 641s + [ ! -d /usr/share/doc/unattended-upgrades ] 641s + [ ! -d /usr/share/doc/lxd ] 641s + [ ! -d /usr/share/doc/lxd-client ] 641s + [ ! -d /usr/share/doc/snapd ] 641s + type iptables 641s + cat 641s + chmod 755 /etc/rc.local 641s + . /etc/rc.local 641s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 641s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 641s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 641s + uname -m 641s + [ s390x = ppc64le ] 641s + [ -d /run/systemd/system ] 641s + systemd-detect-virt --quiet --vm 641s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 641s + cat 641s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 641s + echo COMPRESS=lz4 641s autopkgtest: DBG: testbed command exited with code 0 641s autopkgtest [12:44:14]: upgrading testbed (apt dist-upgrade and autopurge) 641s autopkgtest: DBG: testbed command ['/bin/sh', '-ec', '"$@" 3>&2 2>&1', 'run_apt_command', '/usr/bin/eatmydata', 'apt-get', '--quiet', '--assume-yes', '-o=APT::Status-Fd=3', '-o=APT::Install-Recommends=false', '-o=Dpkg::Options::=--force-confnew', '-o=Debug::pkgProblemResolver=true', 'dist-upgrade'], kind install, sout raw, serr pipe, env ['DEBIAN_FRONTEND=noninteractive', 'APT_LISTBUGS_FRONTEND=none', 'APT_LISTCHANGES_FRONTEND=none'] 641s Reading package lists... 641s Building dependency tree... 641s Reading state information... 642s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 642s Starting 2 pkgProblemResolver with broken count: 0 642s Done 642s Entering ResolveByKeep 642s 642s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 642s autopkgtest: DBG: testbed command exited with code 0 642s autopkgtest: DBG: testbed command ['/bin/sh', '-ec', '"$@" 3>&2 2>&1', 'run_apt_command', '/usr/bin/eatmydata', 'apt-get', '--quiet', '--assume-yes', '-o=APT::Status-Fd=3', '-o=APT::Install-Recommends=false', '-o=Dpkg::Options::=--force-confnew', '-o=Debug::pkgProblemResolver=true', '--purge', 'autoremove'], kind install, sout raw, serr pipe, env ['DEBIAN_FRONTEND=noninteractive', 'APT_LISTBUGS_FRONTEND=none', 'APT_LISTCHANGES_FRONTEND=none'] 642s Reading package lists... 642s Building dependency tree... 642s Reading state information... 642s Starting pkgProblemResolver with broken count: 0 643s Starting 2 pkgProblemResolver with broken count: 0 643s Done 643s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 643s autopkgtest: DBG: testbed command exited with code 0 643s autopkgtest: DBG: testbed command ['bash', '-ec', '[ ! -e /run/autopkgtest_no_reboot.stamp ] || exit 0;for d in /boot /boot/efi /boot/grub /etc/init /etc/init.d /etc/systemd/system /lib/systemd/system; do s=/tmp/autopkgtest.IaIWjt/${d//\\//_}.stamp; [ ! -d $d ] || [ `stat -c %Y $d` = `stat -c %Y $s` ]; done'], kind short, sout raw, serr raw, env [] 643s autopkgtest: DBG: testbed command exited with code 1 643s autopkgtest [12:44:16]: rebooting testbed after setup commands that affected boot 643s autopkgtest: DBG: sending command to testbed: reboot 647s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 662s autopkgtest: DBG: got reply from testbed: ok 662s autopkgtest: DBG: testbed supports reboot, creating /tmp/autopkgtest-reboot 662s autopkgtest: DBG: testbed command ['mkdir', '-p', '/tmp/autopkgtest.IaIWjt'], kind short, sout raw, serr pipe, env [] 662s autopkgtest: DBG: testbed command exited with code 0 662s autopkgtest: DBG: sending command to testbed: copydown /home/ubuntu/autopkgtest/lib/in-testbed/reboot.sh /tmp/autopkgtest.IaIWjt/autopkgtest-reboot 663s autopkgtest: DBG: got reply from testbed: ok 663s autopkgtest: DBG: testbed command ['chmod', '-R', '0755', '--', '/tmp/autopkgtest.IaIWjt/autopkgtest-reboot'], kind short, sout raw, serr pipe, env [] 663s autopkgtest: DBG: testbed command exited with code 0 663s autopkgtest: DBG: testbed command ['ln', '-fns', '/tmp/autopkgtest.IaIWjt/autopkgtest-reboot', '/tmp/autopkgtest-reboot'], kind short, sout raw, serr pipe, env [] 663s autopkgtest: DBG: testbed command exited with code 0 663s autopkgtest: DBG: testbed command ['ln', '-fns', '/tmp/autopkgtest.IaIWjt/autopkgtest-reboot', '/sbin/autopkgtest-reboot'], kind short, sout raw, serr pipe, env [] 663s autopkgtest: DBG: testbed command exited with code 0 663s autopkgtest: DBG: testbed command ['mkdir', '-p', '/tmp/autopkgtest.IaIWjt'], kind short, sout raw, serr pipe, env [] 663s autopkgtest: DBG: testbed command exited with code 0 663s autopkgtest: DBG: sending command to testbed: copydown /home/ubuntu/autopkgtest/lib/in-testbed/reboot-prepare.sh /tmp/autopkgtest.IaIWjt/autopkgtest-reboot-prepare 663s autopkgtest: DBG: got reply from testbed: ok 663s autopkgtest: DBG: testbed command ['chmod', '-R', '0755', '--', '/tmp/autopkgtest.IaIWjt/autopkgtest-reboot-prepare'], kind short, sout raw, serr pipe, env [] 664s autopkgtest: DBG: testbed command exited with code 0 664s autopkgtest: DBG: testbed command ['ln', '-fns', '/tmp/autopkgtest.IaIWjt/autopkgtest-reboot-prepare', '/tmp/autopkgtest-reboot-prepare'], kind short, sout raw, serr pipe, env [] 664s autopkgtest: DBG: testbed command exited with code 0 664s autopkgtest: DBG: testbed command ['uname', '-srv'], kind short, sout pipe, serr pipe, env [] 664s autopkgtest: DBG: testbed command exited with code 0 664s autopkgtest: DBG: testbed command ['sh', '-ec', "dpkg-query --show -f '${Package}\\t${Version}\\n' > /tmp/autopkgtest.IaIWjt/testbed-packages"], kind short, sout raw, serr pipe, env [] 664s autopkgtest: DBG: testbed command exited with code 0 664s autopkgtest: DBG: sending command to testbed: copyup /tmp/autopkgtest.IaIWjt/testbed-packages /tmp/autopkgtest-work.by5by6hj/out/testbed-packages 664s autopkgtest: DBG: got reply from testbed: ok 664s autopkgtest: DBG: testbed supports reboot, creating /tmp/autopkgtest-reboot 664s autopkgtest: DBG: testbed command ['mkdir', '-p', '/tmp/autopkgtest.IaIWjt'], kind short, sout raw, serr pipe, env [] 665s autopkgtest: DBG: testbed command exited with code 0 665s autopkgtest: DBG: sending command to testbed: copydown /home/ubuntu/autopkgtest/lib/in-testbed/reboot.sh /tmp/autopkgtest.IaIWjt/autopkgtest-reboot 665s autopkgtest: DBG: got reply from testbed: ok 665s autopkgtest: DBG: testbed command ['chmod', '-R', '0755', '--', '/tmp/autopkgtest.IaIWjt/autopkgtest-reboot'], kind short, sout raw, serr pipe, env [] 665s autopkgtest: DBG: testbed command exited with code 0 665s autopkgtest: DBG: testbed command ['ln', '-fns', '/tmp/autopkgtest.IaIWjt/autopkgtest-reboot', '/tmp/autopkgtest-reboot'], kind short, sout raw, serr pipe, env [] 665s autopkgtest: DBG: testbed command exited with code 0 665s autopkgtest: DBG: testbed command ['ln', '-fns', '/tmp/autopkgtest.IaIWjt/autopkgtest-reboot', '/sbin/autopkgtest-reboot'], kind short, sout raw, serr pipe, env [] 665s autopkgtest: DBG: testbed command exited with code 0 665s autopkgtest: DBG: testbed command ['mkdir', '-p', '/tmp/autopkgtest.IaIWjt'], kind short, sout raw, serr pipe, env [] 666s autopkgtest: DBG: testbed command exited with code 0 666s autopkgtest: DBG: sending command to testbed: copydown /home/ubuntu/autopkgtest/lib/in-testbed/reboot-prepare.sh /tmp/autopkgtest.IaIWjt/autopkgtest-reboot-prepare 666s autopkgtest: DBG: got reply from testbed: ok 666s autopkgtest: DBG: testbed command ['chmod', '-R', '0755', '--', '/tmp/autopkgtest.IaIWjt/autopkgtest-reboot-prepare'], kind short, sout raw, serr pipe, env [] 666s autopkgtest: DBG: testbed command exited with code 0 666s autopkgtest: DBG: testbed command ['ln', '-fns', '/tmp/autopkgtest.IaIWjt/autopkgtest-reboot-prepare', '/tmp/autopkgtest-reboot-prepare'], kind short, sout raw, serr pipe, env [] 666s autopkgtest: DBG: testbed command exited with code 0 666s autopkgtest: DBG: testbed command ['uname', '-srv'], kind short, sout pipe, serr pipe, env [] 666s autopkgtest: DBG: testbed command exited with code 0 666s autopkgtest: DBG: Binaries: no registered binaries, not publishing anything 666s autopkgtest: DBG: install_deps: deps_new=['python3-biopython', 'python-biopython-doc', 'python3-biopython-sql', 'debhelper-compat (= 13)', 'dh-sequence-python3', 'python3-all-dev:native', 'libpython3-all-dev', 'python3-numpy', 'flex', 'python3-reportlab (>= 4.0.4-1~) ', 'hevea', 'texlive-latex-base', 'texlive-latex-extra', 'texlive-fonts-recommended', 'bwa ', 'clustalo ', 'clustalw [any-amd64] ', 'dialign ', 'dssp ', 'emboss [!armel !armhf !i386 !hppa !m68k !powerpc !s390x !sh4] ', 'fasttree ', 'mafft ', 'muscle3 [i386 amd64 x32] ', 'ncbi-blast+ ', 'phylip ', 'phyml [any-amd64] ', 'prank ', 'probcons ', 'python3-networkx ', 'python3-numpydoc ', 'python3-mysqldb ', 'python3-matplotlib ', 'python3-mmtf ', 'python3-pil ', 'python3-rdflib ', 'python3-psycopg2 [any-amd64] ', 'python3-pygments ', 'python3-igraph ', 'python3-scipy ', 'python3-setuptools', 'python3-sphinx ', 'python3-sphinx-rtd-theme ', 'raxml [any-amd64 any-i386] ', 'samtools [any-amd64] ', 't-coffee ', 'wise ', 'build-essential'] 666s autopkgtest: DBG: install-deps: satisfying python3-biopython, python-biopython-doc, python3-biopython-sql, debhelper-compat (= 13), dh-sequence-python3, python3-all-dev:native, libpython3-all-dev, python3-numpy, flex, python3-reportlab (>= 4.0.4-1~) , hevea, texlive-latex-base, texlive-latex-extra, texlive-fonts-recommended, bwa , clustalo , clustalw [any-amd64] , dialign , dssp , emboss [!armel !armhf !i386 !hppa !m68k !powerpc !s390x !sh4] , fasttree , mafft , muscle3 [i386 amd64 x32] , ncbi-blast+ , phylip , phyml [any-amd64] , prank , probcons , python3-networkx , python3-numpydoc , python3-mysqldb , python3-matplotlib , python3-mmtf , python3-pil , python3-rdflib , python3-psycopg2 [any-amd64] , python3-pygments , python3-igraph , python3-scipy , python3-setuptools, python3-sphinx , python3-sphinx-rtd-theme , raxml [any-amd64 any-i386] , samtools [any-amd64] , t-coffee , wise , build-essential 666s autopkgtest: DBG: can use apt-get on testbed: True 666s autopkgtest: DBG: testbed command ['/bin/sh', '-ec', '"$@" 3>&2 2>&1', 'run_apt_command', '/usr/bin/eatmydata', 'apt-get', '--quiet', '--assume-yes', '-o=APT::Status-Fd=3', '-o=APT::Install-Recommends=false', '-o=Dpkg::Options::=--force-confnew', '-o=Debug::pkgProblemResolver=true', 'satisfy', 'python3-biopython, python-biopython-doc, python3-biopython-sql, debhelper-compat (= 13), dh-sequence-python3, python3-all-dev:native, libpython3-all-dev, python3-numpy, flex, python3-reportlab (>= 4.0.4-1~) , hevea, texlive-latex-base, texlive-latex-extra, texlive-fonts-recommended, bwa , clustalo , clustalw [any-amd64] , dialign , dssp , emboss [!armel !armhf !i386 !hppa !m68k !powerpc !s390x !sh4] , fasttree , mafft , muscle3 [i386 amd64 x32] , ncbi-blast+ , phylip , phyml [any-amd64] , prank , probcons , python3-networkx , python3-numpydoc , python3-mysqldb , python3-matplotlib , python3-mmtf , python3-pil , python3-rdflib , python3-psycopg2 [any-amd64] , python3-pygments , python3-igraph , python3-scipy , python3-setuptools, python3-sphinx , python3-sphinx-rtd-theme , raxml [any-amd64 any-i386] , samtools [any-amd64] , t-coffee , wise , build-essential'], kind install, sout raw, serr pipe, env ['DEBIAN_FRONTEND=noninteractive', 'APT_LISTBUGS_FRONTEND=none', 'APT_LISTCHANGES_FRONTEND=none'] 667s Reading package lists... 667s Building dependency tree... 667s Reading state information... 667s Starting pkgProblemResolver with broken count: 0 667s Starting 2 pkgProblemResolver with broken count: 0 667s Done 667s The following NEW packages will be installed: 667s autoconf automake autopoint autotools-dev blt build-essential bwa clustalo 667s cpp cpp-14 cpp-14-s390x-linux-gnu cpp-s390x-linux-gnu debhelper debugedit 667s dh-autoreconf dh-python dh-strip-nondeterminism dialign docutils-common dssp 667s dwz fasttree flex fontconfig-config fonts-dejavu-core fonts-dejavu-mono 667s fonts-font-awesome fonts-lato fonts-lmodern fonts-lyx fonts-urw-base35 g++ 667s g++-14 g++-14-s390x-linux-gnu g++-s390x-linux-gnu gcc gcc-14 667s gcc-14-s390x-linux-gnu gcc-s390x-linux-gnu gettext ghostscript hevea 667s hicolor-icon-theme imagemagick imagemagick-7-common imagemagick-7.q16 667s intltool-debian libamd3 libaom3 libapache-pom-java libarchive-zip-perl 667s libargtable2-0 libarpack2t64 libasan8 libavahi-client3 libavahi-common-data 667s libavahi-common3 libblas3 libcairo2 libcc1-0 libcifpp-data libcifpp7 667s libcolamd3 libcommons-logging-java libcommons-parent-java libcups2t64 667s libde265-0 libdebhelper-perl libdeflate0 libexpat1-dev libfftw3-double3 667s libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 667s libfreetype6 libgcc-14-dev libgfortran5 libglpk40 libgomp1 libgraphite2-3 667s libgs-common libgs10 libgs10-common libharfbuzz0b libheif-plugin-aomdec 667s libheif-plugin-libde265 libheif1 libice6 libidn12 libigraph3t64 libijs-0.35 667s libimagequant0 libisl23 libitm1 libjbig0 libjbig2dec0 libjpeg-turbo8 667s libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore 667s libjson-perl libkpathsea6 liblapack3 liblbfgsb0 liblcms2-2 liblqr-1-0 667s libltdl7 libmagickcore-7.q16-10 libmagickwand-7.q16-10 libmbedcrypto16 667s libmbedtls21 libmbedx509-7 libmpc3 libmpfi0 libmysqlclient21 libnetpbm11t64 667s libnsl2 libopenjp2-7 libpaper-utils libpaper2 libpdfbox-java libpixman-1-0 667s libplfit0 libpotrace0 libptexenc1 libpython3-all-dev libpython3-dev 667s libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib 667s libpython3.12t64 libpython3.13-dev libqhull-r8.0 libraqm0 libraw23t64 667s libsharpyuv0 libsm6 libstdc++-14-dev libsuitesparseconfig7 libsynctex2 667s libtcl8.6 libteckit0 libtexlua53-5 libtiff6 libtk8.6 libtool libubsan1 667s libwebp7 libwebpdemux2 libwebpmux3 libxaw7 libxcb-render0 libxcb-shm0 667s libxft2 libxi6 libxmu6 libxpm4 libxrender1 libxslt1.1 libxss1 libxt6t64 667s libzzip-0-13t64 m4 mafft mysql-common ncbi-blast+ ncbi-data netpbm phylip 667s po-debconf poppler-data prank preview-latex-style probcons 667s python-biopython-doc python-matplotlib-data python3-alabaster python3-all 667s python3-all-dev python3-biopython python3-biopython-sql python3-brotli 667s python3-cairo python3-contourpy python3-cycler python3-dateutil 667s python3-decorator python3-defusedxml python3-dev python3-docutils 667s python3-fonttools python3-freetype python3-fs python3-igraph 667s python3-imagesize python3-kiwisolver python3-lxml python3-lz4 667s python3-matplotlib python3-mmtf python3-mpmath python3-msgpack 667s python3-mysqldb python3-networkx python3-numpy python3-numpydoc 667s python3-packaging python3-pil python3-pil.imagetk python3-platformdirs 667s python3-pytz python3-rdflib python3-reportlab python3-rlpycairo 667s python3-roman python3-scipy python3-snowballstemmer python3-sphinx 667s python3-sphinx-rtd-theme python3-sphinxcontrib.jquery python3-sympy 667s python3-tabulate python3-texttable python3-tk python3-tz python3-ufolib2 667s python3.12 python3.12-dev python3.12-minimal python3.12-tk python3.13-dev 667s python3.13-tk sgml-base sphinx-common sphinx-rtd-theme-common t-coffee 667s t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended 667s texlive-latex-base texlive-latex-extra texlive-latex-recommended 667s texlive-pictures tk8.6-blt2.5 unicode-data w3c-sgml-lib wise wise-data 667s x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zlib1g-dev 667s 0 upgraded, 259 newly installed, 0 to remove and 0 not upgraded. 