0s autopkgtest [20:34:42]: starting date and time: 2024-11-23 20:34:42+0000 0s autopkgtest [20:34:42]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time 0s autopkgtest [20:34:42]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.mxfdtq5v/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade augur --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-9.secgroup --name adt-plucky-amd64-augur-20241123-203441-juju-7f2275-prod-proposed-migration-environment-2-319e1b7b-1fdd-465f-bb1c-7707ec04bc09 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-amd64 -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'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 49s autopkgtest [20:35:31]: testbed dpkg architecture: amd64 49s autopkgtest [20:35:31]: testbed apt version: 2.9.8 49s autopkgtest [20:35:31]: @@@@@@@@@@@@@@@@@@@@ test bed setup 50s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 51s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [930 kB] 51s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [54.8 kB] 51s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9704 B] 51s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.6 kB] 51s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [91.3 kB] 51s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [43.4 kB] 51s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2408 B] 51s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [40.1 kB] 51s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [295 kB] 51s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [806 kB] 51s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [5528 B] 51s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [20.0 kB] 51s Fetched 2386 kB in 1s (2656 kB/s) 51s Reading package lists... 54s Reading package lists... 54s Building dependency tree... 54s Reading state information... 54s Calculating upgrade... 54s The following package was automatically installed and is no longer required: 54s libsgutils2-1.46-2 54s Use 'sudo apt autoremove' to remove it. 54s The following NEW packages will be installed: 54s libsgutils2-1.48 54s The following packages will be upgraded: 54s amd64-microcode bash bpftrace curl debconf debconf-i18n distro-info 54s fwupd-signed gir1.2-girepository-2.0 gir1.2-glib-2.0 hostname 54s intel-microcode libaudit-common libaudit1 libcurl3t64-gnutls libcurl4t64 54s libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-data libpam-modules 54s libpam-modules-bin libpam-runtime libpam0g libplymouth5 libpython3-stdlib 54s libselinux1 libsemanage-common libsemanage2 linux-base lxd-installer 54s openssh-client openssh-server openssh-sftp-server plymouth 54s plymouth-theme-ubuntu-text python3 python3-blinker python3-dbus 54s python3-debconf python3-gi python3-jsonschema-specifications python3-minimal 54s python3-rpds-py python3-yaml sg3-utils sg3-utils-udev vim-common vim-tiny 54s xxd 55s 49 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 55s Need to get 19.9 MB of archives. 55s After this operation, 4441 kB of additional disk space will be used. 55s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 bash amd64 5.2.32-1ubuntu2 [918 kB] 55s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 hostname amd64 3.25 [11.1 kB] 55s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu1 [6578 B] 55s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu1 [53.9 kB] 55s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 debconf-i18n all 1.5.87ubuntu1 [204 kB] 55s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 55s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 55s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 55s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-debconf all 1.5.87ubuntu1 [4156 B] 55s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 debconf all 1.5.87ubuntu1 [124 kB] 56s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam0g amd64 1.5.3-7ubuntu4 [69.6 kB] 56s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu1 [86.9 kB] 56s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-modules-bin amd64 1.5.3-7ubuntu4 [53.7 kB] 56s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-modules amd64 1.5.3-7ubuntu4 [294 kB] 56s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 openssh-sftp-server amd64 1:9.9p1-3ubuntu2 [41.2 kB] 56s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 openssh-server amd64 1:9.9p1-3ubuntu2 [625 kB] 56s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 openssh-client amd64 1:9.9p1-3ubuntu2 [1080 kB] 56s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-runtime all 1.5.3-7ubuntu4 [40.8 kB] 56s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage-common all 3.7-2build1 [7186 B] 56s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage2 amd64 3.7-2build1 [105 kB] 56s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 distro-info amd64 1.12 [20.0 kB] 56s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.82.0-2 [25.3 kB] 56s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.82.2-3 [182 kB] 56s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.82.2-3 [1655 kB] 56s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.82.0-2 [88.7 kB] 56s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.82.2-3 [51.7 kB] 56s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build4 [110 kB] 56s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-3build1 [293 kB] 56s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build1 [187 kB] 56s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 vim-tiny amd64 2:9.1.0861-1ubuntu1 [1037 kB] 56s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 vim-common all 2:9.1.0861-1ubuntu1 [395 kB] 56s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 xxd amd64 2:9.1.0861-1ubuntu1 [67.8 kB] 56s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libplymouth5 amd64 24.004.60-2ubuntu3 [145 kB] 56s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 plymouth-theme-ubuntu-text amd64 24.004.60-2ubuntu3 [10.3 kB] 56s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 plymouth amd64 24.004.60-2ubuntu3 [140 kB] 56s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftrace amd64 0.21.2-2ubuntu3 [1787 kB] 56s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.9.1-2ubuntu3 [243 kB] 56s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.9.1-2ubuntu3 [420 kB] 56s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd-signed amd64 1.55+1.7-1 [30.6 kB] 56s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.9.1-2ubuntu3 [412 kB] 56s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libsgutils2-1.48 amd64 1.48-0ubuntu1 [124 kB] 56s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-base all 4.10.1ubuntu1 [34.8 kB] 56s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 lxd-installer all 10 [5264 B] 56s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-blinker all 1.9.0-1 [10.7 kB] 56s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-rpds-py amd64 0.21.0-2ubuntu1 [323 kB] 56s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jsonschema-specifications all 2023.12.1-2 [9116 B] 56s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 sg3-utils amd64 1.48-0ubuntu1 [1042 kB] 56s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 sg3-utils-udev all 1.48-0ubuntu1 [6608 B] 56s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 amd64-microcode amd64 3.20240820.1ubuntu1 [187 kB] 56s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 intel-microcode amd64 3.20241112.1ubuntu2 [7055 kB] 57s Preconfiguring packages ... 