0s autopkgtest [16:58:35]: starting date and time: 2025-03-15 16:58:35+0000 0s autopkgtest [16:58:35]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [16:58:35]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.m18o7a_8/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade pscan-tfbs --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-s390x-27.secgroup --name adt-plucky-s390x-pscan-tfbs-20250315-165834-juju-7f2275-prod-proposed-migration-environment-15-9eec5969-f06b-49d3-b55c-60ad8982911e --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/ 139s autopkgtest [17:00:54]: testbed dpkg architecture: s390x 139s autopkgtest [17:00:54]: testbed apt version: 2.9.33 139s autopkgtest [17:00:54]: @@@@@@@@@@@@@@@@@@@@ test bed setup 140s autopkgtest [17:00:55]: testbed release detected to be: None 140s autopkgtest [17:00:55]: updating testbed package index (apt update) 141s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 141s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 141s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 141s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 141s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 141s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 142s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 142s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [113 kB] 142s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 142s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 142s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [320 kB] 142s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.4 kB] 142s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B] 142s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 143s Fetched 1073 kB in 2s (527 kB/s) 143s Reading package lists... 144s + lsb_release --codename --short 144s + RELEASE=plucky 144s + cat 144s + [ plucky != trusty ] 144s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 144s Reading package lists... 144s Building dependency tree... 144s Reading state information... 144s Calculating upgrade... 144s Calculating upgrade... 144s The following packages were automatically installed and are no longer required: 144s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 144s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 144s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 144s linux-tools-6.11.0-8-generic 144s Use 'sudo apt autoremove' to remove them. 144s The following packages will be upgraded: 144s pinentry-curses python3-jinja2 strace 144s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 144s Need to get 652 kB of archives. 144s After this operation, 27.6 kB of additional disk space will be used. 144s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 145s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 145s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 145s Fetched 652 kB in 1s (647 kB/s) 145s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81428 files and directories currently installed.) 145s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 145s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 145s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 145s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 145s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 146s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 146s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 146s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 146s Setting up strace (6.13+ds-1ubuntu1) ... 146s Processing triggers for man-db (2.13.0-1) ... 146s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 146s + /usr/lib/apt/apt-helper analyze-pattern ?true 146s Reading package lists...+ uname -r 146s + sed s/\./\\./g 146s + running_kernel_pattern=^linux-.*6\.14\.0-10-generic.* 146s + apt list ?obsolete 146s + tail -n+2 146s + grep -v ^linux-.*6\.14\.0-10-generic.* 146s + cut -d/ -f1 146s + obsolete_pkgs=linux-headers-6.11.0-8-generic 146s linux-headers-6.11.0-8 146s linux-modules-6.11.0-8-generic 146s linux-tools-6.11.0-8-generic 146s linux-tools-6.11.0-8 146s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove linux-headers-6.11.0-8-generic linux-headers-6.11.0-8 linux-modules-6.11.0-8-generic linux-tools-6.11.0-8-generic linux-tools-6.11.0-8 146s 146s Building dependency tree... 146s Reading state information... 147s Solving dependencies... 147s The following packages will be REMOVED: 147s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 147s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 147s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 147s linux-tools-6.11.0-8-generic* 147s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 147s After this operation, 167 MB disk space will be freed. 147s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81428 files and directories currently installed.) 147s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 147s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 147s Removing libpython3.12t64:s390x (3.12.9-1) ... 147s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 147s Removing libnsl2:s390x (1.3.0-3build3) ... 147s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 147s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 147s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 148s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 148s Processing triggers for libc-bin (2.41-1ubuntu1) ... 148s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 56328 files and directories currently installed.) 148s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 148s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 148s + grep -q trusty /etc/lsb-release 148s + [ ! -d /usr/share/doc/unattended-upgrades ] 148s + [ ! -d /usr/share/doc/lxd ] 148s + [ ! -d /usr/share/doc/lxd-client ] 148s + [ ! -d /usr/share/doc/snapd ] 148s + type iptables 148s + cat 148s + chmod 755 /etc/rc.local 148s + . /etc/rc.local 148s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 148s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 148s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 148s + uname -m 148s + [ s390x = ppc64le ] 148s + [ -d /run/systemd/system ] 148s + systemd-detect-virt --quiet --vm 148s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 148s + cat 148s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 148s + echo COMPRESS=lz4 148s autopkgtest [17:01:03]: upgrading testbed (apt dist-upgrade and autopurge) 148s Reading package lists... 148s Building dependency tree... 148s Reading state information... 149s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 149s Starting 2 pkgProblemResolver with broken count: 0 149s Done 149s Entering ResolveByKeep 149s 149s Calculating upgrade... 