667s Need to get 341 MB of archives. 667s After this operation, 1310 MB of additional disk space will be used. 667s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.12-minimal s390x 3.12.9-1 [836 kB] 668s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x python3.12-minimal s390x 3.12.9-1 [2403 kB] 668s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x m4 s390x 1.4.19-5 [259 kB] 668s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x flex s390x 2.6.4-8.2build1 [311 kB] 668s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-lato all 2.015-1 [2781 kB] 668s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 15-20250213-1ubuntu1 [151 kB] 668s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libfftw3-double3 s390x 3.3.10-2fakesync1build1 [511 kB] 668s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB] 668s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 668s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 668s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libfontenc1 s390x 1:1.1.8-1build1 [14.8 kB] 668s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x x11-common all 1:7.7+23ubuntu3 [21.7 kB] 668s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 668s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x xfonts-utils s390x 1:7.7+7 [101 kB] 668s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-urw-base35 all 20200910-8 [11.0 MB] 669s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig-config s390x 2.15.0-2ubuntu1 [37.5 kB] 669s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x libfontconfig1 s390x 2.15.0-2ubuntu1 [150 kB] 669s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x libsharpyuv0 s390x 1.5.0-0.1 [16.7 kB] 669s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x libaom3 s390x 3.12.0-1 [1492 kB] 669s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x libheif-plugin-aomdec s390x 1.19.5-1build1 [11.6 kB] 669s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x libde265-0 s390x 1.0.15-1build4 [175 kB] 669s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x libheif-plugin-libde265 s390x 1.19.5-1build1 [9066 B] 669s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x libheif1 s390x 1.19.5-1build1 [410 kB] 669s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] 669s Get:25 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8 s390x 2.1.5-3ubuntu2 [147 kB] 669s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 669s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x liblcms2-2 s390x 2.16-2 [175 kB] 669s Get:28 http://ftpmaster.internal/ubuntu plucky/universe s390x liblqr-1-0 s390x 0.4.2-2.1build2 [32.6 kB] 669s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x libltdl7 s390x 2.5.4-3build1 [43.9 kB] 669s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x libopenjp2-7 s390x 2.5.0-2ubuntu3 [208 kB] 669s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x libraw23t64 s390x 0.21.3-1 [415 kB] 669s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.23-1 [46.1 kB] 669s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x libwebp7 s390x 1.5.0-0.1 [210 kB] 669s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu4 [217 kB] 669s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x libwebpdemux2 s390x 1.5.0-0.1 [12.6 kB] 669s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x libwebpmux3 s390x 1.5.0-0.1 [25.8 kB] 669s Get:37 http://ftpmaster.internal/ubuntu plucky/universe s390x imagemagick-7-common all 8:7.1.1.43+dfsg1-1 [69.7 kB] 669s Get:38 http://ftpmaster.internal/ubuntu plucky/universe s390x libmagickcore-7.q16-10 s390x 8:7.1.1.43+dfsg1-1 [2040 kB] 669s Get:39 http://ftpmaster.internal/ubuntu plucky/universe s390x libmagickwand-7.q16-10 s390x 8:7.1.1.43+dfsg1-1 [375 kB] 669s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x poppler-data all 0.4.12-1 [2060 kB] 669s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x sgml-base all 1.31 [11.4 kB] 669s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x libnsl2 s390x 1.3.0-3build3 [44.1 kB] 669s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.12-stdlib s390x 3.12.9-1 [2071 kB] 669s Get:44 http://ftpmaster.internal/ubuntu plucky/main s390x python3.12 s390x 3.12.9-1 [671 kB] 669s Get:45 http://ftpmaster.internal/ubuntu plucky/main s390x autoconf all 2.72-3 [382 kB] 669s Get:46 http://ftpmaster.internal/ubuntu plucky/main s390x autotools-dev all 20220109.1 [44.9 kB] 669s Get:47 http://ftpmaster.internal/ubuntu plucky/main s390x automake all 1:1.17-3 [572 kB] 669s Get:48 http://ftpmaster.internal/ubuntu plucky/main s390x autopoint all 0.23.1-1 [619 kB] 669s Get:49 http://ftpmaster.internal/ubuntu plucky/main s390x libtcl8.6 s390x 8.6.16+dfsg-1 [1034 kB] 669s Get:50 http://ftpmaster.internal/ubuntu plucky/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB] 669s Get:51 http://ftpmaster.internal/ubuntu plucky/main s390x libxft2 s390x 2.3.6-1build1 [49.6 kB] 669s Get:52 http://ftpmaster.internal/ubuntu plucky/main s390x libxss1 s390x 1:1.2.3-1build3 [7396 B] 669s Get:53 http://ftpmaster.internal/ubuntu plucky/main s390x libtk8.6 s390x 8.6.16-1 [830 kB] 670s Get:54 http://ftpmaster.internal/ubuntu plucky/main s390x tk8.6-blt2.5 s390x 2.5.3+dfsg-7build1 [662 kB] 670s Get:55 http://ftpmaster.internal/ubuntu plucky/main s390x blt s390x 2.5.3+dfsg-7build1 [4840 B] 670s Get:56 http://ftpmaster.internal/ubuntu plucky/main s390x libisl23 s390x 0.27-1 [704 kB] 670s Get:57 http://ftpmaster.internal/ubuntu plucky/main s390x libmpc3 s390x 1.3.1-1build2 [57.8 kB] 670s Get:58 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-14-s390x-linux-gnu s390x 14.2.0-17ubuntu1 [9571 kB] 670s Get:59 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-14 s390x 14.2.0-17ubuntu1 [1030 B] 670s Get:60 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [5556 B] 670s Get:61 http://ftpmaster.internal/ubuntu plucky/main s390x cpp s390x 4:14.2.0-1ubuntu1 [22.4 kB] 670s Get:62 http://ftpmaster.internal/ubuntu plucky/main s390x libcc1-0 s390x 15-20250213-1ubuntu1 [49.2 kB] 670s Get:63 http://ftpmaster.internal/ubuntu plucky/main s390x libitm1 s390x 15-20250213-1ubuntu1 [31.2 kB] 670s Get:64 http://ftpmaster.internal/ubuntu plucky/main s390x libasan8 s390x 15-20250213-1ubuntu1 [2970 kB] 670s Get:65 http://ftpmaster.internal/ubuntu plucky/main s390x libubsan1 s390x 15-20250213-1ubuntu1 [1213 kB] 670s Get:66 http://ftpmaster.internal/ubuntu plucky/main s390x libgcc-14-dev s390x 14.2.0-17ubuntu1 [1037 kB] 670s Get:67 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-14-s390x-linux-gnu s390x 14.2.0-17ubuntu1 [18.7 MB] 671s Get:68 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-14 s390x 14.2.0-17ubuntu1 [526 kB] 671s Get:69 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [1204 B] 671s Get:70 http://ftpmaster.internal/ubuntu plucky/main s390x gcc s390x 4:14.2.0-1ubuntu1 [5004 B] 671s Get:71 http://ftpmaster.internal/ubuntu plucky/main s390x libstdc++-14-dev s390x 14.2.0-17ubuntu1 [2611 kB] 671s Get:72 http://ftpmaster.internal/ubuntu plucky/main s390x g++-14-s390x-linux-gnu s390x 14.2.0-17ubuntu1 [11.0 MB] 671s Get:73 http://ftpmaster.internal/ubuntu plucky/main s390x g++-14 s390x 14.2.0-17ubuntu1 [21.8 kB] 671s Get:74 http://ftpmaster.internal/ubuntu plucky/main s390x g++-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [956 B] 671s Get:75 http://ftpmaster.internal/ubuntu plucky/main s390x g++ s390x 4:14.2.0-1ubuntu1 [1080 B] 671s Get:76 http://ftpmaster.internal/ubuntu plucky/main s390x build-essential s390x 12.10ubuntu1 [4930 B] 671s Get:77 http://ftpmaster.internal/ubuntu plucky/universe s390x bwa s390x 0.7.18-1 [249 kB] 671s Get:78 http://ftpmaster.internal/ubuntu plucky/universe s390x libargtable2-0 s390x 13-3 [16.9 kB] 671s Get:79 http://ftpmaster.internal/ubuntu plucky/universe s390x clustalo s390x 1.2.4-8build1 [218 kB] 671s Get:80 http://ftpmaster.internal/ubuntu plucky/main s390x libdebhelper-perl all 13.24.1ubuntu2 [95.4 kB] 671s Get:81 http://ftpmaster.internal/ubuntu plucky/main s390x libtool all 2.5.4-3build1 [168 kB] 671s Get:82 http://ftpmaster.internal/ubuntu plucky/main s390x dh-autoreconf all 20 [16.1 kB] 671s Get:83 http://ftpmaster.internal/ubuntu plucky/main s390x libarchive-zip-perl all 1.68-1 [90.2 kB] 671s Get:84 http://ftpmaster.internal/ubuntu plucky/main s390x libfile-stripnondeterminism-perl all 1.14.1-2 [20.3 kB] 671s Get:85 http://ftpmaster.internal/ubuntu plucky/main s390x dh-strip-nondeterminism all 1.14.1-2 [5064 B] 671s Get:86 http://ftpmaster.internal/ubuntu plucky/main s390x debugedit s390x 1:5.1-2 [50.1 kB] 671s Get:87 http://ftpmaster.internal/ubuntu plucky/main s390x dwz s390x 0.15-1build6 [122 kB] 671s Get:88 http://ftpmaster.internal/ubuntu plucky/main s390x gettext s390x 0.23.1-1 [1065 kB] 671s Get:89 http://ftpmaster.internal/ubuntu plucky/main s390x intltool-debian all 0.35.0+20060710.6 [23.2 kB] 671s Get:90 http://ftpmaster.internal/ubuntu plucky/main s390x po-debconf all 1.0.21+nmu1 [233 kB] 671s Get:91 http://ftpmaster.internal/ubuntu plucky/main s390x debhelper all 13.24.1ubuntu2 [895 kB] 672s Get:92 http://ftpmaster.internal/ubuntu plucky/universe s390x dh-python all 6.20250108 [117 kB] 672s Get:93 http://ftpmaster.internal/ubuntu plucky/universe s390x dialign s390x 2.2.1-13 [155 kB] 672s Get:94 http://ftpmaster.internal/ubuntu plucky/main s390x xml-core all 0.19 [20.3 kB] 672s Get:95 http://ftpmaster.internal/ubuntu plucky/main s390x docutils-common all 0.21.2+dfsg-2 [131 kB] 672s Get:96 http://ftpmaster.internal/ubuntu plucky/universe s390x libcifpp-data all 7.0.9-1 [481 kB] 672s Get:97 http://ftpmaster.internal/ubuntu plucky/universe s390x libcifpp7 s390x 7.0.9-1 [1103 kB] 672s Get:98 http://ftpmaster.internal/ubuntu plucky/universe s390x dssp s390x 4.4.10-1 [784 kB] 672s Get:99 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 672s Get:100 http://ftpmaster.internal/ubuntu plucky/universe s390x fonts-lmodern all 2.005-1 [4799 kB] 672s Get:101 http://ftpmaster.internal/ubuntu plucky/universe s390x fonts-lyx all 2.4.3-1 [171 kB] 672s Get:102 http://ftpmaster.internal/ubuntu plucky/main s390x libgs-common all 10.04.0~dfsg1-2ubuntu1 [176 kB] 672s Get:103 http://ftpmaster.internal/ubuntu plucky/main s390x libgs10-common all 10.04.0~dfsg1-2ubuntu1 [488 kB] 672s Get:104 http://ftpmaster.internal/ubuntu plucky/main s390x libavahi-common-data s390x 0.8-14ubuntu1 [30.5 kB] 672s Get:105 http://ftpmaster.internal/ubuntu plucky/main s390x libavahi-common3 s390x 0.8-14ubuntu1 [23.6 kB] 672s Get:106 http://ftpmaster.internal/ubuntu plucky/main s390x libavahi-client3 s390x 0.8-14ubuntu1 [26.8 kB] 672s Get:107 http://ftpmaster.internal/ubuntu plucky/main s390x libcups2t64 s390x 2.4.11-0ubuntu2 [282 kB] 673s Get:108 http://ftpmaster.internal/ubuntu plucky/main s390x libidn12 s390x 1.42-3 [56.9 kB] 673s Get:109 http://ftpmaster.internal/ubuntu plucky/main s390x libijs-0.35 s390x 0.35-15.1build1 [15.5 kB] 673s Get:110 http://ftpmaster.internal/ubuntu plucky/main s390x libjbig2dec0 s390x 0.20-1build3 [69.3 kB] 673s Get:111 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper2 s390x 2.2.5-0.3 [17.2 kB] 673s Get:112 http://ftpmaster.internal/ubuntu plucky/main s390x libice6 s390x 2:1.1.1-1 [45.4 kB] 673s Get:113 http://ftpmaster.internal/ubuntu plucky/main s390x libsm6 s390x 2:1.2.4-1 [18.4 kB] 673s Get:114 http://ftpmaster.internal/ubuntu plucky/main s390x libxt6t64 s390x 1:1.2.1-1.2build1 [184 kB] 673s Get:115 http://ftpmaster.internal/ubuntu plucky/main s390x libgs10 s390x 10.04.0~dfsg1-2ubuntu1 [3964 kB] 674s Get:116 http://ftpmaster.internal/ubuntu plucky/main s390x ghostscript s390x 10.04.0~dfsg1-2ubuntu1 [43.7 kB] 674s Get:117 http://ftpmaster.internal/ubuntu plucky/universe s390x libnetpbm11t64 s390x 2:11.09.02-2 [124 kB] 674s Get:118 http://ftpmaster.internal/ubuntu plucky/universe s390x netpbm s390x 2:11.09.02-2 [2207 kB] 674s Get:119 http://ftpmaster.internal/ubuntu plucky/universe s390x tex-common all 6.18 [32.8 kB] 674s Get:120 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper-utils s390x 2.2.5-0.3 [15.3 kB] 674s Get:121 http://ftpmaster.internal/ubuntu plucky/main s390x libkpathsea6 s390x 2024.20240313.70630+ds-5build2 [66.9 kB] 674s Get:122 http://ftpmaster.internal/ubuntu plucky/main s390x libptexenc1 s390x 2024.20240313.70630+ds-5build2 [43.4 kB] 674s Get:123 http://ftpmaster.internal/ubuntu plucky/main s390x libsynctex2 s390x 2024.20240313.70630+ds-5build2 [64.6 kB] 674s Get:124 http://ftpmaster.internal/ubuntu plucky/main s390x libtexlua53-5 s390x 2024.20240313.70630+ds-5build2 [131 kB] 674s Get:125 http://ftpmaster.internal/ubuntu plucky/main s390x t1utils s390x 1.41-4build3 [65.6 kB] 674s Get:126 http://ftpmaster.internal/ubuntu plucky/main s390x libpixman-1-0 s390x 0.44.0-3 [201 kB] 674s Get:127 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-render0 s390x 1.17.0-2 [17.0 kB] 674s Get:128 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-shm0 s390x 1.17.0-2 [5862 B] 674s Get:129 http://ftpmaster.internal/ubuntu plucky/main s390x libcairo2 s390x 1.18.2-2 [580 kB] 674s Get:130 http://ftpmaster.internal/ubuntu plucky/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB] 674s Get:131 http://ftpmaster.internal/ubuntu plucky/main s390x libharfbuzz0b s390x 10.2.0-1 [538 kB] 674s Get:132 http://ftpmaster.internal/ubuntu plucky/universe s390x libmpfi0 s390x 1.5.4+ds-4 [34.1 kB] 674s Get:133 http://ftpmaster.internal/ubuntu plucky/universe s390x libpotrace0 s390x 1.16-2build1 [18.7 kB] 674s Get:134 http://ftpmaster.internal/ubuntu plucky/universe s390x libteckit0 s390x 2.5.12+ds1-1 [433 kB] 674s Get:135 http://ftpmaster.internal/ubuntu plucky/main s390x libxmu6 s390x 2:1.1.3-3build2 [53.0 kB] 674s Get:136 http://ftpmaster.internal/ubuntu plucky/main s390x libxpm4 s390x 1:3.5.17-1build2 [41.2 kB] 674s Get:137 http://ftpmaster.internal/ubuntu plucky/main s390x libxaw7 s390x 2:1.0.16-1 [201 kB] 674s Get:138 http://ftpmaster.internal/ubuntu plucky/main s390x libxi6 s390x 2:1.8.2-1 [35.4 kB] 674s Get:139 http://ftpmaster.internal/ubuntu plucky/universe s390x libzzip-0-13t64 s390x 0.13.72+dfsg.1-1.2build1 [28.6 kB] 674s Get:140 http://ftpmaster.internal/ubuntu plucky/universe s390x texlive-binaries s390x 2024.20240313.70630+ds-5build2 [9171 kB] 675s Get:141 http://ftpmaster.internal/ubuntu plucky/main s390x xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 675s Get:142 http://ftpmaster.internal/ubuntu plucky/universe s390x texlive-base all 2024.20241115-1 [22.5 MB] 676s Get:143 http://ftpmaster.internal/ubuntu plucky/main s390x hicolor-icon-theme all 0.18-2 [13.3 kB] 676s Get:144 http://ftpmaster.internal/ubuntu plucky/universe s390x imagemagick-7.q16 s390x 8:7.1.1.43+dfsg1-1 [703 kB] 676s Get:145 http://ftpmaster.internal/ubuntu plucky/universe s390x imagemagick s390x 8:7.1.1.43+dfsg1-1 [14.1 kB] 676s Get:146 http://ftpmaster.internal/ubuntu plucky/universe s390x hevea s390x 2.36-2 [2045 kB] 676s Get:147 http://ftpmaster.internal/ubuntu plucky/main s390x libsuitesparseconfig7 s390x 1:7.8.3+dfsg-3 [13.2 kB] 676s Get:148 http://ftpmaster.internal/ubuntu plucky/universe s390x libamd3 s390x 1:7.8.3+dfsg-3 [35.1 kB] 676s Get:149 http://ftpmaster.internal/ubuntu plucky/universe s390x libapache-pom-java all 33-2 [5874 B] 676s Get:150 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.1-2 [252 kB] 676s Get:151 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 15-20250213-1ubuntu1 [620 kB] 676s Get:152 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.1-2 [2971 kB] 677s Get:153 http://ftpmaster.internal/ubuntu plucky/universe s390x libarpack2t64 s390x 3.9.1-4 [110 kB] 677s Get:154 http://ftpmaster.internal/ubuntu plucky/main s390x libcolamd3 s390x 1:7.8.3+dfsg-3 [23.4 kB] 677s Get:155 http://ftpmaster.internal/ubuntu plucky/universe s390x libcommons-parent-java all 56-1 [10.7 kB] 677s Get:156 http://ftpmaster.internal/ubuntu plucky/universe s390x libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 677s Get:157 http://ftpmaster.internal/ubuntu plucky/main s390x libexpat1-dev s390x 2.6.4-1 [146 kB] 677s Get:158 http://ftpmaster.internal/ubuntu plucky/universe s390x libglpk40 s390x 5.0-1build2 [406 kB] 677s Get:159 http://ftpmaster.internal/ubuntu plucky/universe s390x libplfit0 s390x 0.9.4+ds-1ubuntu5 [29.6 kB] 677s Get:160 http://ftpmaster.internal/ubuntu plucky/universe s390x libigraph3t64 s390x 0.10.15+ds-2 [1015 kB] 677s Get:161 http://ftpmaster.internal/ubuntu plucky/main s390x libimagequant0 s390x 2.18.0-1build1 [43.3 kB] 677s Get:162 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 677s Get:163 http://ftpmaster.internal/ubuntu plucky/universe s390x libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 677s Get:164 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 677s Get:165 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 677s Get:166 http://ftpmaster.internal/ubuntu plucky/main s390x libjson-perl all 4.10000-1 [81.9 kB] 677s Get:167 http://ftpmaster.internal/ubuntu plucky/universe s390x liblbfgsb0 s390x 3.0+dfsg.4-1build1 [32.4 kB] 677s Get:168 http://ftpmaster.internal/ubuntu plucky/universe s390x libmbedcrypto16 s390x 3.6.2-3ubuntu1 [261 kB] 677s Get:169 http://ftpmaster.internal/ubuntu plucky/universe s390x libmbedx509-7 s390x 3.6.2-3ubuntu1 [34.9 kB] 677s Get:170 http://ftpmaster.internal/ubuntu plucky/universe s390x libmbedtls21 s390x 3.6.2-3ubuntu1 [122 kB] 677s Get:171 http://ftpmaster.internal/ubuntu plucky/main s390x mysql-common all 5.8+1.1.1 [6800 B] 677s Get:172 http://ftpmaster.internal/ubuntu plucky/main s390x libmysqlclient21 s390x 8.0.40-1 [1294 kB] 677s Get:173 http://ftpmaster.internal/ubuntu plucky/main s390x zlib1g-dev s390x 1:1.3.dfsg+really1.3.1-1ubuntu1 [898 kB] 677s Get:174 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.13-dev s390x 3.13.2-1 [5596 kB] 677s Get:175 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3-dev s390x 3.13.1-1~exp2 [10.5 kB] 677s Get:176 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.12t64 s390x 3.12.9-1 [2508 kB] 677s Get:177 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.12-dev s390x 3.12.9-1 [5849 kB] 678s Get:178 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3-all-dev s390x 3.13.1-1~exp2 [922 B] 678s Get:179 http://ftpmaster.internal/ubuntu plucky/universe s390x libqhull-r8.0 s390x 2020.2-6build1 [199 kB] 678s Get:180 http://ftpmaster.internal/ubuntu plucky/main s390x libraqm0 s390x 0.10.2-1 [15.8 kB] 678s Get:181 http://ftpmaster.internal/ubuntu plucky/main s390x libxslt1.1 s390x 1.1.39-0exp1ubuntu2 [169 kB] 678s Get:182 http://ftpmaster.internal/ubuntu plucky/universe s390x mafft s390x 7.505-1 [766 kB] 678s Get:183 http://ftpmaster.internal/ubuntu plucky/universe s390x ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 678s Get:184 http://ftpmaster.internal/ubuntu plucky/universe s390x ncbi-blast+ s390x 2.16.0+ds-6build1 [15.2 MB] 679s Get:185 http://ftpmaster.internal/ubuntu plucky/universe s390x phylip s390x 1:3.697+dfsg-4build1 [1051 kB] 679s Get:186 http://ftpmaster.internal/ubuntu plucky/universe s390x prank s390x 0.0.170427+dfsg-3 [357 kB] 679s Get:187 http://ftpmaster.internal/ubuntu plucky/universe s390x preview-latex-style all 13.2-1 [347 kB] 679s Get:188 http://ftpmaster.internal/ubuntu plucky/universe s390x probcons s390x 1.12-14 [109 kB] 679s Get:189 http://ftpmaster.internal/ubuntu plucky/universe s390x python-biopython-doc all 1.85+dfsg-2 [18.2 MB] 679s Get:190 http://ftpmaster.internal/ubuntu plucky/universe s390x python-matplotlib-data all 3.8.3-3ubuntu2 [2929 kB] 680s Get:191 http://ftpmaster.internal/ubuntu plucky/main s390x python3-all s390x 3.13.1-1~exp2 [898 B] 680s Get:192 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-dev s390x 3.13.2-1 [508 kB] 680s Get:193 http://ftpmaster.internal/ubuntu plucky/main s390x python3-dev s390x 3.13.1-1~exp2 [26.7 kB] 680s Get:194 http://ftpmaster.internal/ubuntu plucky/main s390x python3.12-dev s390x 3.12.9-1 [504 kB] 680s Get:195 http://ftpmaster.internal/ubuntu plucky/main s390x python3-all-dev s390x 3.13.1-1~exp2 [918 B] 680s Get:196 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:1.26.4+ds-13 [4601 kB] 680s Get:197 http://ftpmaster.internal/ubuntu plucky/main s390x python3.12-tk s390x 3.12.9-1 [117 kB] 680s Get:198 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-tk s390x 3.13.2-1 [108 kB] 680s Get:199 http://ftpmaster.internal/ubuntu plucky/main s390x python3-tk s390x 3.13.1-1 [9770 B] 680s Get:200 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pil.imagetk s390x 11.1.0-5 [9766 B] 680s Get:201 http://ftpmaster.internal/ubuntu plucky/main s390x python3-pil s390x 11.1.0-5 [527 kB] 680s Get:202 http://ftpmaster.internal/ubuntu plucky/main s390x python3-cairo s390x 1.26.1-2build1 [138 kB] 680s Get:203 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-freetype all 2.5.1-1 [92.3 kB] 680s Get:204 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-rlpycairo all 0.3.0-3 [9130 B] 680s Get:205 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-reportlab all 4.3.0-1 [1137 kB] 680s Get:206 http://ftpmaster.internal/ubuntu plucky/universe s390x w3c-sgml-lib all 1.3-3 [280 kB] 680s Get:207 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-biopython s390x 1.85+dfsg-2 [1756 kB] 681s Get:208 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-biopython-sql all 1.85+dfsg-2 [26.4 kB] 681s Get:209 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-brotli s390x 1.1.0-2build3 [381 kB] 681s Get:210 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-contourpy s390x 1.3.1-1 [235 kB] 681s Get:211 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-cycler all 0.12.1-1 [9716 B] 681s Get:212 http://ftpmaster.internal/ubuntu plucky/main s390x python3-dateutil all 2.9.0-3 [80.2 kB] 681s Get:213 http://ftpmaster.internal/ubuntu plucky/main s390x python3-decorator all 5.1.1-5 [10.1 kB] 681s Get:214 http://ftpmaster.internal/ubuntu plucky/main s390x python3-defusedxml all 0.7.1-3 [42.2 kB] 681s Get:215 http://ftpmaster.internal/ubuntu plucky/main s390x python3-roman all 5.0-1 [10.3 kB] 681s Get:216 http://ftpmaster.internal/ubuntu plucky/main s390x python3-docutils all 0.21.2+dfsg-2 [409 kB] 681s Get:217 http://ftpmaster.internal/ubuntu plucky/main s390x python3-pytz all 2025.1-3 [162 kB] 681s Get:218 http://ftpmaster.internal/ubuntu plucky/main s390x python3-tz all 2025.1-3 [1866 B] 681s Get:219 http://ftpmaster.internal/ubuntu plucky/main s390x python3-platformdirs all 4.3.6-1 [16.8 kB] 681s Get:220 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-fs all 2.4.16-6 [90.7 kB] 681s Get:221 http://ftpmaster.internal/ubuntu plucky/main s390x python3-lxml s390x 5.3.1-1 [1773 kB] 681s Get:222 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-lz4 s390x 4.4.0+dfsg-1 [27.0 kB] 681s Get:223 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-scipy s390x 1.14.1-4ubuntu1 [21.2 MB] 682s Get:224 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-mpmath all 1.3.0-1 [425 kB] 682s Get:225 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-sympy all 1.13.3-1 [4228 kB] 682s Get:226 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 682s Get:227 http://ftpmaster.internal/ubuntu plucky/universe s390x unicode-data all 15.1.0-1 [8878 kB] 683s Get:228 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-fonttools s390x 4.55.3-2 [1723 kB] 683s Get:229 http://ftpmaster.internal/ubuntu plucky/main s390x python3-imagesize all 1.4.1-1 [6844 B] 683s Get:230 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-kiwisolver s390x 1.4.7-3 [65.6 kB] 683s Get:231 http://ftpmaster.internal/ubuntu plucky/main s390x python3-packaging all 24.2-1 [51.5 kB] 683s Get:232 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-matplotlib s390x 3.8.3-3ubuntu2 [4657 kB] 683s Get:233 http://ftpmaster.internal/ubuntu plucky/main s390x python3-msgpack s390x 1.0.3-3build3 [117 kB] 683s Get:234 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-mmtf all 1.1.3-1 [16.2 kB] 683s Get:235 http://ftpmaster.internal/ubuntu plucky/main s390x python3-mysqldb s390x 1.4.6-2build4 [49.9 kB] 683s Get:236 http://ftpmaster.internal/ubuntu plucky/main s390x python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 684s Get:237 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x sphinx-common all 8.1.3-5 [663 kB] 684s Get:238 http://ftpmaster.internal/ubuntu plucky/main s390x python3-alabaster all 0.7.16-0.1 [18.5 kB] 684s Get:239 http://ftpmaster.internal/ubuntu plucky/main s390x python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 684s Get:240 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-sphinx all 8.1.3-5 [474 kB] 684s Get:241 http://ftpmaster.internal/ubuntu plucky/main s390x python3-tabulate all 0.9.0-1 [45.3 kB] 684s Get:242 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-numpydoc all 1.8.0-1 [52.4 kB] 684s Get:243 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-rdflib all 7.1.1-2 [426 kB] 684s Get:244 http://ftpmaster.internal/ubuntu plucky/main s390x sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB] 684s Get:245 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 684s Get:246 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-sphinx-rtd-theme all 3.0.2+dfsg-2 [23.5 kB] 684s Get:247 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-texttable all 1.7.0-1 [11.2 kB] 684s Get:248 http://ftpmaster.internal/ubuntu plucky/universe s390x t-coffee s390x 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [945 kB] 684s Get:249 http://ftpmaster.internal/ubuntu plucky/universe s390x texlive-fonts-recommended all 2024.20241115-1 [4973 kB] 684s Get:250 http://ftpmaster.internal/ubuntu plucky/universe s390x texlive-latex-base all 2024.20241115-1 [1260 kB] 684s Get:251 http://ftpmaster.internal/ubuntu plucky/universe s390x libfontbox-java all 1:1.8.16-5 [208 kB] 684s Get:252 http://ftpmaster.internal/ubuntu plucky/universe s390x libpdfbox-java all 1:1.8.16-5 [5521 kB] 685s Get:253 http://ftpmaster.internal/ubuntu plucky/universe s390x texlive-latex-recommended all 2024.20241115-1 [8739 kB] 685s Get:254 http://ftpmaster.internal/ubuntu plucky/universe s390x texlive-pictures all 2024.20241115-1 [17.0 MB] 686s Get:255 http://ftpmaster.internal/ubuntu plucky/universe s390x texlive-latex-extra all 2024.20250114-1 [24.3 MB] 687s Get:256 http://ftpmaster.internal/ubuntu plucky/universe s390x wise-data all 2.4.1-25 [83.0 kB] 687s Get:257 http://ftpmaster.internal/ubuntu plucky/universe s390x wise s390x 2.4.1-25 [935 kB] 687s Get:258 http://ftpmaster.internal/ubuntu plucky/universe s390x fasttree s390x 2.1.11-2 [190 kB] 687s Get:259 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-igraph s390x 0.11.8+ds-1build1 [340 kB] 688s Preconfiguring packages ... 688s Fetched 341 MB in 20s (17.1 MB/s) 688s Selecting previously unselected package libpython3.12-minimal:s390x. 688s (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 ... 55929 files and directories currently installed.) 688s Preparing to unpack .../000-libpython3.12-minimal_3.12.9-1_s390x.deb ... 688s Unpacking libpython3.12-minimal:s390x (3.12.9-1) ... 688s Selecting previously unselected package python3.12-minimal. 688s Preparing to unpack .../001-python3.12-minimal_3.12.9-1_s390x.deb ... 688s Unpacking python3.12-minimal (3.12.9-1) ... 688s Selecting previously unselected package m4. 688s Preparing to unpack .../002-m4_1.4.19-5_s390x.deb ... 688s Unpacking m4 (1.4.19-5) ... 688s Selecting previously unselected package flex. 688s Preparing to unpack .../003-flex_2.6.4-8.2build1_s390x.deb ... 688s Unpacking flex (2.6.4-8.2build1) ... 688s Selecting previously unselected package fonts-lato. 688s Preparing to unpack .../004-fonts-lato_2.015-1_all.deb ... 688s Unpacking fonts-lato (2.015-1) ... 689s Selecting previously unselected package libgomp1:s390x. 689s Preparing to unpack .../005-libgomp1_15-20250213-1ubuntu1_s390x.deb ... 689s Unpacking libgomp1:s390x (15-20250213-1ubuntu1) ... 689s Selecting previously unselected package libfftw3-double3:s390x. 689s Preparing to unpack .../006-libfftw3-double3_3.3.10-2fakesync1build1_s390x.deb ... 689s Unpacking libfftw3-double3:s390x (3.3.10-2fakesync1build1) ... 689s Selecting previously unselected package libfreetype6:s390x. 689s Preparing to unpack .../007-libfreetype6_2.13.3+dfsg-1_s390x.deb ... 689s Unpacking libfreetype6:s390x (2.13.3+dfsg-1) ... 689s Selecting previously unselected package fonts-dejavu-mono. 689s Preparing to unpack .../008-fonts-dejavu-mono_2.37-8_all.deb ... 689s Unpacking fonts-dejavu-mono (2.37-8) ... 689s Selecting previously unselected package fonts-dejavu-core. 689s Preparing to unpack .../009-fonts-dejavu-core_2.37-8_all.deb ... 