57s Fetched 19.9 MB in 2s (8699 kB/s) 57s (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 ... 75620 files and directories currently installed.) 57s Preparing to unpack .../bash_5.2.32-1ubuntu2_amd64.deb ... 57s Unpacking bash (5.2.32-1ubuntu2) over (5.2.32-1ubuntu1) ... 57s Setting up bash (5.2.32-1ubuntu2) ... 57s update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode 58s (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 ... 75620 files and directories currently installed.) 58s Preparing to unpack .../hostname_3.25_amd64.deb ... 58s Unpacking hostname (3.25) over (3.23+nmu2ubuntu2) ... 58s Setting up hostname (3.25) ... 58s (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 ... 75620 files and directories currently installed.) 58s Preparing to unpack .../libaudit-common_1%3a4.0.2-2ubuntu1_all.deb ... 58s Unpacking libaudit-common (1:4.0.2-2ubuntu1) over (1:4.0.1-1ubuntu2) ... 58s Setting up libaudit-common (1:4.0.2-2ubuntu1) ... 58s (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 ... 75620 files and directories currently installed.) 58s Preparing to unpack .../libaudit1_1%3a4.0.2-2ubuntu1_amd64.deb ... 58s Unpacking libaudit1:amd64 (1:4.0.2-2ubuntu1) over (1:4.0.1-1ubuntu2) ... 58s Setting up libaudit1:amd64 (1:4.0.2-2ubuntu1) ... 58s (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 ... 75620 files and directories currently installed.) 58s Preparing to unpack .../debconf-i18n_1.5.87ubuntu1_all.deb ... 58s Unpacking debconf-i18n (1.5.87ubuntu1) over (1.5.86ubuntu1) ... 58s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 58s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 58s Setting up python3-minimal (3.12.7-1) ... 58s (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 ... 75620 files and directories currently installed.) 58s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 58s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 58s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 58s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 58s Preparing to unpack .../python3-debconf_1.5.87ubuntu1_all.deb ... 58s Unpacking python3-debconf (1.5.87ubuntu1) over (1.5.86ubuntu1) ... 58s Preparing to unpack .../debconf_1.5.87ubuntu1_all.deb ... 58s Unpacking debconf (1.5.87ubuntu1) over (1.5.86ubuntu1) ... 58s Setting up debconf (1.5.87ubuntu1) ... 58s (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 ... 75620 files and directories currently installed.) 58s Preparing to unpack .../libpam0g_1.5.3-7ubuntu4_amd64.deb ... 58s Unpacking libpam0g:amd64 (1.5.3-7ubuntu4) over (1.5.3-7ubuntu2) ... 59s Setting up libpam0g:amd64 (1.5.3-7ubuntu4) ... 59s (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 ... 75620 files and directories currently installed.) 59s Preparing to unpack .../libselinux1_3.7-3ubuntu1_amd64.deb ... 59s Unpacking libselinux1:amd64 (3.7-3ubuntu1) over (3.5-2ubuntu5) ... 59s Setting up libselinux1:amd64 (3.7-3ubuntu1) ... 59s (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 ... 75620 files and directories currently installed.) 59s Preparing to unpack .../libpam-modules-bin_1.5.3-7ubuntu4_amd64.deb ... 59s Unpacking libpam-modules-bin (1.5.3-7ubuntu4) over (1.5.3-7ubuntu2) ... 59s Setting up libpam-modules-bin (1.5.3-7ubuntu4) ... 59s pam_namespace.service is a disabled or a static unit not running, not starting it. 59s (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 ... 75620 files and directories currently installed.) 59s Preparing to unpack .../libpam-modules_1.5.3-7ubuntu4_amd64.deb ... 59s Unpacking libpam-modules:amd64 (1.5.3-7ubuntu4) over (1.5.3-7ubuntu2) ... 59s Setting up libpam-modules:amd64 (1.5.3-7ubuntu4) ... 59s (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 ... 75620 files and directories currently installed.) 59s Preparing to unpack .../openssh-sftp-server_1%3a9.9p1-3ubuntu2_amd64.deb ... 59s Unpacking openssh-sftp-server (1:9.9p1-3ubuntu2) over (1:9.7p1-7ubuntu5) ... 59s Preparing to unpack .../openssh-server_1%3a9.9p1-3ubuntu2_amd64.deb ... 59s Unpacking openssh-server (1:9.9p1-3ubuntu2) over (1:9.7p1-7ubuntu5) ... 59s Preparing to unpack .../openssh-client_1%3a9.9p1-3ubuntu2_amd64.deb ... 59s Unpacking openssh-client (1:9.9p1-3ubuntu2) over (1:9.7p1-7ubuntu5) ... 59s Preparing to unpack .../libpam-runtime_1.5.3-7ubuntu4_all.deb ... 59s Unpacking libpam-runtime (1.5.3-7ubuntu4) over (1.5.3-7ubuntu2) ... 60s Setting up libpam-runtime (1.5.3-7ubuntu4) ... 60s (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 ... 75622 files and directories currently installed.) 60s Preparing to unpack .../libsemanage-common_3.7-2build1_all.deb ... 60s Unpacking libsemanage-common (3.7-2build1) over (3.5-1build6) ... 60s Setting up libsemanage-common (3.7-2build1) ... 60s (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 ... 75621 files and directories currently installed.) 60s Preparing to unpack .../libsemanage2_3.7-2build1_amd64.deb ... 60s Unpacking libsemanage2:amd64 (3.7-2build1) over (3.5-1build6) ... 60s Setting up libsemanage2:amd64 (3.7-2build1) ... 60s (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 ... 75621 files and directories currently installed.) 60s Preparing to unpack .../00-distro-info_1.12_amd64.deb ... 60s Unpacking distro-info (1.12) over (1.9) ... 60s Preparing to unpack .../01-gir1.2-girepository-2.0_1.82.0-2_amd64.deb ... 60s Unpacking gir1.2-girepository-2.0:amd64 (1.82.0-2) over (1.80.1-4) ... 60s Preparing to unpack .../02-gir1.2-glib-2.0_2.82.2-3_amd64.deb ... 60s Unpacking gir1.2-glib-2.0:amd64 (2.82.2-3) over (2.82.1-0ubuntu1) ... 60s Preparing to unpack .../03-libglib2.0-0t64_2.82.2-3_amd64.deb ... 60s Unpacking libglib2.0-0t64:amd64 (2.82.2-3) over (2.82.1-0ubuntu1) ... 60s Preparing to unpack .../04-libgirepository-1.0-1_1.82.0-2_amd64.deb ... 60s Unpacking libgirepository-1.0-1:amd64 (1.82.0-2) over (1.80.1-4) ... 60s Preparing to unpack .../05-libglib2.0-data_2.82.2-3_all.deb ... 60s Unpacking libglib2.0-data (2.82.2-3) over (2.82.1-0ubuntu1) ... 60s Preparing to unpack .../06-python3-dbus_1.3.2-5build4_amd64.deb ... 60s Unpacking python3-dbus (1.3.2-5build4) over (1.3.2-5build3) ... 60s Preparing to unpack .../07-python3-gi_3.50.0-3build1_amd64.deb ... 60s Unpacking python3-gi (3.50.0-3build1) over (3.50.0-3) ... 60s Preparing to unpack .../08-python3-yaml_6.0.2-1build1_amd64.deb ... 60s Unpacking python3-yaml (6.0.2-1build1) over (6.0.2-1) ... 60s Preparing to unpack .../09-vim-tiny_2%3a9.1.0861-1ubuntu1_amd64.deb ... 60s Unpacking vim-tiny (2:9.1.0861-1ubuntu1) over (2:9.1.0777-1ubuntu1) ... 60s Preparing to unpack .../10-vim-common_2%3a9.1.0861-1ubuntu1_all.deb ... 60s Unpacking vim-common (2:9.1.0861-1ubuntu1) over (2:9.1.0777-1ubuntu1) ... 60s Preparing to unpack .../11-xxd_2%3a9.1.0861-1ubuntu1_amd64.deb ... 60s Unpacking xxd (2:9.1.0861-1ubuntu1) over (2:9.1.0777-1ubuntu1) ... 60s Preparing to unpack .../12-libplymouth5_24.004.60-2ubuntu3_amd64.deb ... 60s Unpacking libplymouth5:amd64 (24.004.60-2ubuntu3) over (24.004.60-1ubuntu11) ... 60s Preparing to unpack .../13-plymouth-theme-ubuntu-text_24.004.60-2ubuntu3_amd64.deb ... 60s Unpacking plymouth-theme-ubuntu-text (24.004.60-2ubuntu3) over (24.004.60-1ubuntu11) ... 60s Preparing to unpack .../14-plymouth_24.004.60-2ubuntu3_amd64.deb ... 60s Unpacking plymouth (24.004.60-2ubuntu3) over (24.004.60-1ubuntu11) ... 60s Preparing to unpack .../15-bpftrace_0.21.2-2ubuntu3_amd64.deb ... 60s Unpacking bpftrace (0.21.2-2ubuntu3) over (0.21.2-2ubuntu2) ... 