149s The following packages will be upgraded: 149s libc-bin libc-dev-bin libc6 libc6-dev locales 149s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 149s Need to get 9512 kB of archives. 149s After this operation, 8192 B of additional disk space will be used. 149s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 152s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 152s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 154s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 155s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 160s Preconfiguring packages ... 160s Fetched 9512 kB in 11s (848 kB/s) 160s (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 ... 56326 files and directories currently installed.) 160s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 160s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 161s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 161s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 161s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 161s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 161s Setting up libc6:s390x (2.41-1ubuntu2) ... 161s (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 ... 56326 files and directories currently installed.) 161s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 161s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 161s Setting up libc-bin (2.41-1ubuntu2) ... 161s (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 ... 56326 files and directories currently installed.) 161s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 161s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 161s Setting up locales (2.41-1ubuntu2) ... 161s Generating locales (this might take a while)... 162s en_US.UTF-8... done 162s Generation complete. 162s Setting up libc-dev-bin (2.41-1ubuntu2) ... 162s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 162s Processing triggers for man-db (2.13.0-1) ... 163s Processing triggers for systemd (257.3-1ubuntu3) ... 164s Reading package lists... 164s Building dependency tree... 164s Reading state information... 164s Starting pkgProblemResolver with broken count: 0 164s Starting 2 pkgProblemResolver with broken count: 0 164s Done 164s Solving dependencies... 164s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 164s autopkgtest [17:01:19]: rebooting testbed after setup commands that affected boot 185s autopkgtest [17:01:40]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 187s autopkgtest [17:01:42]: @@@@@@@@@@@@@@@@@@@@ apt-source pscan-tfbs 189s Get:1 http://ftpmaster.internal/ubuntu plucky/universe pscan-tfbs 1.2.2-4build2 (dsc) [2067 B] 189s Get:2 http://ftpmaster.internal/ubuntu plucky/universe pscan-tfbs 1.2.2-4build2 (tar) [42.9 kB] 189s Get:3 http://ftpmaster.internal/ubuntu plucky/universe pscan-tfbs 1.2.2-4build2 (diff) [7476 B] 189s gpgv: Signature made Tue Jul 30 06:52:29 2024 UTC 189s gpgv: using RSA key 92978A6E195E4921825F7FF0F34F09744E9F5DD9 189s gpgv: Can't check signature: No public key 189s dpkg-source: warning: cannot verify inline signature for ./pscan-tfbs_1.2.2-4build2.dsc: no acceptable signature found 189s autopkgtest [17:01:44]: testing package pscan-tfbs version 1.2.2-4build2 190s autopkgtest [17:01:45]: build not needed 190s autopkgtest [17:01:45]: test run-unit-test: preparing testbed 190s Reading package lists... 190s Building dependency tree... 190s Reading state information... 190s Starting pkgProblemResolver with broken count: 0 190s Starting 2 pkgProblemResolver with broken count: 0 190s Done 191s The following NEW packages will be installed: 191s libgsl28 libgslcblas0 pscan-tfbs 191s 0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. 191s Need to get 1366 kB of archives. 191s After this operation, 4018 kB of additional disk space will be used. 191s Get:1 http://ftpmaster.internal/ubuntu plucky/universe s390x libgslcblas0 s390x 2.8+dfsg-5 [153 kB] 191s Get:2 http://ftpmaster.internal/ubuntu plucky/universe s390x libgsl28 s390x 2.8+dfsg-5 [1126 kB] 192s Get:3 http://ftpmaster.internal/ubuntu plucky/universe s390x pscan-tfbs s390x 1.2.2-4build2 [87.1 kB] 192s Fetched 1366 kB in 2s (799 kB/s) 193s Selecting previously unselected package libgslcblas0:s390x. 193s (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 ... 56326 files and directories currently installed.) 193s Preparing to unpack .../libgslcblas0_2.8+dfsg-5_s390x.deb ... 193s Unpacking libgslcblas0:s390x (2.8+dfsg-5) ... 193s Selecting previously unselected package libgsl28:s390x. 193s Preparing to unpack .../libgsl28_2.8+dfsg-5_s390x.deb ... 193s Unpacking libgsl28:s390x (2.8+dfsg-5) ... 193s Selecting previously unselected package pscan-tfbs. 193s Preparing to unpack .../pscan-tfbs_1.2.2-4build2_s390x.deb ... 193s Unpacking pscan-tfbs (1.2.2-4build2) ... 193s Setting up libgslcblas0:s390x (2.8+dfsg-5) ... 193s Setting up libgsl28:s390x (2.8+dfsg-5) ... 193s Setting up pscan-tfbs (1.2.2-4build2) ... 193s Processing triggers for man-db (2.13.0-1) ... 193s Processing triggers for libc-bin (2.41-1ubuntu2) ... 194s autopkgtest [17:01:49]: test run-unit-test: [----------------------- 194s Test 1 194s sh: 1: dos2unix: not found 194s 194s Reading matrix file(s)... 2 matrices acquired. 194s 194s Reading background sequence file... 1[SHORT TFBS MATRIX] 194s NFY 1 0.816888 0.816888 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 194s 1 0.944058 0.944058 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 194s PASS 194s Test 2 194s [SHORT TFBS MATRIX] 194s NFY 1 0.816888 0.816888 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 194s PASS 194s background sequences acquired. 194s Processing >NM_000546.3 Homo sapien (1) 194s Writing short matrix output...done 194s 194s sh: 1: dos2unix: not found 194s 194s Reading matrix file(s)... 1 matrices acquired. 194s 194s Reading background sequence file... 1 background sequences acquired. 194s Processing >NM_000546.3 Homo sapien (1) 194s Writing short matrix output...done 194s 194s autopkgtest [17:01:49]: test run-unit-test: -----------------------] 195s autopkgtest [17:01:50]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 195s run-unit-test PASS 195s autopkgtest [17:01:50]: @@@@@@@@@@@@@@@@@@@@ summary 195s run-unit-test PASS 200s nova [W] Using flock in prodstack6-s390x 200s Creating nova instance adt-plucky-s390x-pscan-tfbs-20250315-165834-juju-7f2275-prod-proposed-migration-environment-15-9eec5969-f06b-49d3-b55c-60ad8982911e from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 200s nova [W] Timed out waiting for 5530a31b-3185-41ad-bf2b-4bd609e3324c to get deleted.