689s Unpacking fonts-dejavu-core (2.37-8) ... 689s Selecting previously unselected package libfontenc1:s390x. 689s Preparing to unpack .../010-libfontenc1_1%3a1.1.8-1build1_s390x.deb ... 689s Unpacking libfontenc1:s390x (1:1.1.8-1build1) ... 689s Selecting previously unselected package x11-common. 689s Preparing to unpack .../011-x11-common_1%3a7.7+23ubuntu3_all.deb ... 689s Unpacking x11-common (1:7.7+23ubuntu3) ... 689s Selecting previously unselected package xfonts-encodings. 689s Preparing to unpack .../012-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 689s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 689s Selecting previously unselected package xfonts-utils. 689s Preparing to unpack .../013-xfonts-utils_1%3a7.7+7_s390x.deb ... 689s Unpacking xfonts-utils (1:7.7+7) ... 689s Selecting previously unselected package fonts-urw-base35. 689s Preparing to unpack .../014-fonts-urw-base35_20200910-8_all.deb ... 689s Unpacking fonts-urw-base35 (20200910-8) ... 689s Selecting previously unselected package fontconfig-config. 689s Preparing to unpack .../015-fontconfig-config_2.15.0-2ubuntu1_s390x.deb ... 689s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 689s Selecting previously unselected package libfontconfig1:s390x. 689s Preparing to unpack .../016-libfontconfig1_2.15.0-2ubuntu1_s390x.deb ... 689s Unpacking libfontconfig1:s390x (2.15.0-2ubuntu1) ... 689s Selecting previously unselected package libsharpyuv0:s390x. 689s Preparing to unpack .../017-libsharpyuv0_1.5.0-0.1_s390x.deb ... 689s Unpacking libsharpyuv0:s390x (1.5.0-0.1) ... 689s Selecting previously unselected package libaom3:s390x. 689s Preparing to unpack .../018-libaom3_3.12.0-1_s390x.deb ... 689s Unpacking libaom3:s390x (3.12.0-1) ... 689s Selecting previously unselected package libheif-plugin-aomdec:s390x. 689s Preparing to unpack .../019-libheif-plugin-aomdec_1.19.5-1build1_s390x.deb ... 689s Unpacking libheif-plugin-aomdec:s390x (1.19.5-1build1) ... 689s Selecting previously unselected package libde265-0:s390x. 689s Preparing to unpack .../020-libde265-0_1.0.15-1build4_s390x.deb ... 689s Unpacking libde265-0:s390x (1.0.15-1build4) ... 689s Selecting previously unselected package libheif-plugin-libde265:s390x. 689s Preparing to unpack .../021-libheif-plugin-libde265_1.19.5-1build1_s390x.deb ... 689s Unpacking libheif-plugin-libde265:s390x (1.19.5-1build1) ... 689s Selecting previously unselected package libheif1:s390x. 689s Preparing to unpack .../022-libheif1_1.19.5-1build1_s390x.deb ... 689s Unpacking libheif1:s390x (1.19.5-1build1) ... 689s Selecting previously unselected package libjbig0:s390x. 689s Preparing to unpack .../023-libjbig0_2.1-6.1ubuntu2_s390x.deb ... 689s Unpacking libjbig0:s390x (2.1-6.1ubuntu2) ... 689s Selecting previously unselected package libjpeg-turbo8:s390x. 689s Preparing to unpack .../024-libjpeg-turbo8_2.1.5-3ubuntu2_s390x.deb ... 689s Unpacking libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 689s Selecting previously unselected package libjpeg8:s390x. 689s Preparing to unpack .../025-libjpeg8_8c-2ubuntu11_s390x.deb ... 689s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 689s Selecting previously unselected package liblcms2-2:s390x. 689s Preparing to unpack .../026-liblcms2-2_2.16-2_s390x.deb ... 689s Unpacking liblcms2-2:s390x (2.16-2) ... 689s Selecting previously unselected package liblqr-1-0:s390x. 689s Preparing to unpack .../027-liblqr-1-0_0.4.2-2.1build2_s390x.deb ... 689s Unpacking liblqr-1-0:s390x (0.4.2-2.1build2) ... 689s Selecting previously unselected package libltdl7:s390x. 689s Preparing to unpack .../028-libltdl7_2.5.4-3build1_s390x.deb ... 689s Unpacking libltdl7:s390x (2.5.4-3build1) ... 689s Selecting previously unselected package libopenjp2-7:s390x. 689s Preparing to unpack .../029-libopenjp2-7_2.5.0-2ubuntu3_s390x.deb ... 689s Unpacking libopenjp2-7:s390x (2.5.0-2ubuntu3) ... 689s Selecting previously unselected package libraw23t64:s390x. 689s Preparing to unpack .../030-libraw23t64_0.21.3-1_s390x.deb ... 689s Unpacking libraw23t64:s390x (0.21.3-1) ... 689s Selecting previously unselected package libdeflate0:s390x. 689s Preparing to unpack .../031-libdeflate0_1.23-1_s390x.deb ... 689s Unpacking libdeflate0:s390x (1.23-1) ... 689s Selecting previously unselected package libwebp7:s390x. 689s Preparing to unpack .../032-libwebp7_1.5.0-0.1_s390x.deb ... 689s Unpacking libwebp7:s390x (1.5.0-0.1) ... 689s Selecting previously unselected package libtiff6:s390x. 689s Preparing to unpack .../033-libtiff6_4.5.1+git230720-4ubuntu4_s390x.deb ... 689s Unpacking libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 689s Selecting previously unselected package libwebpdemux2:s390x. 689s Preparing to unpack .../034-libwebpdemux2_1.5.0-0.1_s390x.deb ... 689s Unpacking libwebpdemux2:s390x (1.5.0-0.1) ... 689s Selecting previously unselected package libwebpmux3:s390x. 689s Preparing to unpack .../035-libwebpmux3_1.5.0-0.1_s390x.deb ... 689s Unpacking libwebpmux3:s390x (1.5.0-0.1) ... 689s Selecting previously unselected package imagemagick-7-common. 689s Preparing to unpack .../036-imagemagick-7-common_8%3a7.1.1.43+dfsg1-1_all.deb ... 689s Unpacking imagemagick-7-common (8:7.1.1.43+dfsg1-1) ... 689s Selecting previously unselected package libmagickcore-7.q16-10:s390x. 689s Preparing to unpack .../037-libmagickcore-7.q16-10_8%3a7.1.1.43+dfsg1-1_s390x.deb ... 689s Unpacking libmagickcore-7.q16-10:s390x (8:7.1.1.43+dfsg1-1) ... 689s Selecting previously unselected package libmagickwand-7.q16-10:s390x. 689s Preparing to unpack .../038-libmagickwand-7.q16-10_8%3a7.1.1.43+dfsg1-1_s390x.deb ... 689s Unpacking libmagickwand-7.q16-10:s390x (8:7.1.1.43+dfsg1-1) ... 689s Selecting previously unselected package poppler-data. 689s Preparing to unpack .../039-poppler-data_0.4.12-1_all.deb ... 689s Unpacking poppler-data (0.4.12-1) ... 689s Selecting previously unselected package sgml-base. 689s Preparing to unpack .../040-sgml-base_1.31_all.deb ... 689s Unpacking sgml-base (1.31) ... 689s Selecting previously unselected package libnsl2:s390x. 689s Preparing to unpack .../041-libnsl2_1.3.0-3build3_s390x.deb ... 689s Unpacking libnsl2:s390x (1.3.0-3build3) ... 689s Selecting previously unselected package libpython3.12-stdlib:s390x. 689s Preparing to unpack .../042-libpython3.12-stdlib_3.12.9-1_s390x.deb ... 689s Unpacking libpython3.12-stdlib:s390x (3.12.9-1) ... 690s Selecting previously unselected package python3.12. 690s Preparing to unpack .../043-python3.12_3.12.9-1_s390x.deb ... 690s Unpacking python3.12 (3.12.9-1) ... 690s Selecting previously unselected package autoconf. 690s Preparing to unpack .../044-autoconf_2.72-3_all.deb ... 690s Unpacking autoconf (2.72-3) ... 690s Selecting previously unselected package autotools-dev. 690s Preparing to unpack .../045-autotools-dev_20220109.1_all.deb ... 690s Unpacking autotools-dev (20220109.1) ... 690s Selecting previously unselected package automake. 690s Preparing to unpack .../046-automake_1%3a1.17-3_all.deb ... 690s Unpacking automake (1:1.17-3) ... 690s Selecting previously unselected package autopoint. 690s Preparing to unpack .../047-autopoint_0.23.1-1_all.deb ... 690s Unpacking autopoint (0.23.1-1) ... 690s Selecting previously unselected package libtcl8.6:s390x. 690s Preparing to unpack .../048-libtcl8.6_8.6.16+dfsg-1_s390x.deb ... 690s Unpacking libtcl8.6:s390x (8.6.16+dfsg-1) ... 690s Selecting previously unselected package libxrender1:s390x. 690s Preparing to unpack .../049-libxrender1_1%3a0.9.10-1.1build1_s390x.deb ... 690s Unpacking libxrender1:s390x (1:0.9.10-1.1build1) ... 690s Selecting previously unselected package libxft2:s390x. 690s Preparing to unpack .../050-libxft2_2.3.6-1build1_s390x.deb ... 690s Unpacking libxft2:s390x (2.3.6-1build1) ... 690s Selecting previously unselected package libxss1:s390x. 690s Preparing to unpack .../051-libxss1_1%3a1.2.3-1build3_s390x.deb ... 690s Unpacking libxss1:s390x (1:1.2.3-1build3) ... 690s Selecting previously unselected package libtk8.6:s390x. 690s Preparing to unpack .../052-libtk8.6_8.6.16-1_s390x.deb ... 690s Unpacking libtk8.6:s390x (8.6.16-1) ... 690s Selecting previously unselected package tk8.6-blt2.5. 690s Preparing to unpack .../053-tk8.6-blt2.5_2.5.3+dfsg-7build1_s390x.deb ... 690s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 690s Selecting previously unselected package blt. 690s Preparing to unpack .../054-blt_2.5.3+dfsg-7build1_s390x.deb ... 690s Unpacking blt (2.5.3+dfsg-7build1) ... 690s Selecting previously unselected package libisl23:s390x. 690s Preparing to unpack .../055-libisl23_0.27-1_s390x.deb ... 690s Unpacking libisl23:s390x (0.27-1) ... 690s Selecting previously unselected package libmpc3:s390x. 690s Preparing to unpack .../056-libmpc3_1.3.1-1build2_s390x.deb ... 690s Unpacking libmpc3:s390x (1.3.1-1build2) ... 690s Selecting previously unselected package cpp-14-s390x-linux-gnu. 690s Preparing to unpack .../057-cpp-14-s390x-linux-gnu_14.2.0-17ubuntu1_s390x.deb ... 690s Unpacking cpp-14-s390x-linux-gnu (14.2.0-17ubuntu1) ... 690s Selecting previously unselected package cpp-14. 690s Preparing to unpack .../058-cpp-14_14.2.0-17ubuntu1_s390x.deb ... 690s Unpacking cpp-14 (14.2.0-17ubuntu1) ... 690s Selecting previously unselected package cpp-s390x-linux-gnu. 690s Preparing to unpack .../059-cpp-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 690s Unpacking cpp-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 690s Selecting previously unselected package cpp. 690s Preparing to unpack .../060-cpp_4%3a14.2.0-1ubuntu1_s390x.deb ... 690s Unpacking cpp (4:14.2.0-1ubuntu1) ... 690s Selecting previously unselected package libcc1-0:s390x. 690s Preparing to unpack .../061-libcc1-0_15-20250213-1ubuntu1_s390x.deb ... 690s Unpacking libcc1-0:s390x (15-20250213-1ubuntu1) ... 690s Selecting previously unselected package libitm1:s390x. 690s Preparing to unpack .../062-libitm1_15-20250213-1ubuntu1_s390x.deb ... 690s Unpacking libitm1:s390x (15-20250213-1ubuntu1) ... 690s Selecting previously unselected package libasan8:s390x. 690s Preparing to unpack .../063-libasan8_15-20250213-1ubuntu1_s390x.deb ... 690s Unpacking libasan8:s390x (15-20250213-1ubuntu1) ... 690s Selecting previously unselected package libubsan1:s390x. 690s Preparing to unpack .../064-libubsan1_15-20250213-1ubuntu1_s390x.deb ... 690s Unpacking libubsan1:s390x (15-20250213-1ubuntu1) ... 690s Selecting previously unselected package libgcc-14-dev:s390x. 690s Preparing to unpack .../065-libgcc-14-dev_14.2.0-17ubuntu1_s390x.deb ... 690s Unpacking libgcc-14-dev:s390x (14.2.0-17ubuntu1) ... 690s Selecting previously unselected package gcc-14-s390x-linux-gnu. 690s Preparing to unpack .../066-gcc-14-s390x-linux-gnu_14.2.0-17ubuntu1_s390x.deb ... 690s Unpacking gcc-14-s390x-linux-gnu (14.2.0-17ubuntu1) ... 690s Selecting previously unselected package gcc-14. 690s Preparing to unpack .../067-gcc-14_14.2.0-17ubuntu1_s390x.deb ... 690s Unpacking gcc-14 (14.2.0-17ubuntu1) ... 690s Selecting previously unselected package gcc-s390x-linux-gnu. 690s Preparing to unpack .../068-gcc-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 690s Unpacking gcc-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 690s Selecting previously unselected package gcc. 690s Preparing to unpack .../069-gcc_4%3a14.2.0-1ubuntu1_s390x.deb ... 690s Unpacking gcc (4:14.2.0-1ubuntu1) ... 690s Selecting previously unselected package libstdc++-14-dev:s390x. 690s Preparing to unpack .../070-libstdc++-14-dev_14.2.0-17ubuntu1_s390x.deb ... 690s Unpacking libstdc++-14-dev:s390x (14.2.0-17ubuntu1) ... 691s Selecting previously unselected package g++-14-s390x-linux-gnu. 691s Preparing to unpack .../071-g++-14-s390x-linux-gnu_14.2.0-17ubuntu1_s390x.deb ... 691s Unpacking g++-14-s390x-linux-gnu (14.2.0-17ubuntu1) ... 691s Selecting previously unselected package g++-14. 691s Preparing to unpack .../072-g++-14_14.2.0-17ubuntu1_s390x.deb ... 691s Unpacking g++-14 (14.2.0-17ubuntu1) ... 691s Selecting previously unselected package g++-s390x-linux-gnu. 691s Preparing to unpack .../073-g++-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 691s Unpacking g++-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 691s Selecting previously unselected package g++. 691s Preparing to unpack .../074-g++_4%3a14.2.0-1ubuntu1_s390x.deb ... 691s Unpacking g++ (4:14.2.0-1ubuntu1) ... 691s Selecting previously unselected package build-essential. 691s Preparing to unpack .../075-build-essential_12.10ubuntu1_s390x.deb ... 691s Unpacking build-essential (12.10ubuntu1) ... 691s Selecting previously unselected package bwa. 691s Preparing to unpack .../076-bwa_0.7.18-1_s390x.deb ... 691s Unpacking bwa (0.7.18-1) ... 691s Selecting previously unselected package libargtable2-0. 691s Preparing to unpack .../077-libargtable2-0_13-3_s390x.deb ... 691s Unpacking libargtable2-0 (13-3) ... 691s Selecting previously unselected package clustalo. 691s Preparing to unpack .../078-clustalo_1.2.4-8build1_s390x.deb ... 691s Unpacking clustalo (1.2.4-8build1) ... 691s Selecting previously unselected package libdebhelper-perl. 691s Preparing to unpack .../079-libdebhelper-perl_13.24.1ubuntu2_all.deb ... 691s Unpacking libdebhelper-perl (13.24.1ubuntu2) ... 691s Selecting previously unselected package libtool. 691s Preparing to unpack .../080-libtool_2.5.4-3build1_all.deb ... 691s Unpacking libtool (2.5.4-3build1) ... 691s Selecting previously unselected package dh-autoreconf. 691s Preparing to unpack .../081-dh-autoreconf_20_all.deb ... 691s Unpacking dh-autoreconf (20) ... 691s Selecting previously unselected package libarchive-zip-perl. 691s Preparing to unpack .../082-libarchive-zip-perl_1.68-1_all.deb ... 691s Unpacking libarchive-zip-perl (1.68-1) ... 691s Selecting previously unselected package libfile-stripnondeterminism-perl. 691s Preparing to unpack .../083-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... 691s Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... 691s Selecting previously unselected package dh-strip-nondeterminism. 691s Preparing to unpack .../084-dh-strip-nondeterminism_1.14.1-2_all.deb ... 691s Unpacking dh-strip-nondeterminism (1.14.1-2) ... 691s Selecting previously unselected package debugedit. 691s Preparing to unpack .../085-debugedit_1%3a5.1-2_s390x.deb ... 691s Unpacking debugedit (1:5.1-2) ... 691s Selecting previously unselected package dwz. 691s Preparing to unpack .../086-dwz_0.15-1build6_s390x.deb ... 691s Unpacking dwz (0.15-1build6) ... 691s Selecting previously unselected package gettext. 691s Preparing to unpack .../087-gettext_0.23.1-1_s390x.deb ... 691s Unpacking gettext (0.23.1-1) ... 