61s Preparing to unpack .../16-curl_8.9.1-2ubuntu3_amd64.deb ... 61s Unpacking curl (8.9.1-2ubuntu3) over (8.9.1-2ubuntu2) ... 61s Preparing to unpack .../17-libcurl4t64_8.9.1-2ubuntu3_amd64.deb ... 61s Unpacking libcurl4t64:amd64 (8.9.1-2ubuntu3) over (8.9.1-2ubuntu2) ... 61s Preparing to unpack .../18-fwupd-signed_1.55+1.7-1_amd64.deb ... 61s Unpacking fwupd-signed (1.55+1.7-1) over (1.54+1.6-1build1) ... 61s Preparing to unpack .../19-libcurl3t64-gnutls_8.9.1-2ubuntu3_amd64.deb ... 61s Unpacking libcurl3t64-gnutls:amd64 (8.9.1-2ubuntu3) over (8.9.1-2ubuntu2) ... 61s Selecting previously unselected package libsgutils2-1.48:amd64. 61s Preparing to unpack .../20-libsgutils2-1.48_1.48-0ubuntu1_amd64.deb ... 61s Unpacking libsgutils2-1.48:amd64 (1.48-0ubuntu1) ... 61s Preparing to unpack .../21-linux-base_4.10.1ubuntu1_all.deb ... 61s Unpacking linux-base (4.10.1ubuntu1) over (4.5ubuntu9) ... 61s Preparing to unpack .../22-lxd-installer_10_all.deb ... 61s Unpacking lxd-installer (10) over (9) ... 61s Preparing to unpack .../23-python3-blinker_1.9.0-1_all.deb ... 61s Unpacking python3-blinker (1.9.0-1) over (1.8.2-1) ... 61s Preparing to unpack .../24-python3-rpds-py_0.21.0-2ubuntu1_amd64.deb ... 61s Unpacking python3-rpds-py (0.21.0-2ubuntu1) over (0.20.0-0ubuntu3) ... 61s Preparing to unpack .../25-python3-jsonschema-specifications_2023.12.1-2_all.deb ... 61s Unpacking python3-jsonschema-specifications (2023.12.1-2) over (2023.12.1-1ubuntu1) ... 61s Preparing to unpack .../26-sg3-utils_1.48-0ubuntu1_amd64.deb ... 61s Unpacking sg3-utils (1.48-0ubuntu1) over (1.46-3ubuntu5) ... 61s Preparing to unpack .../27-sg3-utils-udev_1.48-0ubuntu1_all.deb ... 61s Unpacking sg3-utils-udev (1.48-0ubuntu1) over (1.46-3ubuntu5) ... 61s Preparing to unpack .../28-amd64-microcode_3.20240820.1ubuntu1_amd64.deb ... 61s Unpacking amd64-microcode (3.20240820.1ubuntu1) over (3.20240116.2+nmu1ubuntu1.1) ... 61s Preparing to unpack .../29-intel-microcode_3.20241112.1ubuntu2_amd64.deb ... 61s Unpacking intel-microcode (3.20241112.1ubuntu2) over (3.20240910.0ubuntu1) ... 61s Setting up distro-info (1.12) ... 61s Setting up linux-base (4.10.1ubuntu1) ... 61s Setting up libcurl4t64:amd64 (8.9.1-2ubuntu3) ... 61s Setting up bpftrace (0.21.2-2ubuntu3) ... 61s Setting up openssh-client (1:9.9p1-3ubuntu2) ... 61s Setting up intel-microcode (3.20241112.1ubuntu2) ... 61s intel-microcode: microcode will be updated at next boot 61s Setting up libcurl3t64-gnutls:amd64 (8.9.1-2ubuntu3) ... 61s Setting up fwupd-signed (1.55+1.7-1) ... 61s Setting up libsgutils2-1.48:amd64 (1.48-0ubuntu1) ... 61s Setting up debconf-i18n (1.5.87ubuntu1) ... 61s Setting up amd64-microcode (3.20240820.1ubuntu1) ... 61s amd64-microcode: microcode will be updated at next boot 61s Setting up xxd (2:9.1.0861-1ubuntu1) ... 61s Setting up libglib2.0-0t64:amd64 (2.82.2-3) ... 61s No schema files found: doing nothing. 61s Setting up libglib2.0-data (2.82.2-3) ... 61s Setting up vim-common (2:9.1.0861-1ubuntu1) ... 61s Setting up gir1.2-glib-2.0:amd64 (2.82.2-3) ... 61s Setting up lxd-installer (10) ... 62s Setting up libplymouth5:amd64 (24.004.60-2ubuntu3) ... 62s Setting up libgirepository-1.0-1:amd64 (1.82.0-2) ... 62s Setting up curl (8.9.1-2ubuntu3) ... 62s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 62s Setting up sg3-utils (1.48-0ubuntu1) ... 62s Setting up openssh-sftp-server (1:9.9p1-3ubuntu2) ... 62s Setting up openssh-server (1:9.9p1-3ubuntu2) ... 62s Installing new version of config file /etc/ssh/moduli ... 62s Replacing config file /etc/ssh/sshd_config with new version 63s Setting up plymouth (24.004.60-2ubuntu3) ... 63s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 63s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 70s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 70s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 71s Setting up python3 (3.12.7-1) ... 71s Setting up vim-tiny (2:9.1.0861-1ubuntu1) ... 71s Setting up sg3-utils-udev (1.48-0ubuntu1) ... 71s update-initramfs: deferring update (trigger activated) 71s Setting up plymouth-theme-ubuntu-text (24.004.60-2ubuntu3) ... 71s update-initramfs: deferring update (trigger activated) 71s Setting up gir1.2-girepository-2.0:amd64 (1.82.0-2) ... 71s Setting up python3-gi (3.50.0-3build1) ... 71s Setting up python3-rpds-py (0.21.0-2ubuntu1) ... 71s Setting up python3-jsonschema-specifications (2023.12.1-2) ... 71s Setting up python3-blinker (1.9.0-1) ... 71s Setting up python3-dbus (1.3.2-5build4) ... 71s Setting up python3-debconf (1.5.87ubuntu1) ... 72s Setting up python3-yaml (6.0.2-1build1) ... 72s Processing triggers for man-db (2.13.0-1) ... 73s Processing triggers for debianutils (5.21) ... 73s Processing triggers for install-info (7.1.1-1) ... 73s Processing triggers for initramfs-tools (0.142ubuntu35) ... 73s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 73s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 80s Processing triggers for libc-bin (2.40-1ubuntu3) ... 80s Processing triggers for ufw (0.36.2-8) ... 80s Reading package lists... 80s Building dependency tree... 80s Reading state information... 81s The following packages will be REMOVED: 81s libsgutils2-1.46-2* 81s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 81s After this operation, 294 kB disk space will be freed. 81s (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 ... 75656 files and directories currently installed.) 81s Removing libsgutils2-1.46-2:amd64 (1.46-3ubuntu5) ... 81s Processing triggers for libc-bin (2.40-1ubuntu3) ... 81s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 82s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 82s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 82s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 82s Reading package lists... 82s Reading package lists... 83s Building dependency tree... 83s Reading state information... 83s Calculating upgrade... 83s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 83s Reading package lists... 83s Building dependency tree... 83s Reading state information... 83s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 83s autopkgtest [20:36:05]: rebooting testbed after setup commands that affected boot 100s autopkgtest [20:36:22]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 103s autopkgtest [20:36:25]: @@@@@@@@@@@@@@@@@@@@ apt-source augur 106s Get:1 http://ftpmaster.internal/ubuntu plucky/universe augur 24.4.0-1 (dsc) [2754 B] 106s Get:2 http://ftpmaster.internal/ubuntu plucky/universe augur 24.4.0-1 (tar) [6802 kB] 106s Get:3 http://ftpmaster.internal/ubuntu plucky/universe augur 24.4.0-1 (diff) [16.5 kB] 106s gpgv: Signature made Wed May 22 16:59:51 2024 UTC 106s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 106s gpgv: issuer "emollier@debian.org" 106s gpgv: Can't check signature: No public key 106s dpkg-source: warning: cannot verify inline signature for ./augur_24.4.0-1.dsc: no acceptable signature found 106s autopkgtest [20:36:28]: testing package augur version 24.4.0-1 106s autopkgtest [20:36:28]: build not needed 108s autopkgtest [20:36:30]: test run-unit-test: preparing testbed 109s Reading package lists... 109s Building dependency tree... 109s Reading state information... 