691s Selecting previously unselected package intltool-debian. 691s Preparing to unpack .../088-intltool-debian_0.35.0+20060710.6_all.deb ... 691s Unpacking intltool-debian (0.35.0+20060710.6) ... 691s Selecting previously unselected package po-debconf. 691s Preparing to unpack .../089-po-debconf_1.0.21+nmu1_all.deb ... 691s Unpacking po-debconf (1.0.21+nmu1) ... 691s Selecting previously unselected package debhelper. 691s Preparing to unpack .../090-debhelper_13.24.1ubuntu2_all.deb ... 691s Unpacking debhelper (13.24.1ubuntu2) ... 691s Selecting previously unselected package dh-python. 691s Preparing to unpack .../091-dh-python_6.20250108_all.deb ... 691s Unpacking dh-python (6.20250108) ... 691s Selecting previously unselected package dialign. 691s Preparing to unpack .../092-dialign_2.2.1-13_s390x.deb ... 691s Unpacking dialign (2.2.1-13) ... 691s Selecting previously unselected package xml-core. 691s Preparing to unpack .../093-xml-core_0.19_all.deb ... 691s Unpacking xml-core (0.19) ... 691s Selecting previously unselected package docutils-common. 691s Preparing to unpack .../094-docutils-common_0.21.2+dfsg-2_all.deb ... 691s Unpacking docutils-common (0.21.2+dfsg-2) ... 691s Selecting previously unselected package libcifpp-data. 691s Preparing to unpack .../095-libcifpp-data_7.0.9-1_all.deb ... 691s Unpacking libcifpp-data (7.0.9-1) ... 691s Selecting previously unselected package libcifpp7:s390x. 691s Preparing to unpack .../096-libcifpp7_7.0.9-1_s390x.deb ... 691s Unpacking libcifpp7:s390x (7.0.9-1) ... 691s Selecting previously unselected package dssp. 691s Preparing to unpack .../097-dssp_4.4.10-1_s390x.deb ... 691s Unpacking dssp (4.4.10-1) ... 691s Selecting previously unselected package fonts-font-awesome. 691s Preparing to unpack .../098-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 691s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 691s Selecting previously unselected package fonts-lmodern. 691s Preparing to unpack .../099-fonts-lmodern_2.005-1_all.deb ... 691s Unpacking fonts-lmodern (2.005-1) ... 691s Selecting previously unselected package fonts-lyx. 691s Preparing to unpack .../100-fonts-lyx_2.4.3-1_all.deb ... 691s Unpacking fonts-lyx (2.4.3-1) ... 691s Selecting previously unselected package libgs-common. 691s Preparing to unpack .../101-libgs-common_10.04.0~dfsg1-2ubuntu1_all.deb ... 691s Unpacking libgs-common (10.04.0~dfsg1-2ubuntu1) ... 691s Selecting previously unselected package libgs10-common. 691s Preparing to unpack .../102-libgs10-common_10.04.0~dfsg1-2ubuntu1_all.deb ... 691s Unpacking libgs10-common (10.04.0~dfsg1-2ubuntu1) ... 692s Selecting previously unselected package libavahi-common-data:s390x. 692s Preparing to unpack .../103-libavahi-common-data_0.8-14ubuntu1_s390x.deb ... 692s Unpacking libavahi-common-data:s390x (0.8-14ubuntu1) ... 692s Selecting previously unselected package libavahi-common3:s390x. 692s Preparing to unpack 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.../109-libjbig2dec0_0.20-1build3_s390x.deb ... 692s Unpacking libjbig2dec0:s390x (0.20-1build3) ... 692s Selecting previously unselected package libpaper2:s390x. 692s Preparing to unpack .../110-libpaper2_2.2.5-0.3_s390x.deb ... 692s Unpacking libpaper2:s390x (2.2.5-0.3) ... 692s Selecting previously unselected package libice6:s390x. 692s Preparing to unpack .../111-libice6_2%3a1.1.1-1_s390x.deb ... 692s Unpacking libice6:s390x (2:1.1.1-1) ... 692s Selecting previously unselected package libsm6:s390x. 692s Preparing to unpack .../112-libsm6_2%3a1.2.4-1_s390x.deb ... 692s Unpacking libsm6:s390x (2:1.2.4-1) ... 692s Selecting previously unselected package libxt6t64:s390x. 692s Preparing to unpack .../113-libxt6t64_1%3a1.2.1-1.2build1_s390x.deb ... 692s Unpacking libxt6t64:s390x (1:1.2.1-1.2build1) ... 692s Selecting previously unselected package libgs10:s390x. 692s Preparing to unpack .../114-libgs10_10.04.0~dfsg1-2ubuntu1_s390x.deb ... 692s Unpacking libgs10:s390x (10.04.0~dfsg1-2ubuntu1) ... 692s Selecting previously unselected package ghostscript. 692s Preparing to unpack .../115-ghostscript_10.04.0~dfsg1-2ubuntu1_s390x.deb ... 692s Unpacking ghostscript (10.04.0~dfsg1-2ubuntu1) ... 692s Selecting previously unselected package libnetpbm11t64:s390x. 692s Preparing to unpack .../116-libnetpbm11t64_2%3a11.09.02-2_s390x.deb ... 692s Unpacking libnetpbm11t64:s390x (2:11.09.02-2) ... 692s Selecting previously unselected package netpbm. 692s Preparing to unpack .../117-netpbm_2%3a11.09.02-2_s390x.deb ... 692s Unpacking netpbm (2:11.09.02-2) ... 692s Selecting previously unselected package tex-common. 692s Preparing to unpack .../118-tex-common_6.18_all.deb ... 692s Unpacking tex-common (6.18) ... 692s Selecting previously unselected package libpaper-utils. 692s Preparing to unpack .../119-libpaper-utils_2.2.5-0.3_s390x.deb ... 692s Unpacking libpaper-utils (2.2.5-0.3) ... 692s Selecting previously unselected package libkpathsea6:s390x. 692s Preparing to unpack .../120-libkpathsea6_2024.20240313.70630+ds-5build2_s390x.deb ... 692s Unpacking libkpathsea6:s390x (2024.20240313.70630+ds-5build2) ... 692s Selecting previously unselected package libptexenc1:s390x. 692s Preparing to unpack .../121-libptexenc1_2024.20240313.70630+ds-5build2_s390x.deb ... 692s Unpacking libptexenc1:s390x (2024.20240313.70630+ds-5build2) ... 692s Selecting previously unselected package libsynctex2:s390x. 692s Preparing to unpack .../122-libsynctex2_2024.20240313.70630+ds-5build2_s390x.deb ... 692s Unpacking libsynctex2:s390x (2024.20240313.70630+ds-5build2) ... 692s Selecting previously unselected package libtexlua53-5:s390x. 692s Preparing to unpack .../123-libtexlua53-5_2024.20240313.70630+ds-5build2_s390x.deb ... 692s Unpacking libtexlua53-5:s390x (2024.20240313.70630+ds-5build2) ... 692s Selecting previously unselected package t1utils. 692s Preparing to unpack .../124-t1utils_1.41-4build3_s390x.deb ... 692s Unpacking t1utils (1.41-4build3) ... 692s Selecting previously unselected package libpixman-1-0:s390x. 692s Preparing to unpack .../125-libpixman-1-0_0.44.0-3_s390x.deb ... 692s Unpacking libpixman-1-0:s390x (0.44.0-3) ... 692s Selecting previously unselected package libxcb-render0:s390x. 692s Preparing to unpack .../126-libxcb-render0_1.17.0-2_s390x.deb ... 692s Unpacking libxcb-render0:s390x (1.17.0-2) ... 692s Selecting previously unselected package libxcb-shm0:s390x. 692s Preparing to unpack .../127-libxcb-shm0_1.17.0-2_s390x.deb ... 692s Unpacking libxcb-shm0:s390x (1.17.0-2) ... 692s Selecting previously unselected package libcairo2:s390x. 692s Preparing to unpack .../128-libcairo2_1.18.2-2_s390x.deb ... 692s Unpacking libcairo2:s390x (1.18.2-2) ... 692s Selecting previously unselected package libgraphite2-3:s390x. 692s Preparing to unpack .../129-libgraphite2-3_1.3.14-2ubuntu1_s390x.deb ... 692s Unpacking libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 692s Selecting previously unselected package libharfbuzz0b:s390x. 692s Preparing to unpack .../130-libharfbuzz0b_10.2.0-1_s390x.deb ... 692s Unpacking libharfbuzz0b:s390x (10.2.0-1) ... 692s Selecting previously unselected package libmpfi0:s390x. 692s Preparing to unpack .../131-libmpfi0_1.5.4+ds-4_s390x.deb ... 692s Unpacking libmpfi0:s390x (1.5.4+ds-4) ... 692s Selecting previously unselected package libpotrace0:s390x. 692s Preparing to unpack .../132-libpotrace0_1.16-2build1_s390x.deb ... 692s Unpacking libpotrace0:s390x (1.16-2build1) ... 692s Selecting previously unselected package libteckit0:s390x. 692s Preparing to unpack .../133-libteckit0_2.5.12+ds1-1_s390x.deb ... 692s Unpacking libteckit0:s390x (2.5.12+ds1-1) ... 692s Selecting previously unselected package libxmu6:s390x. 692s Preparing to unpack .../134-libxmu6_2%3a1.1.3-3build2_s390x.deb ... 692s Unpacking libxmu6:s390x (2:1.1.3-3build2) ... 692s Selecting previously unselected package libxpm4:s390x. 692s Preparing to unpack .../135-libxpm4_1%3a3.5.17-1build2_s390x.deb ... 692s Unpacking libxpm4:s390x (1:3.5.17-1build2) ... 692s Selecting previously unselected package libxaw7:s390x. 692s Preparing to unpack .../136-libxaw7_2%3a1.0.16-1_s390x.deb ... 692s Unpacking libxaw7:s390x (2:1.0.16-1) ... 692s Selecting previously unselected package libxi6:s390x. 692s Preparing to unpack .../137-libxi6_2%3a1.8.2-1_s390x.deb ... 692s Unpacking libxi6:s390x (2:1.8.2-1) ... 692s Selecting previously unselected package libzzip-0-13t64:s390x. 692s Preparing to unpack .../138-libzzip-0-13t64_0.13.72+dfsg.1-1.2build1_s390x.deb ... 692s Unpacking libzzip-0-13t64:s390x (0.13.72+dfsg.1-1.2build1) ... 692s Selecting previously unselected package texlive-binaries. 692s Preparing to unpack .../139-texlive-binaries_2024.20240313.70630+ds-5build2_s390x.deb ... 692s Unpacking texlive-binaries (2024.20240313.70630+ds-5build2) ... 693s Selecting previously unselected package xdg-utils. 693s Preparing to unpack .../140-xdg-utils_1.2.1-2ubuntu1_all.deb ... 693s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 693s Selecting previously unselected package texlive-base. 693s Preparing to unpack .../141-texlive-base_2024.20241115-1_all.deb ... 693s Unpacking texlive-base (2024.20241115-1) ... 694s Selecting previously unselected package hicolor-icon-theme. 694s Preparing to unpack .../142-hicolor-icon-theme_0.18-2_all.deb ... 694s Unpacking hicolor-icon-theme (0.18-2) ... 694s Selecting previously unselected package imagemagick-7.q16. 694s Preparing to unpack .../143-imagemagick-7.q16_8%3a7.1.1.43+dfsg1-1_s390x.deb ... 694s Unpacking imagemagick-7.q16 (8:7.1.1.43+dfsg1-1) ... 694s Selecting previously unselected package imagemagick. 694s Preparing to unpack .../144-imagemagick_8%3a7.1.1.43+dfsg1-1_s390x.deb ... 694s Unpacking imagemagick (8:7.1.1.43+dfsg1-1) ... 694s Selecting previously unselected package hevea. 694s Preparing to unpack .../145-hevea_2.36-2_s390x.deb ... 694s Unpacking hevea (2.36-2) ... 694s Selecting previously unselected package libsuitesparseconfig7:s390x. 694s Preparing to unpack .../146-libsuitesparseconfig7_1%3a7.8.3+dfsg-3_s390x.deb ... 694s Unpacking libsuitesparseconfig7:s390x (1:7.8.3+dfsg-3) ... 694s Selecting previously unselected package libamd3:s390x. 694s Preparing to unpack .../147-libamd3_1%3a7.8.3+dfsg-3_s390x.deb ... 694s Unpacking libamd3:s390x (1:7.8.3+dfsg-3) ... 694s Selecting previously unselected package libapache-pom-java. 694s Preparing to unpack .../148-libapache-pom-java_33-2_all.deb ... 694s Unpacking libapache-pom-java (33-2) ... 694s Selecting previously unselected package libblas3:s390x. 694s Preparing to unpack .../149-libblas3_3.12.1-2_s390x.deb ... 694s Unpacking libblas3:s390x (3.12.1-2) ... 694s Selecting previously unselected package libgfortran5:s390x. 694s Preparing to unpack .../150-libgfortran5_15-20250213-1ubuntu1_s390x.deb ... 694s Unpacking libgfortran5:s390x (15-20250213-1ubuntu1) ... 694s Selecting previously unselected package liblapack3:s390x. 694s Preparing to unpack .../151-liblapack3_3.12.1-2_s390x.deb ... 694s Unpacking liblapack3:s390x (3.12.1-2) ... 694s Selecting previously unselected package libarpack2t64:s390x. 694s Preparing to unpack .../152-libarpack2t64_3.9.1-4_s390x.deb ... 694s Unpacking libarpack2t64:s390x (3.9.1-4) ... 694s Selecting previously unselected package libcolamd3:s390x. 694s Preparing to unpack .../153-libcolamd3_1%3a7.8.3+dfsg-3_s390x.deb ... 694s Unpacking libcolamd3:s390x (1:7.8.3+dfsg-3) ... 694s Selecting previously unselected package libcommons-parent-java. 694s Preparing to unpack .../154-libcommons-parent-java_56-1_all.deb ... 694s Unpacking libcommons-parent-java (56-1) ... 694s Selecting previously unselected package libcommons-logging-java. 694s Preparing to unpack .../155-libcommons-logging-java_1.3.0-1ubuntu1_all.deb ... 694s Unpacking libcommons-logging-java (1.3.0-1ubuntu1) ... 694s Selecting previously unselected package libexpat1-dev:s390x. 694s Preparing to unpack .../156-libexpat1-dev_2.6.4-1_s390x.deb 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unselected package libmbedcrypto16:s390x. 694s Preparing to unpack .../167-libmbedcrypto16_3.6.2-3ubuntu1_s390x.deb ... 694s Unpacking libmbedcrypto16:s390x (3.6.2-3ubuntu1) ... 694s Selecting previously unselected package libmbedx509-7:s390x. 694s Preparing to unpack .../168-libmbedx509-7_3.6.2-3ubuntu1_s390x.deb ... 694s Unpacking libmbedx509-7:s390x (3.6.2-3ubuntu1) ... 694s Selecting previously unselected package libmbedtls21:s390x. 694s Preparing to unpack .../169-libmbedtls21_3.6.2-3ubuntu1_s390x.deb ... 694s Unpacking libmbedtls21:s390x (3.6.2-3ubuntu1) ... 694s Selecting previously unselected package mysql-common. 694s Preparing to unpack .../170-mysql-common_5.8+1.1.1_all.deb ... 695s Unpacking mysql-common (5.8+1.1.1) ... 695s Selecting previously unselected package libmysqlclient21:s390x. 695s Preparing to unpack .../171-libmysqlclient21_8.0.40-1_s390x.deb ... 695s Unpacking libmysqlclient21:s390x (8.0.40-1) ... 695s Selecting previously unselected package zlib1g-dev:s390x. 695s Preparing to unpack .../172-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_s390x.deb ... 695s Unpacking zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 695s Selecting previously unselected package libpython3.13-dev:s390x. 695s Preparing to unpack .../173-libpython3.13-dev_3.13.2-1_s390x.deb ... 695s Unpacking libpython3.13-dev:s390x (3.13.2-1) ... 695s Selecting previously unselected package libpython3-dev:s390x. 695s Preparing to unpack .../174-libpython3-dev_3.13.1-1~exp2_s390x.deb ... 695s Unpacking libpython3-dev:s390x (3.13.1-1~exp2) ... 695s Selecting previously unselected package libpython3.12t64:s390x. 695s Preparing to unpack .../175-libpython3.12t64_3.12.9-1_s390x.deb ... 695s Unpacking libpython3.12t64:s390x (3.12.9-1) ... 695s Selecting previously unselected package libpython3.12-dev:s390x. 695s Preparing to unpack .../176-libpython3.12-dev_3.12.9-1_s390x.deb ... 695s Unpacking libpython3.12-dev:s390x (3.12.9-1) ... 695s Selecting previously unselected package libpython3-all-dev:s390x. 695s Preparing to unpack .../177-libpython3-all-dev_3.13.1-1~exp2_s390x.deb ... 695s Unpacking libpython3-all-dev:s390x (3.13.1-1~exp2) ... 695s Selecting previously unselected package libqhull-r8.0:s390x. 695s Preparing to unpack .../178-libqhull-r8.0_2020.2-6build1_s390x.deb ... 695s Unpacking libqhull-r8.0:s390x (2020.2-6build1) ... 695s Selecting previously unselected package libraqm0:s390x. 695s Preparing to unpack .../179-libraqm0_0.10.2-1_s390x.deb ... 695s Unpacking libraqm0:s390x (0.10.2-1) ... 695s Selecting previously unselected package libxslt1.1:s390x. 695s Preparing to unpack .../180-libxslt1.1_1.1.39-0exp1ubuntu2_s390x.deb ... 