109s Starting pkgProblemResolver with broken count: 0 109s Starting 2 pkgProblemResolver with broken count: 0 109s Done 110s The following additional packages will be installed: 110s augur blt fasttree flake8 fontconfig-config fonts-dejavu-core 110s fonts-dejavu-mono fonts-lyx fonts-urw-base35 libamd3 libblas3 libcairo2 110s libcamd3 libccolamd3 libcholmod5 libcolamd3 libdeflate0 libdsdp-5.8t64 110s libfftw3-double3 libfontconfig1 libfontenc1 libgfortran5 libglpk40 libgomp1 110s libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b libimagequant0 libjbig0 110s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 110s liblcms2-2 liblerc4 libltdl7 libopenjp2-7 libpixman-1-0 110s libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 110s libsharpyuv0 libsuitesparseconfig7 libtcl8.6 libtiff6 libtk8.6 libumfpack6 110s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 110s libxrender1 libxslt1.1 libxss1 mafft mypy pigz python-matplotlib-data 110s python3-all python3-appdirs python3-asttokens python3-bcbio-gff 110s python3-biopython python3-boto3 python3-botocore python3-brotli 110s python3-cairo python3-contourpy python3-cvxopt python3-cycler 110s python3-dateutil python3-decorator python3-dendropy python3-executing 110s python3-flake8 python3-fonttools python3-freetype python3-freezegun 110s python3-fs python3-importlib-metadata python3-iniconfig python3-ipdb 110s python3-ipython python3-isodate python3-jedi python3-jmespath 110s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 110s python3-matplotlib-inline python3-mccabe python3-mpmath python3-mypy 110s python3-mypy-extensions python3-networkx python3-numpy python3-packaging 110s python3-pandas python3-pandas-lib python3-parso python3-pexpect python3-pil 110s python3-pil.imagetk python3-pluggy python3-prompt-toolkit python3-psutil 110s python3-ptyprocess python3-pure-eval python3-pycodestyle python3-pyfaidx 110s python3-pyfastx python3-pyflakes python3-pygtrie python3-pytest 110s python3-pytest-mock python3-reportlab python3-rlpycairo python3-s3transfer 110s python3-schedule python3-scipy python3-seaborn python3-six 110s python3-stack-data python3-sympy python3-tk python3-traitlets 110s python3-treetime python3-typeshed python3-tz python3-ufolib2 110s python3-unicodedata2 python3-wcwidth python3-xopen python3-zstandard 110s python3.12-tk python3.13 python3.13-minimal python3.13-tk raxml seqmagick 110s sgml-base tk8.6-blt2.5 unicode-data vcftools w3c-sgml-lib x11-common 110s xfonts-encodings xfonts-utils xml-core 110s Suggested packages: 110s blt-demo fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre libfftw3-bin 110s libfftw3-dev libiodbc2-dev default-libmysqlclient-dev gsl-ref-psdoc 110s | gsl-doc-pdf | gsl-doc-info | gsl-ref-html libjs-jquery-ui-docs 110s liblcms2-utils tcl8.6 tk8.6 mypy-doc bwa clustalo clustalw dialign dssp 110s emboss muscle3 phylip phyml prank probcons python3-mysqldb python3-mmtf 110s python3-rdflib python3-psycopg2 samtools t-coffee wise python-cvxopt-doc 110s python-cycler-doc python-ipython-doc python-lxml-doc cm-super-minimal dvipng 110s ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 110s librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi-cairo 110s python3-gobject python3-pyqt5 python3-sip python3-tornado 110s texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 110s python3-gdal python3-pydot python3-pygraphviz gcc gfortran python-numpy-doc 110s python3-dev python-pandas-doc python3-statsmodels python-pexpect-doc 110s python-pil-doc python-pygtrie-doc python-pytest-mock-doc pdf-viewer 110s python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm 110s python-scipy-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg 110s python-traitlets-doc python-zstandard-doc python3.13-venv python3.13-doc 110s binfmt-support sgml-base-doc debhelper 110s Recommended packages: 110s iqtree javascript-common blast2 libwww-perl lynx ruby python-biopython-doc 110s ncbi-blast+ python3-bs4 python3-cssselect python3-html5lib python3-orjson 110s python3-bottleneck python3-numexpr python3-odf python3-openpyxl 110s python3-tables python3-numba python3-olefile pyflakes3 fonts-dejavu-extra 110s g++ | c++-compiler isympy-common tabix 110s The following NEW packages will be installed: 110s augur autopkgtest-satdep blt fasttree flake8 fontconfig-config 110s fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 libamd3 110s libblas3 libcairo2 libcamd3 libccolamd3 libcholmod5 libcolamd3 libdeflate0 110s libdsdp-5.8t64 libfftw3-double3 libfontconfig1 libfontenc1 libgfortran5 110s libglpk40 libgomp1 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b 110s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 110s liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libltdl7 libopenjp2-7 110s libpixman-1-0 libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 110s libraqm0 libsharpyuv0 libsuitesparseconfig7 libtcl8.6 libtiff6 libtk8.6 110s libumfpack6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 110s libxft2 libxrender1 libxslt1.1 libxss1 mafft mypy pigz 110s python-matplotlib-data python3-all python3-appdirs python3-asttokens 110s python3-bcbio-gff python3-biopython python3-boto3 python3-botocore 110s python3-brotli python3-cairo python3-contourpy python3-cvxopt python3-cycler 110s python3-dateutil python3-decorator python3-dendropy python3-executing 110s python3-flake8 python3-fonttools python3-freetype python3-freezegun 110s python3-fs python3-importlib-metadata python3-iniconfig python3-ipdb 110s python3-ipython python3-isodate python3-jedi python3-jmespath 110s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 110s python3-matplotlib-inline python3-mccabe python3-mpmath python3-mypy 110s python3-mypy-extensions python3-networkx python3-numpy python3-packaging 110s python3-pandas python3-pandas-lib python3-parso python3-pexpect python3-pil 110s python3-pil.imagetk python3-pluggy python3-prompt-toolkit python3-psutil 110s python3-ptyprocess python3-pure-eval python3-pycodestyle python3-pyfaidx 110s python3-pyfastx python3-pyflakes python3-pygtrie python3-pytest 110s python3-pytest-mock python3-reportlab python3-rlpycairo python3-s3transfer 110s python3-schedule python3-scipy python3-seaborn python3-six 110s python3-stack-data python3-sympy python3-tk python3-traitlets 110s python3-treetime python3-typeshed python3-tz python3-ufolib2 110s python3-unicodedata2 python3-wcwidth python3-xopen python3-zstandard 110s python3.12-tk python3.13 python3.13-minimal python3.13-tk raxml seqmagick 110s sgml-base tk8.6-blt2.5 unicode-data vcftools w3c-sgml-lib x11-common 110s xfonts-encodings xfonts-utils xml-core 110s 0 upgraded, 157 newly installed, 0 to remove and 0 not upgraded. 110s Need to get 146 MB/146 MB of archives. 110s After this operation, 757 MB of additional disk space will be used. 110s Get:1 /tmp/autopkgtest.qYTrYA/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [756 B] 110s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB] 111s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB] 111s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 111s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 pigz amd64 2.8-1 [65.6 kB] 111s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 111s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 111s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 111s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11ubuntu1 [5319 kB] 111s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1085 kB] 111s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 111s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 111s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 111s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 111s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 111s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 111s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 112s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 112s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 112s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 112s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 112s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 112s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.15-1 [862 kB] 112s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.7-3 [116 kB] 112s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.0-2 [106 kB] 112s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 112s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 112s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tk amd64 3.12.7-1 [9752 B] 112s Get:29 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 10.4.0-1ubuntu2 [9568 B] 112s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 112s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 112s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 112s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 112s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 112s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 112s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 112s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 112s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 112s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 112s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 112s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 112s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 112s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 112s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 112s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 112s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 112s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu2 [580 kB] 112s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 112s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 112s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 112s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 112s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2build1 [143 kB] 112s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 112s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 112s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 112s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 112s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 112s Get:58 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.84+dfsg-4build1 [1719 kB] 112s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 112s Get:60 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-bcbio-gff all 0.7.1-2 [33.9 kB] 112s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libsuitesparseconfig7 amd64 1:7.8.3+dfsg-2 [13.4 kB] 112s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamd3 amd64 1:7.8.3+dfsg-2 [31.1 kB] 112s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcamd3 amd64 1:7.8.3+dfsg-2 [27.6 kB] 112s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 libccolamd3 amd64 1:7.8.3+dfsg-2 [27.5 kB] 112s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 libcolamd3 amd64 1:7.8.3+dfsg-2 [19.5 kB] 112s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcholmod5 amd64 1:7.8.3+dfsg-2 [876 kB] 112s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 libdsdp-5.8t64 amd64 5.8-10.1build1 [199 kB] 112s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libfftw3-double3 amd64 3.3.10-1ubuntu4 [839 kB] 112s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 libltdl7 amd64 2.4.7-8 [43.9 kB] 112s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 libglpk40 amd64 5.0-1build2 [369 kB] 112s Get:71 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgslcblas0 amd64 2.8+dfsg-5 [290 kB] 112s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgsl28 amd64 2.8+dfsg-5 [1285 kB] 112s Get:73 http://ftpmaster.internal/ubuntu plucky/universe amd64 libumfpack6 amd64 1:7.8.3+dfsg-2 [337 kB] 112s Get:74 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cvxopt amd64 1.3.0+dfsg-1build8 [296 kB] 112s Get:75 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-isodate all 0.7.0-1 [18.6 kB] 112s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 113s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB] 113s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-3 [80.2 kB] 113s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 113s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5ubuntu1 [8271 kB] 113s Get:81 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5ubuntu1 [3112 kB] 113s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-importlib-metadata all 8.5.0-1 [20.7 kB] 113s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 113s Get:84 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyfastx amd64 2.1.0-2 [56.7 kB] 113s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 113s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 113s Get:87 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5ubuntu1 [21.7 MB] 114s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 114s Get:89 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 114s Get:90 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.2.1-1 [171 kB] 114s Get:91 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3ubuntu1 [2928 kB] 114s Get:92 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.0-2build1 [271 kB] 114s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 114s Get:94 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build3 [368 kB] 114s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 114s Get:96 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-4 [91.3 kB] 114s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu1 [169 kB] 114s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.0-1build1 [1834 kB] 114s Get:99 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build5 [27.5 kB] 114s Get:100 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 114s Get:101 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB] 114s Get:102 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 114s Get:103 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build2 [360 kB] 114s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB] 115s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB] 115s Get:106 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B] 115s Get:107 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 115s Get:108 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.55.0-3 [1759 kB] 115s Get:109 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-2build1 [70.3 kB] 115s Get:110 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 115s Get:111 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3ubuntu1 [4691 kB] 115s Get:112 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-treetime all 0.11.4-1 [941 kB] 115s Get:113 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-xopen all 1.7.0-2 [17.0 kB] 115s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jmespath all 1.0.1-1 [21.3 kB] 115s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-botocore all 1.34.46+repack-1ubuntu1 [6211 kB] 115s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-s3transfer all 0.10.1-1ubuntu2 [54.3 kB] 115s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-boto3 all 