695s Unpacking libxslt1.1:s390x (1.1.39-0exp1ubuntu2) ... 695s Selecting previously unselected package mafft. 695s Preparing to unpack .../181-mafft_7.505-1_s390x.deb ... 695s Unpacking mafft (7.505-1) ... 695s Selecting previously unselected package ncbi-data. 695s Preparing to unpack .../182-ncbi-data_6.1.20170106+dfsg2-5_all.deb ... 695s Unpacking ncbi-data (6.1.20170106+dfsg2-5) ... 695s Selecting previously unselected package ncbi-blast+. 695s Preparing to unpack .../183-ncbi-blast+_2.16.0+ds-6build1_s390x.deb ... 695s Unpacking ncbi-blast+ (2.16.0+ds-6build1) ... 695s Selecting previously unselected package phylip. 695s Preparing to unpack .../184-phylip_1%3a3.697+dfsg-4build1_s390x.deb ... 695s Unpacking phylip (1:3.697+dfsg-4build1) ... 696s Selecting previously unselected package prank. 696s Preparing to unpack .../185-prank_0.0.170427+dfsg-3_s390x.deb ... 696s Unpacking prank (0.0.170427+dfsg-3) ... 696s Selecting previously unselected package preview-latex-style. 696s Preparing to unpack .../186-preview-latex-style_13.2-1_all.deb ... 696s Unpacking preview-latex-style (13.2-1) ... 696s Selecting previously unselected package probcons. 696s Preparing to unpack .../187-probcons_1.12-14_s390x.deb ... 696s Unpacking probcons (1.12-14) ... 696s Selecting previously unselected package python-biopython-doc. 696s Preparing to unpack .../188-python-biopython-doc_1.85+dfsg-2_all.deb ... 696s Unpacking python-biopython-doc (1.85+dfsg-2) ... 696s Selecting previously unselected package python-matplotlib-data. 696s Preparing to unpack .../189-python-matplotlib-data_3.8.3-3ubuntu2_all.deb ... 696s Unpacking python-matplotlib-data (3.8.3-3ubuntu2) ... 696s Selecting previously unselected package python3-all. 696s Preparing to unpack .../190-python3-all_3.13.1-1~exp2_s390x.deb ... 696s Unpacking python3-all (3.13.1-1~exp2) ... 696s Selecting previously unselected package python3.13-dev. 696s Preparing to unpack .../191-python3.13-dev_3.13.2-1_s390x.deb ... 696s Unpacking python3.13-dev (3.13.2-1) ... 696s Selecting previously unselected package python3-dev. 696s Preparing to unpack .../192-python3-dev_3.13.1-1~exp2_s390x.deb ... 696s Unpacking python3-dev (3.13.1-1~exp2) ... 696s Selecting previously unselected package python3.12-dev. 696s Preparing to unpack .../193-python3.12-dev_3.12.9-1_s390x.deb ... 696s Unpacking python3.12-dev (3.12.9-1) ... 696s Selecting previously unselected package python3-all-dev. 696s Preparing to unpack .../194-python3-all-dev_3.13.1-1~exp2_s390x.deb ... 696s Unpacking python3-all-dev (3.13.1-1~exp2) ... 696s Selecting previously unselected package python3-numpy. 696s Preparing to unpack .../195-python3-numpy_1%3a1.26.4+ds-13_s390x.deb ... 696s Unpacking python3-numpy (1:1.26.4+ds-13) ... 696s Selecting previously unselected package python3.12-tk. 696s Preparing to unpack .../196-python3.12-tk_3.12.9-1_s390x.deb ... 696s Unpacking python3.12-tk (3.12.9-1) ... 696s Selecting previously unselected package python3.13-tk. 696s Preparing to unpack .../197-python3.13-tk_3.13.2-1_s390x.deb ... 696s Unpacking python3.13-tk (3.13.2-1) ... 696s Selecting previously unselected package python3-tk:s390x. 696s Preparing to unpack .../198-python3-tk_3.13.1-1_s390x.deb ... 696s Unpacking python3-tk:s390x (3.13.1-1) ... 696s Selecting previously unselected package python3-pil.imagetk:s390x. 696s Preparing to unpack .../199-python3-pil.imagetk_11.1.0-5_s390x.deb ... 696s Unpacking python3-pil.imagetk:s390x (11.1.0-5) ... 696s Selecting previously unselected package python3-pil:s390x. 696s Preparing to unpack .../200-python3-pil_11.1.0-5_s390x.deb ... 696s Unpacking python3-pil:s390x (11.1.0-5) ... 696s Selecting previously unselected package python3-cairo. 696s Preparing to unpack .../201-python3-cairo_1.26.1-2build1_s390x.deb ... 696s Unpacking python3-cairo (1.26.1-2build1) ... 696s Selecting previously unselected package python3-freetype. 696s Preparing to unpack .../202-python3-freetype_2.5.1-1_all.deb ... 696s Unpacking python3-freetype (2.5.1-1) ... 696s Selecting previously unselected package python3-rlpycairo. 696s Preparing to unpack .../203-python3-rlpycairo_0.3.0-3_all.deb ... 696s Unpacking python3-rlpycairo (0.3.0-3) ... 696s Selecting previously unselected package python3-reportlab. 696s Preparing to unpack .../204-python3-reportlab_4.3.0-1_all.deb ... 696s Unpacking python3-reportlab (4.3.0-1) ... 696s Selecting previously unselected package w3c-sgml-lib. 696s Preparing to unpack .../205-w3c-sgml-lib_1.3-3_all.deb ... 696s Unpacking w3c-sgml-lib (1.3-3) ... 697s Selecting previously unselected package python3-biopython. 697s Preparing to unpack .../206-python3-biopython_1.85+dfsg-2_s390x.deb ... 697s Unpacking python3-biopython (1.85+dfsg-2) ... 697s Selecting previously unselected package python3-biopython-sql. 697s Preparing to unpack .../207-python3-biopython-sql_1.85+dfsg-2_all.deb ... 697s Unpacking python3-biopython-sql (1.85+dfsg-2) ... 697s Selecting previously unselected package python3-brotli. 697s Preparing to unpack .../208-python3-brotli_1.1.0-2build3_s390x.deb ... 697s Unpacking python3-brotli (1.1.0-2build3) ... 697s Selecting previously unselected package python3-contourpy. 697s Preparing to unpack .../209-python3-contourpy_1.3.1-1_s390x.deb ... 697s Unpacking python3-contourpy (1.3.1-1) ... 697s Selecting previously unselected package python3-cycler. 697s Preparing to unpack .../210-python3-cycler_0.12.1-1_all.deb ... 697s Unpacking python3-cycler (0.12.1-1) ... 697s Selecting previously unselected package python3-dateutil. 697s Preparing to unpack .../211-python3-dateutil_2.9.0-3_all.deb ... 697s Unpacking python3-dateutil (2.9.0-3) ... 697s Selecting previously unselected package python3-decorator. 697s Preparing to unpack .../212-python3-decorator_5.1.1-5_all.deb ... 697s Unpacking python3-decorator (5.1.1-5) ... 697s Selecting previously unselected package python3-defusedxml. 697s Preparing to unpack .../213-python3-defusedxml_0.7.1-3_all.deb ... 697s Unpacking python3-defusedxml (0.7.1-3) ... 697s Selecting previously unselected package python3-roman. 697s Preparing to unpack .../214-python3-roman_5.0-1_all.deb ... 697s Unpacking python3-roman (5.0-1) ... 697s Selecting previously unselected package python3-docutils. 697s Preparing to unpack .../215-python3-docutils_0.21.2+dfsg-2_all.deb ... 697s Unpacking python3-docutils (0.21.2+dfsg-2) ... 697s Selecting previously unselected package python3-pytz. 697s Preparing to unpack .../216-python3-pytz_2025.1-3_all.deb ... 697s Unpacking python3-pytz (2025.1-3) ... 697s Selecting previously unselected package python3-tz. 697s Preparing to unpack .../217-python3-tz_2025.1-3_all.deb ... 697s Unpacking python3-tz (2025.1-3) ... 697s Selecting previously unselected package python3-platformdirs. 697s Preparing to unpack .../218-python3-platformdirs_4.3.6-1_all.deb ... 697s Unpacking python3-platformdirs (4.3.6-1) ... 697s Selecting previously unselected package python3-fs. 697s Preparing to unpack .../219-python3-fs_2.4.16-6_all.deb ... 697s Unpacking python3-fs (2.4.16-6) ... 697s Selecting previously unselected package python3-lxml:s390x. 697s Preparing to unpack .../220-python3-lxml_5.3.1-1_s390x.deb ... 697s Unpacking python3-lxml:s390x (5.3.1-1) ... 697s Selecting previously unselected package python3-lz4. 697s Preparing to unpack .../221-python3-lz4_4.4.0+dfsg-1_s390x.deb ... 697s Unpacking python3-lz4 (4.4.0+dfsg-1) ... 697s Selecting previously unselected package python3-scipy. 697s Preparing to unpack .../222-python3-scipy_1.14.1-4ubuntu1_s390x.deb ... 697s Unpacking python3-scipy (1.14.1-4ubuntu1) ... 698s Selecting previously unselected package python3-mpmath. 698s Preparing to unpack .../223-python3-mpmath_1.3.0-1_all.deb ... 698s Unpacking python3-mpmath (1.3.0-1) ... 698s Selecting previously unselected package python3-sympy. 698s Preparing to unpack .../224-python3-sympy_1.13.3-1_all.deb ... 698s Unpacking python3-sympy (1.13.3-1) ... 698s Selecting previously unselected package python3-ufolib2. 698s Preparing to unpack .../225-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... 698s Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ... 698s Selecting previously unselected package unicode-data. 698s Preparing to unpack .../226-unicode-data_15.1.0-1_all.deb ... 698s Unpacking unicode-data (15.1.0-1) ... 698s Selecting previously unselected package python3-fonttools. 698s Preparing to unpack .../227-python3-fonttools_4.55.3-2_s390x.deb ... 698s Unpacking python3-fonttools (4.55.3-2) ... 698s Selecting previously unselected package python3-imagesize. 698s Preparing to unpack .../228-python3-imagesize_1.4.1-1_all.deb ... 698s Unpacking python3-imagesize (1.4.1-1) ... 698s Selecting previously unselected package python3-kiwisolver. 699s Preparing to unpack .../229-python3-kiwisolver_1.4.7-3_s390x.deb ... 699s Unpacking python3-kiwisolver (1.4.7-3) ... 699s Selecting previously unselected package python3-packaging. 699s Preparing to unpack .../230-python3-packaging_24.2-1_all.deb ... 699s Unpacking python3-packaging (24.2-1) ... 699s Selecting previously unselected package python3-matplotlib. 699s Preparing to unpack .../231-python3-matplotlib_3.8.3-3ubuntu2_s390x.deb ... 699s 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Setting up libgcc-14-dev:s390x (14.2.0-17ubuntu1) ... 737s Setting up libigraph3t64:s390x (0.10.15+ds-2) ... 737s Setting up libstdc++-14-dev:s390x (14.2.0-17ubuntu1) ... 737s Setting up libsm6:s390x (2:1.2.4-1) ... 737s Setting up libavahi-client3:s390x (0.8-14ubuntu1) ... 737s Setting up liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 737s Setting up libxft2:s390x (2.3.6-1build1) ... 737s Setting up python3-scipy (1.14.1-4ubuntu1) ... 744s Setting up libpython3-dev:s390x (3.13.1-1~exp2) ... 744s Setting up cpp-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 744s Setting up python3.13-dev (3.13.2-1) ... 744s Setting up po-debconf (1.0.21+nmu1) ... 744s Setting up libtk8.6:s390x (8.6.16-1) ... 744s Setting up python3.12-tk (3.12.9-1) ... 745s Setting up libpython3.12-dev:s390x (3.12.9-1) ... 745s Setting up python3-mmtf (1.1.3-1) ... 745s Setting up fonts-urw-base35 (20200910-8) ... 745s Setting up libcairo2:s390x (1.18.2-2) ... 745s Setting up python3.13-tk (3.13.2-1) ... 745s Setting up ncbi-blast+ (2.16.0+ds-6build1) ... 745s Setting up python3-pil:s390x (11.1.0-5) ... 745s Setting up gcc-14-s390x-linux-gnu (14.2.0-17ubuntu1) ... 745s Setting up gcc-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 746s Setting up libpython3-all-dev:s390x (3.13.1-1~exp2) ... 746s Setting up sphinx-common (8.1.3-5) ... 746s Setting up python3-dev (3.13.1-1~exp2) ... 746s Setting up libxt6t64:s390x (1:1.2.1-1.2build1) ... 746s Setting up g++-14-s390x-linux-gnu (14.2.0-17ubuntu1) ... 746s Setting up python3.12-dev (3.12.9-1) ... 746s Setting up netpbm (2:11.09.02-2) ... 746s Setting up python3-igraph (0.11.8+ds-1build1) ... 746s Setting up cpp (4:14.2.0-1ubuntu1) ... 746s Setting up libcups2t64:s390x (2.4.11-0ubuntu2) ... 746s Setting up python3-all-dev (3.13.1-1~exp2) ... 746s Setting up libgs10-common (10.04.0~dfsg1-2ubuntu1) ... 746s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 746s Setting up libxmu6:s390x (2:1.1.3-3build2) ... 746s Setting up python3-cairo (1.26.1-2build1) ... 746s Setting up blt (2.5.3+dfsg-7build1) ... 746s Setting up python3-tk:s390x (3.13.1-1) ... 746s Setting up g++-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 746s Setting up libxaw7:s390x (2:1.0.16-1) ... 746s Setting up gcc-14 (14.2.0-17ubuntu1) ... 746s Setting up python3-pil.imagetk:s390x (11.1.0-5) ... 746s Setting up python3-rlpycairo (0.3.0-3) ... 746s Setting up python3-reportlab (4.3.0-1) ... 748s Setting up texlive-binaries (2024.20240313.70630+ds-5build2) ... 748s update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode 748s update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode 748s Setting up g++-14 (14.2.0-17ubuntu1) ... 748s Setting up texlive-base (2024.20241115-1) ... 748s tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps 749s tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg 749s tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper 749s tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex 749s Setting up libgs10:s390x (10.04.0~dfsg1-2ubuntu1) ... 749s Setting up libtool (2.5.4-3build1) ... 749s Setting up ghostscript (10.04.0~dfsg1-2ubuntu1) ... 749s Setting up gcc (4:14.2.0-1ubuntu1) ... 749s Setting up dh-autoreconf (20) ... 749s Setting up texlive-latex-base (2024.20241115-1) ... 749s Setting up texlive-latex-recommended (2024.20241115-1) ... 749s Setting up texlive-pictures (2024.20241115-1) ... 749s Setting up g++ (4:14.2.0-1ubuntu1) ... 749s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 749s Setting up texlive-fonts-recommended (2024.20241115-1) ... 749s Setting up build-essential (12.10ubuntu1) ... 749s Setting up debhelper (13.24.1ubuntu2) ... 749s Setting up texlive-latex-extra (2024.20250114-1) ... 749s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 750s Setting up libheif-plugin-aomdec:s390x (1.19.5-1build1) ... 750s Setting up libheif-plugin-libde265:s390x (1.19.5-1build1) ... 750s Setting up libheif1:s390x (1.19.5-1build1) ... 750s Setting up python3-fonttools (4.55.3-2) ... 752s Setting up libmagickcore-7.q16-10:s390x (8:7.1.1.43+dfsg1-1) ... 752s Setting up python3-matplotlib (3.8.3-3ubuntu2) ... 754s Setting up libmagickwand-7.q16-10:s390x (8:7.1.1.43+dfsg1-1) ... 754s Setting up imagemagick-7.q16 (8:7.1.1.43+dfsg1-1) ... 