1.34.46+dfsg-1ubuntu1 [72.5 kB] 115s Get:118 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-dendropy all 4.6.1-1 [278 kB] 115s Get:119 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-schedule all 1.2.2-1 [12.2 kB] 115s Get:120 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-seaborn all 0.13.2-4 [225 kB] 115s Get:121 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-zstandard amd64 0.23.0-2build1 [419 kB] 116s Get:122 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pygtrie all 2.2-2 [16.0 kB] 116s Get:123 http://ftpmaster.internal/ubuntu plucky/universe amd64 seqmagick all 0.8.6-3 [38.6 kB] 116s Get:124 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-parso all 0.8.3-1 [67.2 kB] 116s Get:125 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-typeshed all 0.0~git20231111.6764465-3 [1274 kB] 116s Get:126 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-jedi all 0.19.1+ds1-1 [693 kB] 116s Get:127 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 116s Get:128 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib-inline all 0.1.6-2 [8784 B] 116s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-wcwidth all 0.2.13+dfsg1-1 [26.3 kB] 116s Get:130 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-prompt-toolkit all 3.0.48-1 [256 kB] 116s Get:131 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-asttokens all 2.4.1-2 [20.8 kB] 116s Get:132 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-executing all 2.1.0-0.1 [24.4 kB] 116s Get:133 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pure-eval all 0.2.3-1 [11.4 kB] 116s Get:134 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-stack-data all 0.6.3-1 [22.0 kB] 116s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-ptyprocess all 0.7.0-6 [14.8 kB] 116s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pexpect all 4.9-3 [48.1 kB] 116s Get:137 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ipython all 8.29.0-1 [569 kB] 116s Get:138 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ipdb all 0.13.13-2 [15.4 kB] 116s Get:139 http://ftpmaster.internal/ubuntu plucky/universe amd64 mafft amd64 7.505-1 [795 kB] 116s Get:140 http://ftpmaster.internal/ubuntu plucky/universe amd64 raxml amd64 8.2.13+dfsg-1 [1640 kB] 116s Get:141 http://ftpmaster.internal/ubuntu plucky/universe amd64 fasttree amd64 2.1.11-2 [174 kB] 116s Get:142 http://ftpmaster.internal/ubuntu plucky/universe amd64 vcftools amd64 0.1.16-3 [393 kB] 116s Get:143 http://ftpmaster.internal/ubuntu plucky/universe amd64 augur all 24.4.0-1 [238 kB] 116s Get:144 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mccabe all 0.7.0-1 [8678 B] 116s Get:145 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pycodestyle all 2.12.1-1 [30.1 kB] 116s Get:146 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyflakes all 3.2.0-2 [52.9 kB] 116s Get:147 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-flake8 all 7.1.1-2 [44.1 kB] 116s Get:148 http://ftpmaster.internal/ubuntu plucky/universe amd64 flake8 all 7.1.1-2 [6444 B] 116s Get:149 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mypy-extensions all 1.0.0-1 [6148 B] 116s Get:150 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-psutil amd64 5.9.8-2build3 [196 kB] 116s Get:151 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mypy amd64 1.13.0-1build1 [15.7 MB] 116s Get:152 http://ftpmaster.internal/ubuntu plucky/universe amd64 mypy all 1.13.0-1build1 [24.9 kB] 116s Get:153 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freezegun all 1.5.1-1.1 [15.9 kB] 116s Get:154 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 116s Get:155 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 116s Get:156 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.3-1 [251 kB] 116s Get:157 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest-mock all 3.14.0-2 [11.7 kB] 117s Fetched 146 MB in 7s (22.4 MB/s) 117s Selecting previously unselected package libpython3.13-minimal:amd64. 117s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75651 files and directories currently installed.) 117s Preparing to unpack .../000-libpython3.13-minimal_3.13.0-2_amd64.deb ... 117s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... 117s Selecting previously unselected package python3.13-minimal. 117s Preparing to unpack .../001-python3.13-minimal_3.13.0-2_amd64.deb ... 117s Unpacking python3.13-minimal (3.13.0-2) ... 117s Selecting previously unselected package sgml-base. 117s Preparing to unpack .../002-sgml-base_1.31_all.deb ... 117s Unpacking sgml-base (1.31) ... 117s Selecting previously unselected package pigz. 117s Preparing to unpack .../003-pigz_2.8-1_amd64.deb ... 117s Unpacking pigz (2.8-1) ... 117s Selecting previously unselected package libblas3:amd64. 117s Preparing to unpack .../004-libblas3_3.12.0-3build2_amd64.deb ... 117s Unpacking libblas3:amd64 (3.12.0-3build2) ... 117s Selecting previously unselected package libgfortran5:amd64. 117s Preparing to unpack .../005-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 117s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 117s Selecting previously unselected package liblapack3:amd64. 117s Preparing to unpack .../006-liblapack3_3.12.0-3build2_amd64.deb ... 117s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 117s Selecting previously unselected package python3-numpy. 117s Preparing to unpack .../007-python3-numpy_1%3a1.26.4+ds-11ubuntu1_amd64.deb ... 117s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 118s Selecting previously unselected package libtcl8.6:amd64. 118s Preparing to unpack .../008-libtcl8.6_8.6.15+dfsg-2_amd64.deb ... 118s Unpacking libtcl8.6:amd64 (8.6.15+dfsg-2) ... 118s Selecting previously unselected package fonts-dejavu-mono. 118s Preparing to unpack .../009-fonts-dejavu-mono_2.37-8_all.deb ... 118s Unpacking fonts-dejavu-mono (2.37-8) ... 118s Selecting previously unselected package fonts-dejavu-core. 118s Preparing to unpack .../010-fonts-dejavu-core_2.37-8_all.deb ... 118s Unpacking fonts-dejavu-core (2.37-8) ... 118s Selecting previously unselected package libfontenc1:amd64. 118s Preparing to unpack .../011-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 118s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 118s Selecting previously unselected package x11-common. 118s Preparing to unpack .../012-x11-common_1%3a7.7+23ubuntu3_all.deb ... 118s Unpacking x11-common (1:7.7+23ubuntu3) ... 118s Selecting previously unselected package xfonts-encodings. 118s Preparing to unpack .../013-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 118s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 118s Selecting previously unselected package xfonts-utils. 118s Preparing to unpack .../014-xfonts-utils_1%3a7.7+7_amd64.deb ... 118s Unpacking xfonts-utils (1:7.7+7) ... 118s Selecting previously unselected package fonts-urw-base35. 118s Preparing to unpack .../015-fonts-urw-base35_20200910-8_all.deb ... 118s Unpacking fonts-urw-base35 (20200910-8) ... 118s Selecting previously unselected package fontconfig-config. 118s Preparing to unpack .../016-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 118s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 118s Selecting previously unselected package libfontconfig1:amd64. 118s Preparing to unpack .../017-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 118s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 118s Selecting previously unselected package libxrender1:amd64. 118s Preparing to unpack .../018-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 118s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 118s Selecting previously unselected package libxft2:amd64. 118s Preparing to unpack .../019-libxft2_2.3.6-1build1_amd64.deb ... 118s Unpacking libxft2:amd64 (2.3.6-1build1) ... 118s Selecting previously unselected package libxss1:amd64. 118s Preparing to unpack .../020-libxss1_1%3a1.2.3-1build3_amd64.deb ... 118s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 118s Selecting previously unselected package libtk8.6:amd64. 118s Preparing to unpack .../021-libtk8.6_8.6.15-1_amd64.deb ... 118s Unpacking libtk8.6:amd64 (8.6.15-1) ... 118s Selecting previously unselected package python3.12-tk. 118s Preparing to unpack .../022-python3.12-tk_3.12.7-3_amd64.deb ... 118s Unpacking python3.12-tk (3.12.7-3) ... 118s Selecting previously unselected package python3.13-tk. 118s Preparing to unpack .../023-python3.13-tk_3.13.0-2_amd64.deb ... 118s Unpacking python3.13-tk (3.13.0-2) ... 118s Selecting previously unselected package tk8.6-blt2.5. 118s Preparing to unpack .../024-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 118s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 118s Selecting previously unselected package blt. 118s Preparing to unpack .../025-blt_2.5.3+dfsg-7build1_amd64.deb ... 118s Unpacking blt (2.5.3+dfsg-7build1) ... 118s Selecting previously unselected package python3-tk:amd64. 118s Preparing to unpack .../026-python3-tk_3.12.7-1_amd64.deb ... 118s Unpacking python3-tk:amd64 (3.12.7-1) ... 118s Selecting previously unselected package python3-pil.imagetk:amd64. 118s Preparing to unpack .../027-python3-pil.imagetk_10.4.0-1ubuntu2_amd64.deb ... 118s Unpacking python3-pil.imagetk:amd64 (10.4.0-1ubuntu2) ... 118s Selecting previously unselected package libgomp1:amd64. 118s Preparing to unpack .../028-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 118s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 118s Selecting previously unselected package libimagequant0:amd64. 119s Preparing to unpack .../029-libimagequant0_2.18.0-1build1_amd64.deb ... 119s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 119s Selecting previously unselected package libjpeg-turbo8:amd64. 119s Preparing to unpack .../030-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 119s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 119s Selecting previously unselected package libjpeg8:amd64. 119s Preparing to unpack .../031-libjpeg8_8c-2ubuntu11_amd64.deb ... 119s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 119s Selecting previously unselected package liblcms2-2:amd64. 119s Preparing to unpack .../032-liblcms2-2_2.16-2_amd64.deb ... 119s Unpacking liblcms2-2:amd64 (2.16-2) ... 119s Selecting previously unselected package libopenjp2-7:amd64. 119s Preparing to unpack .../033-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ... 119s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 119s Selecting previously unselected package libgraphite2-3:amd64. 119s Preparing to unpack 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liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 119s Selecting previously unselected package libsharpyuv0:amd64. 119s Preparing to unpack .../040-libsharpyuv0_1.4.0-0.1_amd64.deb ... 119s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 119s Selecting previously unselected package libwebp7:amd64. 119s Preparing to unpack .../041-libwebp7_1.4.0-0.1_amd64.deb ... 119s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 119s Selecting previously unselected package libtiff6:amd64. 119s Preparing to unpack .../042-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 119s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 119s Selecting previously unselected package libwebpdemux2:amd64. 119s Preparing to unpack .../043-libwebpdemux2_1.4.0-0.1_amd64.deb ... 119s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 119s Selecting previously unselected package libwebpmux3:amd64. 119s Preparing to unpack .../044-libwebpmux3_1.4.0-0.1_amd64.deb ... 119s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 119s Selecting previously unselected package python3-pil:amd64. 119s Preparing to unpack .../045-python3-pil_10.4.0-1ubuntu2_amd64.deb ... 119s Unpacking python3-pil:amd64 (10.4.0-1ubuntu2) ... 119s Selecting previously unselected package libpixman-1-0:amd64. 119s Preparing to unpack .../046-libpixman-1-0_0.44.0-3_amd64.deb ... 119s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 119s Selecting previously unselected package libxcb-render0:amd64. 119s Preparing to unpack .../047-libxcb-render0_1.17.0-2_amd64.deb ... 119s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 119s Selecting previously unselected package libxcb-shm0:amd64. 119s Preparing to unpack .../048-libxcb-shm0_1.17.0-2_amd64.deb ... 119s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 119s Selecting previously unselected package libcairo2:amd64. 119s Preparing to unpack .../049-libcairo2_1.18.2-2_amd64.deb ... 119s Unpacking libcairo2:amd64 (1.18.2-2) ... 119s Selecting previously unselected package python3-cairo. 119s Preparing to unpack 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python3-biopython. 119s Preparing to unpack .../056-python3-biopython_1.84+dfsg-4build1_amd64.deb ... 119s Unpacking python3-biopython (1.84+dfsg-4build1) ... 119s Selecting previously unselected package python3-six. 119s Preparing to unpack .../057-python3-six_1.16.0-7_all.deb ... 119s Unpacking python3-six (1.16.0-7) ... 119s Selecting previously unselected package python3-bcbio-gff. 119s Preparing to unpack .../058-python3-bcbio-gff_0.7.1-2_all.deb ... 119s Unpacking python3-bcbio-gff (0.7.1-2) ... 119s Selecting previously unselected package libsuitesparseconfig7:amd64. 119s Preparing to unpack .../059-libsuitesparseconfig7_1%3a7.8.3+dfsg-2_amd64.deb ... 119s Unpacking libsuitesparseconfig7:amd64 (1:7.8.3+dfsg-2) ... 119s Selecting previously unselected package libamd3:amd64. 119s Preparing to unpack .../060-libamd3_1%3a7.8.3+dfsg-2_amd64.deb ... 119s Unpacking libamd3:amd64 (1:7.8.3+dfsg-2) ... 119s Selecting previously unselected package libcamd3:amd64. 119s Preparing to unpack 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(1:7.8.3+dfsg-2) ... 120s Selecting previously unselected package python3-cvxopt. 120s Preparing to unpack .../072-python3-cvxopt_1.3.0+dfsg-1build8_amd64.deb ... 120s Unpacking python3-cvxopt (1.3.0+dfsg-1build8) ... 120s Selecting previously unselected package python3-isodate. 120s Preparing to unpack .../073-python3-isodate_0.7.0-1_all.deb ... 120s Unpacking python3-isodate (0.7.0-1) ... 120s Selecting previously unselected package python3-networkx. 120s Preparing to unpack .../074-python3-networkx_3.2.1-4ubuntu1_all.deb ... 120s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 120s Selecting previously unselected package python3-packaging. 120s Preparing to unpack .../075-python3-packaging_24.2-1_all.deb ... 120s Unpacking python3-packaging (24.2-1) ... 120s Selecting previously unselected package python3-dateutil. 120s Preparing to unpack .../076-python3-dateutil_2.9.0-3_all.deb ... 120s Unpacking python3-dateutil (2.9.0-3) ... 120s Selecting previously unselected package python3-tz. 120s Preparing to unpack .../077-python3-tz_2024.1-2_all.deb ... 120s Unpacking python3-tz (2024.1-2) ... 120s Selecting previously unselected package python3-pandas-lib:amd64. 