754s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare (compare) in auto mode 754s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare-im7 (compare-im7) in auto mode 754s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate (animate) in auto mode 754s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate-im7 (animate-im7) in auto mode 754s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert (convert) in auto mode 754s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert-im7 (convert-im7) in auto mode 754s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite (composite) in auto mode 754s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite-im7 (composite-im7) in auto mode 754s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure (conjure) in auto mode 754s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure-im7 (conjure-im7) in auto mode 754s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import (import) in auto mode 754s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import-im7 (import-im7) in auto mode 754s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify (identify) in auto mode 754s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify-im7 (identify-im7) in auto mode 754s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream (stream) in auto mode 754s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream-im7 (stream-im7) in auto mode 754s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display (display) in auto mode 754s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display-im7 (display-im7) in auto mode 754s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage (montage) in auto mode 754s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage-im7 (montage-im7) in auto mode 754s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify (mogrify) in auto mode 754s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify-im7 (mogrify-im7) in auto mode 754s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick (magick) in auto mode 754s update-alternatives: warning: skip creation of /usr/share/man/man1/magick.1.gz because associated file /usr/share/man/man1/magick-im7.q16.1.gz (of link group magick) doesn't exist 754s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick-im7 (magick-im7) in auto mode 754s update-alternatives: warning: skip creation of /usr/share/man/man1/magick-im7.1.gz because associated file /usr/share/man/man1/magick-im7.q16.1.gz (of link group magick-im7) doesn't exist 754s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script (magick-script) in auto mode 754s update-alternatives: warning: skip creation of /usr/share/man/man1/magick-script.1.gz because associated file /usr/share/man/man1/magick-script-im7.q16.1.gz (of link group magick-script) doesn't exist 754s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script-im7 (magick-script-im7) in auto mode 754s update-alternatives: warning: skip creation of /usr/share/man/man1/magick-script-im7.1.gz because associated file /usr/share/man/man1/magick-script-im7.q16.1.gz (of link group magick-script-im7) doesn't exist 754s Setting up hevea (2.36-2) ... 754s Setting up imagemagick (8:7.1.1.43+dfsg1-1) ... 754s Processing triggers for install-info (7.1.1-1) ... 755s Processing triggers for libc-bin (2.40-4ubuntu1) ... 755s Processing triggers for systemd (257.2-3ubuntu1) ... 755s Processing triggers for man-db (2.13.0-1) ... 756s Processing triggers for sgml-base (1.31) ... 756s Setting up docutils-common (0.21.2+dfsg-2) ... 756s Setting up w3c-sgml-lib (1.3-3) ... 781s Setting up python3-biopython (1.85+dfsg-2) ... 783s Setting up python3-biopython-sql (1.85+dfsg-2) ... 783s Processing triggers for sgml-base (1.31) ... 783s Setting up python3-docutils (0.21.2+dfsg-2) ... 783s Setting up python3-sphinx (8.1.3-5) ... 785s Setting up python3-sphinxcontrib.jquery (4.1-5) ... 785s Setting up python3-numpydoc (1.8.0-1) ... 785s Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-2) ... 785s Processing triggers for tex-common (6.18) ... 785s Running updmap-sys. This may take some time... done. 786s Running mktexlsr /var/lib/texmf ... done. 786s Building format(s) --all. 870s This may take some time... done. 870s autopkgtest: DBG: testbed command exited with code 0 870s autopkgtest: DBG: testbed command ['dpkg-query', '--show', '-f', '${Status}', 'python3-biopython'], kind short, sout pipe, serr pipe, env [] 871s autopkgtest: DBG: testbed command exited with code 0 871s autopkgtest: DBG: testbed command ['dpkg-query', '--show', '-f', '${Status}', 'python-biopython-doc'], kind short, sout pipe, serr pipe, env [] 871s autopkgtest: DBG: testbed command exited with code 0 871s autopkgtest: DBG: testbed command ['dpkg-query', '--show', '-f', '${Status}', 'python3-biopython-sql'], kind short, sout pipe, serr pipe, env [] 871s autopkgtest: DBG: testbed command exited with code 0 871s autopkgtest: DBG: testbed command ['sh', '-ec', "dpkg-query --show -f '${Package}\\t${Version}\\n' > /tmp/autopkgtest.IaIWjt/full_suite-packages.all"], kind short, sout raw, serr pipe, env [] 871s autopkgtest: DBG: testbed command exited with code 0 871s autopkgtest: DBG: sending command to testbed: copyup /tmp/autopkgtest.IaIWjt/full_suite-packages.all /tmp/autopkgtest-work.by5by6hj/out/full_suite-packages.all 871s autopkgtest: DBG: got reply from testbed: ok 871s autopkgtest: DBG: testbed command ['test', '-e', '/tmp/autopkgtest.IaIWjt/build.Jxz/src'], kind short, sout raw, serr raw, env [] 872s autopkgtest: DBG: testbed command exited with code 1 872s autopkgtest: DBG: testbed command ['mkdir', '-p', '/tmp/autopkgtest.IaIWjt/build.Jxz'], kind short, sout raw, serr pipe, env [] 872s autopkgtest: DBG: testbed command exited with code 0 872s autopkgtest: DBG: sending command to testbed: copydown /tmp/autopkgtest-work.by5by6hj/out/tests-tree/ /tmp/autopkgtest.IaIWjt/build.Jxz/src/ 886s autopkgtest: DBG: got reply from testbed: ok 886s autopkgtest: DBG: testbed command ['chown', '-R', 'ubuntu', '--', '/tmp/autopkgtest.IaIWjt/build.Jxz/src'], kind short, sout raw, serr pipe, env [] 887s autopkgtest: DBG: testbed command exited with code 0 887s autopkgtest [12:48:20]: test full_suite: sh debian/tests/run-unit-test 887s autopkgtest [12:48:20]: test full_suite: [----------------------- 887s autopkgtest: DBG: testbed command ['su', '-s', '/bin/bash', 'ubuntu', '-c', "set -e; exec /tmp/autopkgtest.IaIWjt/wrapper.sh --debug --artifacts=/tmp/autopkgtest.IaIWjt/full_suite-artifacts --chdir=/tmp/autopkgtest.IaIWjt/build.Jxz/src --env=AUTOPKGTEST_TESTBED_ARCH=s390x --env=AUTOPKGTEST_TEST_ARCH=s390x --env=DEB_BUILD_OPTIONS=parallel=2 --env=DEBIAN_FRONTEND=noninteractive --env=LANG=C.UTF-8 --unset-env=LANGUAGE --unset-env=LC_ADDRESS --unset-env=LC_ALL --unset-env=LC_COLLATE --unset-env=LC_CTYPE --unset-env=LC_IDENTIFICATION --unset-env=LC_MEASUREMENT --unset-env=LC_MESSAGES --unset-env=LC_MONETARY --unset-env=LC_NAME --unset-env=LC_NUMERIC --unset-env=LC_PAPER --unset-env=LC_TELEPHONE --unset-env=LC_TIME --script-pid-file=/tmp/autopkgtest_script_pid --source-profile --stderr=/tmp/autopkgtest.IaIWjt/full_suite-stderr --stdout=/tmp/autopkgtest.IaIWjt/full_suite-stdout --tmp=/tmp/autopkgtest.IaIWjt/autopkgtest_tmp --env=ADT_TEST_TRIGGERS=sphinx/8.1.3-5 -- bash -ec 'sh debian/tests/run-unit-test'"], kind test, sout raw, serr raw, env [] 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: creating AUTOPKGTEST_ARTIFACTS: /tmp/autopkgtest.IaIWjt/full_suite-artifacts 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: changing to directory: /tmp/autopkgtest.IaIWjt/build.Jxz/src 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: setting environment: AUTOPKGTEST_TESTBED_ARCH=s390x 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: setting environment: AUTOPKGTEST_TEST_ARCH=s390x 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: setting environment: DEB_BUILD_OPTIONS=parallel=2 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: setting environment: DEBIAN_FRONTEND=noninteractive 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: setting environment: LANG=C.UTF-8 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: unsetting environment: LANGUAGE 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: unsetting environment: LC_ADDRESS 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: unsetting environment: LC_ALL 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: unsetting environment: LC_COLLATE 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: unsetting environment: LC_CTYPE 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: unsetting environment: LC_IDENTIFICATION 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: unsetting environment: LC_MEASUREMENT 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: unsetting environment: LC_MESSAGES 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: unsetting environment: LC_MONETARY 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: unsetting environment: LC_NAME 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: unsetting environment: LC_NUMERIC 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: unsetting environment: LC_PAPER 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: unsetting environment: LC_TELEPHONE 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: unsetting environment: LC_TIME 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: will create pid file: /tmp/autopkgtest_script_pid 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: pretending to be a login shell 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: will write standard error to /tmp/autopkgtest.IaIWjt/full_suite-stderr 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: will write stdout to /tmp/autopkgtest.IaIWjt/full_suite-stdout 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: creating AUTOPKGTEST_TMP: /tmp/autopkgtest.IaIWjt/autopkgtest_tmp 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: setting environment: ADT_TEST_TRIGGERS=sphinx/8.1.3-5 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: command to run: bash -ec sh debian/tests/run-unit-test 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: copying /tmp/tmp.Vcy0o5BF60/out to stdout and file: /tmp/autopkgtest.IaIWjt/full_suite-stdout 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: copying /tmp/tmp.Vcy0o5BF60/err to standard error and file: /tmp/autopkgtest.IaIWjt/full_suite-stdout 887s /tmp/autopkgtest.IaIWjt/wrapper.sh: writing script pid 6753 to /tmp/autopkgtest_script_pid 888s mkdir: created directory 'Bio' 888s mkdir: created directory 'Bio/Align' 888s mkdir: created directory 'Bio/Align/substitution_matrices' 888s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 888s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 889s test_Ace ... ok 889s test_Affy ... ok 891s test_AlignIO ... ok 891s test_AlignIO_ClustalIO ... ok 891s test_AlignIO_EmbossIO ... ok 891s test_AlignIO_FastaIO ... ok 891s test_AlignIO_MauveIO ... ok 891s test_AlignIO_PhylipIO ... ok 891s test_AlignIO_convert ... ok 891s test_AlignInfo ... ok 892s test_Align_Alignment ... ok 892s test_Align_a2m ... ok 892s test_Align_bed ... ok 892s test_Align_bigbed ... ok 893s test_Align_bigmaf ... ok 893s test_Align_bigpsl ... ok 893s test_Align_chain ... ok 893s test_Align_clustal ... ok 899s test_Align_codonalign ... ok 899s test_Align_emboss ... ok 899s test_Align_exonerate ... ok 899s test_Align_fasta ... ok 900s test_Align_hhr ... ok 901s test_Align_maf ... ok 901s test_Align_mauve ... ok 901s test_Align_msf ... ok 901s test_Align_nexus ... ok 901s test_Align_phylip ... ok 901s test_Align_psl ... ok 902s test_Align_sam ... ok 903s test_Align_stockholm ... ok 904s test_Align_tabular ... ok 904s test_Application ... ok 904s test_BioSQL_MySQLdb_online ... skipping. internet not available 904s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 904s test_BioSQL_mysql_connector_online ... skipping. internet not available 904s test_BioSQL_psycopg2_online ... skipping. internet not available 908s test_BioSQL_sqlite3 ... ok 908s test_BioSQL_sqlite3_online ... skipping. internet not available 908s test_Blast_Record ... ok 908s test_Blast_parser ... ok 909s test_CAPS ... ok 909s test_Chi2 ... ok 911s test_ClustalOmega_tool ... ok 911s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 911s test_Cluster ... ok 911s test_CodonTable ... ok 911s test_ColorSpiral ... ok 911s test_Compass ... ok 912s test_Consensus ... ok 913s test_Dialign_tool ... ok 913s test_EMBL_unittest ... ok 913s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 913s test_EmbossPrimer ... ok 917s test_Entrez ... ok 917s test_Entrez_online ... skipping. internet not available 918s test_Entrez_parser ... ok 918s test_Enzyme ... ok 918s test_ExPASy ... skipping. internet not available 918s test_Fasttree_tool ... ok 918s test_File ... ok 918s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 918s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 918s ok 921s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 923s ok 923s test_GraphicsChromosome ... ok 923s test_GraphicsDistribution ... ok 924s test_GraphicsGeneral ... ok 925s test_HMMCasino ... ok 925s test_HMMGeneral ... ok 925s test_KEGG ... ok 925s test_KEGG_online ... skipping. internet not available 930s test_KGML_graphics ... ok 930s test_KGML_graphics_online ... skipping. internet not available 931s test_KGML_nographics ... ok 932s test_KeyWList ... ok 932s test_LogisticRegression ... ok 933s test_MafIO_index ... ok 934s test_Mafft_tool ... ok 934s test_MarkovModel ... ok 934s test_Medline ... ok 934s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 935s test_NCBIXML ... Exception ignored in: 935s Traceback (most recent call last): 935s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 935s expat_parser.Parse(NULL, True) 935s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 935s ok 936s test_NCBI_BLAST_tools ... ok 937s test_NCBI_qblast ... ok 937s test_NMR ... ok 937s test_NaiveBayes ... ok 937s test_Nexus ... ok 937s test_PAML_baseml ... ok 938s test_PAML_codeml ... ok 938s test_PAML_yn00 ... ok 943s test_PDB_CEAligner ... ok 945s test_PDB_DSSP ... ok 945s test_PDB_Dice ... ok 945s test_PDB_Disordered ... ok 945s test_PDB_Exposure ... ok 945s test_PDB_FragmentMapper ... ok 947s test_PDB_KDTree ... ok 947s test_PDB_MMCIF2Dict ... ok 947s test_PDB_MMCIFIO ... ok 949s test_PDB_MMCIFParser ... ok 949s test_PDB_NACCESS ... ok 949s test_PDB_PDBIO ... ok 949s test_PDB_PDBList ... skipping. internet not available 962s test_PDB_PDBMLParser ... ok 963s test_PDB_PDBParser ... ok 963s test_PDB_PSEA ... skipping. Download and install psea from ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/. Make sure that psea is on path 963s test_PDB_Polypeptide ... ok 963s test_PDB_QCPSuperimposer ... ok 967s test_PDB_SASA ... ok 968s test_PDB_SMCRA ... ok 968s test_PDB_Selection ... ok 968s test_PDB_StructureAlignment ... ok 968s test_PDB_Superimposer ... ok 969s test_PDB_alphafold_db ... skipping. internet not available 979s test_PDB_internal_coords ... ok 979s test_PDB_parse_pdb_header ... ok 980s test_PDB_vectors ... ok 980s test_PQR ... ok 981s test_Pathway ... ok 981s test_Phd ... ok 982s test_Phylo ... ok 982s test_PhyloXML ... ok 983s test_Phylo_CDAO ... ok 983s test_Phylo_NeXML ... ok 985s test_Phylo_igraph ... ok 989s test_Phylo_matplotlib ... ok 989s test_Phylo_networkx ... ok 990s test_PopGen_GenePop_nodepend ... ok 992s test_Prank_tool ... ok 992s test_Probcons_tool ... ok 993s test_ProtParam ... ok 994s test_RCSBFormats ... ok 995s test_Restriction ... ok 996s test_SCOP_Astral ... ok 997s test_SCOP_Cla ... ok 998s test_SCOP_Des ... ok 999s test_SCOP_Dom ... ok 1000s test_SCOP_Hie ... ok 1000s test_SCOP_Raf ... ok 1001s test_SCOP_Residues ... ok 1002s test_SCOP_Scop ... ok 1003s test_SVDSuperimposer ... ok 1004s test_SearchIO_blast_tab ... ok 1005s test_SearchIO_blast_tab_index ... ok 1006s test_SearchIO_blast_xml ... ok 1008s test_SearchIO_blast_xml_index ... ok 1009s test_SearchIO_blat_psl ... ok 1010s test_SearchIO_blat_psl_index ... ok 1011s test_SearchIO_exonerate ... ok 1012s test_SearchIO_exonerate_text_index ... ok 1013s test_SearchIO_exonerate_vulgar_index ... ok 1014s test_SearchIO_fasta_m10 ... ok 1015s test_SearchIO_fasta_m10_index ... ok 1015s test_SearchIO_hhsuite2_text ... ok 1016s test_SearchIO_hmmer2_text ... ok 1017s test_SearchIO_hmmer2_text_index ... ok 1018s test_SearchIO_hmmer3_domtab ... ok 1019s test_SearchIO_hmmer3_domtab_index ... ok 1019s test_SearchIO_hmmer3_tab ... ok 1020s test_SearchIO_hmmer3_tab_index ... ok 1021s test_SearchIO_hmmer3_text ... ok 1022s test_SearchIO_hmmer3_text_index ... ok 1022s test_SearchIO_interproscan_xml ... ok 1023s test_SearchIO_model ... ok 1024s test_SearchIO_write ... ok 1025s test_SeqFeature ... ok 1043s test_SeqIO ... ok 1044s test_SeqIO_AbiIO ... ok 1045s test_SeqIO_FastaIO ... ok 1045s test_SeqIO_Gck ... ok 1046s test_SeqIO_Gfa ... ok 1047s test_SeqIO_Insdc ... ok 1047s test_SeqIO_NibIO ... ok 1050s test_SeqIO_PdbIO ... ok 1051s test_SeqIO_QualityIO ... ok 1052s test_SeqIO_SeqXML ... ok 1053s test_SeqIO_SffIO ... ok 1054s test_SeqIO_SnapGene ... ok 1056s test_SeqIO_TwoBitIO ... ok 1057s test_SeqIO_UniprotIO ... ok 1058s test_SeqIO_Xdna ... ok 1059s test_SeqIO_features ... ok 1074s test_SeqIO_index ... ok 1075s test_SeqIO_online ... skipping. internet not available 1077s test_SeqIO_write ... ok 1077s test_SeqRecord ... ok 1077s test_SeqUtils ... ok 1079s test_Seq_objs ... ok 1080s test_SwissProt ... ok 1083s test_TCoffee_tool ... ok 1084s test_TogoWS ... skipping. internet not available 1085s test_TreeConstruction ... ok 1085s test_UniGene ... ok 1086s test_UniProt ... skipping. internet not available 1087s test_UniProt_GOA ... ok 1088s test_align ... ok 1089s test_align_substitution_matrices ... ok 1093s test_bgzf ... ok 1094s test_cellosaurus ... ok 1100s test_codonalign ... ok 1101s test_geo ... ok 1102s test_kNN ... ok 1103s test_motifs ... ok 1104s test_motifs_online ... skipping. internet not available 1105s test_pairwise2 ... /usr/lib/python3/dist-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module. 1105s warnings.warn( 1105s ok 1106s test_pairwise2_no_C ... ok 1107s test_pairwise_aligner ... ok 1108s test_pairwise_alignment_map ... ok 1116s test_phenotype ... ok 1116s test_phenotype_fit ... ok 1117s test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper. 1118s test_prodoc ... ok 1118s test_prosite ... ok 1119s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 1120s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 1120s test_seq ... ok 1121s test_translate ... ok 1122s Skipping any tests requiring internet access 1122s Python version: 3.12.9 (main, Feb 5 2025, 01:31:18) [GCC 14.2.0] 1122s Operating system: posix linux 1122s ---------------------------------------------------------------------- 1122s Ran 216 tests in 233.156 seconds 1122s 1123s sys:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 1123s sys:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 1124s test_Ace ... ok 1124s test_Affy ... ok 1126s test_AlignIO ... ok 1126s test_AlignIO_ClustalIO ... ok 1126s test_AlignIO_EmbossIO ... ok 1126s test_AlignIO_FastaIO ... ok 1126s test_AlignIO_MauveIO ... ok 1126s test_AlignIO_PhylipIO ... ok 1126s test_AlignIO_convert ... ok 1126s test_AlignInfo ... ok 1126s test_Align_Alignment ... ok 1127s test_Align_a2m ... ok 1127s test_Align_bed ... ok 1127s test_Align_bigbed ... ok 1127s test_Align_bigmaf ... ok 1128s test_Align_bigpsl ... ok 1128s test_Align_chain ... ok 1128s test_Align_clustal ... ok 1134s test_Align_codonalign ... ok 1134s test_Align_emboss ... ok 1134s test_Align_exonerate ... ok 1134s test_Align_fasta ... ok 1134s test_Align_hhr ... ok 1135s test_Align_maf ... ok 1135s test_Align_mauve ... ok 1135s test_Align_msf ... ok 1135s test_Align_nexus ... ok 1135s test_Align_phylip ... ok 1136s test_Align_psl ... ok 1136s test_Align_sam ... ok 1137s test_Align_stockholm ... ok 1138s test_Align_tabular ... ok 1138s test_Application ... ok 1138s test_BioSQL_MySQLdb_online ... skipping. internet not available 1138s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 1138s test_BioSQL_mysql_connector_online ... skipping. internet not available 1138s test_BioSQL_psycopg2_online ... skipping. internet not available 1141s test_BioSQL_sqlite3 ... ok 1141s test_BioSQL_sqlite3_online ... skipping. internet not available 1141s test_Blast_Record ... ok 1142s test_Blast_parser ... ok 1142s test_CAPS ... ok 1142s test_Chi2 ... ok 1144s test_ClustalOmega_tool ... ok 1144s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 1144s test_Cluster ... ok 1144s test_CodonTable ... ok 1144s test_ColorSpiral ... ok 1144s test_Compass ... ok 1145s test_Consensus ... ok 1146s test_Dialign_tool ... ok 1147s test_EMBL_unittest ... ok 1147s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 1147s test_EmbossPrimer ... ok 1151s test_Entrez ... ok 1151s test_Entrez_online ... skipping. internet not available 1151s test_Entrez_parser ... ok 1151s test_Enzyme ... ok 1151s test_ExPASy ... skipping. internet not available 1151s test_Fasttree_tool ... ok 1151s test_File ... ok 1151s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 1151s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 1151s ok 1153s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 1155s ok 1156s test_GraphicsChromosome ... ok 1156s test_GraphicsDistribution ... ok 1157s test_GraphicsGeneral ... ok 1157s test_HMMCasino ... ok 1157s test_HMMGeneral ... ok 1157s test_KEGG ... ok 1157s test_KEGG_online ... skipping. internet not available 1163s test_KGML_graphics ... ok 1163s test_KGML_graphics_online ... skipping. internet not available 1164s test_KGML_nographics ... ok 1164s test_KeyWList ... ok 1164s test_LogisticRegression ... ok 1164s test_MafIO_index ... ok 1165s test_Mafft_tool ... ok 1165s test_MarkovModel ... ok 1165s test_Medline ... ok 1165s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 1166s test_NCBIXML ... Exception ignored in: 1166s Traceback (most recent call last): 1166s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 1166s expat_parser.Parse(NULL, True) 1166s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 1166s ok 1168s test_NCBI_BLAST_tools ... ok 1168s test_NCBI_qblast ... ok 1168s test_NMR ... ok 1168s test_NaiveBayes ... ok 1168s test_Nexus ... ok 1168s test_PAML_baseml ... ok 1169s test_PAML_codeml ... ok 1169s test_PAML_yn00 ... ok 1175s test_PDB_CEAligner ... ok 1176s test_PDB_DSSP ... ok 1176s test_PDB_Dice ... ok 1176s test_PDB_Disordered ... ok 1177s test_PDB_Exposure ... ok 1177s test_PDB_FragmentMapper ... ok 1178s test_PDB_KDTree ... ok 1178s test_PDB_MMCIF2Dict ... ok 1178s test_PDB_MMCIFIO ... ok 1180s test_PDB_MMCIFParser ... ok 1180s test_PDB_NACCESS ... ok 1180s test_PDB_PDBIO ... ok 1180s test_PDB_PDBList ... skipping. internet not available 1190s test_PDB_PDBMLParser ... ok 1190s test_PDB_PDBParser ... ok 1190s test_PDB_PSEA ... skipping. Download and install psea from ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/. Make sure that psea is on path 1190s test_PDB_Polypeptide ... ok 1191s test_PDB_QCPSuperimposer ... ok 1194s test_PDB_SASA ... ok 1195s test_PDB_SMCRA ... ok 1195s test_PDB_Selection ... ok 1195s test_PDB_StructureAlignment ... ok 1196s test_PDB_Superimposer ... ok 1196s test_PDB_alphafold_db ... skipping. internet not available 1204s test_PDB_internal_coords ... ok 1205s test_PDB_parse_pdb_header ... ok 1205s test_PDB_vectors ... ok 1205s test_PQR ... ok 1205s test_Pathway ... ok 1206s test_Phd ... ok 1206s test_Phylo ... ok 1207s test_PhyloXML ... ok 1208s test_Phylo_CDAO ... ok 1208s test_Phylo_NeXML ... ok 1209s test_Phylo_igraph ... ok 1212s test_Phylo_matplotlib ... ok 1213s test_Phylo_networkx ... ok 1214s test_PopGen_GenePop_nodepend ... ok 1216s test_Prank_tool ... ok 1217s test_Probcons_tool ... ok 1217s test_ProtParam ... ok 1219s test_RCSBFormats ... ok 1220s test_Restriction ... ok 1220s test_SCOP_Astral ... ok 1221s test_SCOP_Cla ... ok 1222s test_SCOP_Des ... ok 1223s test_SCOP_Dom ... ok 1224s test_SCOP_Hie ... ok 1225s test_SCOP_Raf ... ok 1225s test_SCOP_Residues ... ok 1227s test_SCOP_Scop ... ok 1228s test_SVDSuperimposer ... ok 1229s test_SearchIO_blast_tab ... ok 1230s test_SearchIO_blast_tab_index ... ok 1230s test_SearchIO_blast_xml ... ok 1233s test_SearchIO_blast_xml_index ... ok 1233s test_SearchIO_blat_psl ... ok 1235s test_SearchIO_blat_psl_index ... ok 1236s test_SearchIO_exonerate ... ok 1237s test_SearchIO_exonerate_text_index ... ok 1237s test_SearchIO_exonerate_vulgar_index ... ok 1238s test_SearchIO_fasta_m10 ... ok 1239s test_SearchIO_fasta_m10_index ... ok 1240s test_SearchIO_hhsuite2_text ... ok 1241s test_SearchIO_hmmer2_text ... ok 1242s test_SearchIO_hmmer2_text_index ... ok 1243s test_SearchIO_hmmer3_domtab ... ok 1244s test_SearchIO_hmmer3_domtab_index ... ok 1245s test_SearchIO_hmmer3_tab ... ok 1246s test_SearchIO_hmmer3_tab_index ... ok 1246s test_SearchIO_hmmer3_text ... ok 1247s test_SearchIO_hmmer3_text_index ... ok 1248s test_SearchIO_interproscan_xml ... ok 1249s test_SearchIO_model ... ok 1250s test_SearchIO_write ... ok 1251s test_SeqFeature ... ok 1271s test_SeqIO ... ok 1272s test_SeqIO_AbiIO ... ok 1273s test_SeqIO_FastaIO ... ok 1274s test_SeqIO_Gck ... ok 1275s test_SeqIO_Gfa ... ok 1275s test_SeqIO_Insdc ... ok 1276s test_SeqIO_NibIO ... ok 1279s test_SeqIO_PdbIO ... ok 1280s test_SeqIO_QualityIO ... ok 1281s test_SeqIO_SeqXML ... ok 1282s test_SeqIO_SffIO ... ok 1283s test_SeqIO_SnapGene ... ok 1284s test_SeqIO_TwoBitIO ... ok 1285s test_SeqIO_UniprotIO ... ok 1286s test_SeqIO_Xdna ... ok 1287s test_SeqIO_features ... ok 1301s test_SeqIO_index ... ok 1301s test_SeqIO_online ... skipping. internet not available 1302s test_SeqIO_write ... ok 1303s test_SeqRecord ... ok 1304s test_SeqUtils ... ok 1306s test_Seq_objs ... ok 1307s test_SwissProt ... ok 1310s test_TCoffee_tool ... ok 1310s test_TogoWS ... skipping. internet not available 1312s test_TreeConstruction ... ok 1313s test_UniGene ... ok 1313s test_UniProt ... skipping. internet not available 1314s test_UniProt_GOA ... ok 1315s test_align ... ok 1316s test_align_substitution_matrices ... ok 1319s test_bgzf ... ok 1320s test_cellosaurus ... ok 1326s test_codonalign ... ok 1327s test_geo ... ok 1328s test_kNN ... ok 1329s test_motifs ... ok 1329s test_motifs_online ... skipping. internet not available 1330s test_pairwise2 ... /usr/lib/python3/dist-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module. 1330s warnings.warn( 1330s ok 1331s test_pairwise2_no_C ... ok 1331s test_pairwise_aligner ... ok 1332s test_pairwise_alignment_map ... ok 1341s test_phenotype ... ok 1341s test_phenotype_fit ... ok 1342s test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper. 1343s test_prodoc ... ok 1344s test_prosite ... ok 1344s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 1345s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 1346s test_seq ... ok 1347s test_translate ... ok 1347s ---------------------------------------------------------------------- 1347s Ran 216 tests in 223.343 seconds 1347s 1347s Skipping any tests requiring internet access 1347s Python version: 3.13.2 (main, Feb 5 2025, 01:23:35) [GCC 14.2.0] 1347s Operating system: posix linux 1348s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 1348s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 1348s /tmp/autopkgtest.IaIWjt/wrapper.sh: checking for leaked background processes... 1348s /tmp/autopkgtest.IaIWjt/wrapper.sh: waiting for tee/cat subprocesses... 1348s /tmp/autopkgtest.IaIWjt/wrapper.sh: cleaning up... 1348s /tmp/autopkgtest.IaIWjt/wrapper.sh: Exit status: 0 1348s autopkgtest: DBG: testbed command exited with code 0 1349s autopkgtest [12:56:02]: test full_suite: -----------------------] 1349s autopkgtest: DBG: testbed executing test finished with exit status 0 1349s autopkgtest: DBG: sending command to testbed: copyup /tmp/autopkgtest.IaIWjt/full_suite-stdout /tmp/autopkgtest-work.by5by6hj/out/full_suite-stdout 1349s autopkgtest: DBG: got reply from testbed: ok 1349s autopkgtest: DBG: sending command to testbed: copyup /tmp/autopkgtest.IaIWjt/full_suite-stderr /tmp/autopkgtest-work.by5by6hj/out/full_suite-stderr 1349s autopkgtest: DBG: got reply from testbed: ok 1349s autopkgtest [12:56:02]: test full_suite: - - - - - - - - - - results - - - - - - - - - - 1349s full_suite PASS 1349s autopkgtest: DBG: sending command to testbed: copyup /tmp/autopkgtest.IaIWjt/full_suite-artifacts/ /tmp/autopkgtest-work.by5by6hj/out/artifacts/ 1349s autopkgtest: DBG: got reply from testbed: ok 1349s autopkgtest: DBG: testbed command ['rm', '-rf', '/tmp/autopkgtest.IaIWjt/full_suite-artifacts', '/tmp/autopkgtest.IaIWjt/autopkgtest_tmp'], kind short, sout raw, serr pipe, env [] 1350s autopkgtest: DBG: testbed command exited with code 0 1350s autopkgtest: DBG: needs_reset, previously=False, requested by run_tests() line 230 1350s autopkgtest [12:56:03]: @@@@@@@@@@@@@@@@@@@@ summary 1350s dependencies PASS 1350s full_suite PASS 1350s autopkgtest: DBG: testbed stop 1350s autopkgtest: DBG: testbed close, scratch=/tmp/autopkgtest.IaIWjt 1350s autopkgtest: DBG: sending command to testbed: close 1367s autopkgtest: DBG: got reply from testbed: ok 1367s autopkgtest: DBG: sending command to testbed: quit 1367s nova [W] Using flock in prodstack6-s390x 1367s Creating nova instance adt-plucky-s390x-python-biopython-20250219-123333-juju-7f2275-prod-proposed-migration-environment-15-5a58a9f7-96a4-41c9-917f-dd7024d665f5 from image adt/ubuntu-plucky-s390x-server-20250219.img (UUID 7af5aa59-4155-4177-a560-02c7dd963d23)... 1367s nova [W] Timed out waiting for a994b359-ce7d-479e-b6c6-974172f4d75c to get deleted. 1367s nova [W] Using flock in prodstack6-s390x 1367s flock: timeout while waiting to get lock 1367s Creating nova instance adt-plucky-s390x-python-biopython-20250219-123333-juju-7f2275-prod-proposed-migration-environment-15-5a58a9f7-96a4-41c9-917f-dd7024d665f5 from image adt/ubuntu-plucky-s390x-server-20250219.img (UUID 7af5aa59-4155-4177-a560-02c7dd963d23)... 1367s nova [W] Timed out waiting for 7da33b9d-0b7d-49b3-aacd-35ff8fbf639a to get deleted.