120s Preparing to unpack .../078-python3-pandas-lib_2.2.3+dfsg-5ubuntu1_amd64.deb ... 120s Unpacking python3-pandas-lib:amd64 (2.2.3+dfsg-5ubuntu1) ... 121s Selecting previously unselected package python3-pandas. 121s Preparing to unpack .../079-python3-pandas_2.2.3+dfsg-5ubuntu1_all.deb ... 121s Unpacking python3-pandas (2.2.3+dfsg-5ubuntu1) ... 121s Selecting previously unselected package python3-importlib-metadata. 121s Preparing to unpack .../080-python3-importlib-metadata_8.5.0-1_all.deb ... 121s Unpacking python3-importlib-metadata (8.5.0-1) ... 121s Selecting previously unselected package python3-pyfaidx. 121s Preparing to unpack .../081-python3-pyfaidx_0.8.1.3-1_all.deb ... 121s Unpacking python3-pyfaidx (0.8.1.3-1) ... 121s Selecting previously unselected package python3-pyfastx. 121s Preparing to unpack .../082-python3-pyfastx_2.1.0-2_amd64.deb ... 121s Unpacking python3-pyfastx (2.1.0-2) ... 121s Selecting previously unselected package python3-decorator. 121s Preparing to unpack .../083-python3-decorator_5.1.1-5_all.deb ... 121s Unpacking python3-decorator (5.1.1-5) ... 121s Selecting previously unselected package liblbfgsb0:amd64. 121s Preparing to unpack .../084-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 121s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 121s Selecting previously unselected package python3-scipy. 121s Preparing to unpack .../085-python3-scipy_1.13.1-5ubuntu1_amd64.deb ... 121s Unpacking python3-scipy (1.13.1-5ubuntu1) ... 121s Selecting previously unselected package libjs-jquery. 121s Preparing to unpack .../086-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 121s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 122s Selecting previously unselected package libjs-jquery-ui. 122s Preparing to unpack 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python3-brotli (1.1.0-2build3) ... 122s Selecting previously unselected package python3-appdirs. 122s Preparing to unpack .../093-python3-appdirs_1.4.4-4_all.deb ... 122s Unpacking python3-appdirs (1.4.4-4) ... 122s Selecting previously unselected package python3-fs. 122s Preparing to unpack .../094-python3-fs_2.4.16-4_all.deb ... 122s Unpacking python3-fs (2.4.16-4) ... 122s Selecting previously unselected package libxslt1.1:amd64. 122s Preparing to unpack .../095-libxslt1.1_1.1.39-0exp1ubuntu1_amd64.deb ... 122s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ... 122s Selecting previously unselected package python3-lxml:amd64. 122s Preparing to unpack .../096-python3-lxml_5.3.0-1build1_amd64.deb ... 122s Unpacking python3-lxml:amd64 (5.3.0-1build1) ... 122s Selecting previously unselected package python3-lz4. 122s Preparing to unpack .../097-python3-lz4_4.0.2+dfsg-1build5_amd64.deb ... 122s Unpacking python3-lz4 (4.0.2+dfsg-1build5) ... 122s Selecting previously unselected package python3-mpmath. 122s Preparing to unpack .../098-python3-mpmath_1.3.0-1_all.deb ... 122s Unpacking python3-mpmath (1.3.0-1) ... 122s Selecting previously unselected package python3-sympy. 122s Preparing to unpack .../099-python3-sympy_1.13.3-1_all.deb ... 122s Unpacking python3-sympy (1.13.3-1) ... 122s Selecting previously unselected package python3-ufolib2. 122s Preparing to unpack .../100-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 122s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 122s Selecting previously unselected package python3-unicodedata2. 122s Preparing to unpack .../101-python3-unicodedata2_15.1.0+ds-1build2_amd64.deb ... 122s Unpacking python3-unicodedata2 (15.1.0+ds-1build2) ... 122s Selecting previously unselected package libpython3.13-stdlib:amd64. 122s Preparing to unpack .../102-libpython3.13-stdlib_3.13.0-2_amd64.deb ... 122s Unpacking libpython3.13-stdlib:amd64 (3.13.0-2) ... 123s Selecting previously unselected package python3.13. 123s Preparing to unpack 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... 123s Selecting previously unselected package python3-matplotlib. 123s Preparing to unpack .../109-python3-matplotlib_3.8.3-3ubuntu1_amd64.deb ... 123s Unpacking python3-matplotlib (3.8.3-3ubuntu1) ... 123s Selecting previously unselected package python3-treetime. 123s Preparing to unpack .../110-python3-treetime_0.11.4-1_all.deb ... 123s Unpacking python3-treetime (0.11.4-1) ... 123s Selecting previously unselected package python3-xopen. 123s Preparing to unpack .../111-python3-xopen_1.7.0-2_all.deb ... 123s Unpacking python3-xopen (1.7.0-2) ... 123s Selecting previously unselected package python3-jmespath. 123s Preparing to unpack .../112-python3-jmespath_1.0.1-1_all.deb ... 123s Unpacking python3-jmespath (1.0.1-1) ... 123s Selecting previously unselected package python3-botocore. 123s Preparing to unpack .../113-python3-botocore_1.34.46+repack-1ubuntu1_all.deb ... 123s Unpacking python3-botocore (1.34.46+repack-1ubuntu1) ... 124s Selecting previously unselected package python3-s3transfer. 124s Preparing to unpack .../114-python3-s3transfer_0.10.1-1ubuntu2_all.deb ... 124s Unpacking python3-s3transfer (0.10.1-1ubuntu2) ... 124s Selecting previously unselected package python3-boto3. 124s Preparing to unpack .../115-python3-boto3_1.34.46+dfsg-1ubuntu1_all.deb ... 124s Unpacking python3-boto3 (1.34.46+dfsg-1ubuntu1) ... 124s Selecting previously unselected package python3-dendropy. 124s Preparing to unpack .../116-python3-dendropy_4.6.1-1_all.deb ... 124s Unpacking python3-dendropy (4.6.1-1) ... 124s Selecting previously unselected package python3-schedule. 124s Preparing to unpack .../117-python3-schedule_1.2.2-1_all.deb ... 124s Unpacking python3-schedule (1.2.2-1) ... 124s Selecting previously unselected package python3-seaborn. 124s Preparing to unpack .../118-python3-seaborn_0.13.2-4_all.deb ... 124s Unpacking python3-seaborn (0.13.2-4) ... 124s Selecting previously unselected package python3-zstandard. 124s Preparing to unpack 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(1:7.8.3+dfsg-2) ... 171s Setting up python3-ipdb (0.13.13-2) ... 171s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 171s Setting up python3-cairo (1.26.1-2build1) ... 171s Setting up python3-cvxopt (1.3.0+dfsg-1build8) ... 171s Setting up blt (2.5.3+dfsg-7build1) ... 171s Setting up python3-tk:amd64 (3.12.7-1) ... 172s Setting up python3-pil.imagetk:amd64 (10.4.0-1ubuntu2) ... 172s Setting up python3-rlpycairo (0.3.0-3) ... 172s Setting up python3-reportlab (4.2.5-1) ... 173s Setting up python3-fonttools (4.55.0-3) ... 174s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 175s Setting up python3-matplotlib (3.8.3-3ubuntu1) ... 177s Setting up python3-seaborn (0.13.2-4) ... 177s Processing triggers for systemd (256.5-2ubuntu4) ... 177s Processing triggers for man-db (2.13.0-1) ... 178s Processing triggers for libc-bin (2.40-1ubuntu3) ... 178s Processing triggers for sgml-base (1.31) ... 178s Setting up w3c-sgml-lib (1.3-3) ... 201s Setting up python3-biopython (1.84+dfsg-4build1) ... 203s Setting up python3-treetime (0.11.4-1) ... 203s Setting up seqmagick (0.8.6-3) ... 203s Setting up python3-bcbio-gff (0.7.1-2) ... 203s Setting up augur (24.4.0-1) ... 203s Setting up autopkgtest-satdep (0) ... 208s (Reading database ... 103599 files and directories currently installed.) 208s Removing autopkgtest-satdep (0) ... 209s autopkgtest [20:38:11]: test run-unit-test: [----------------------- 209s ============================= test session starts ============================== 209s platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.13 209s cachedir: .pytest_cache 209s rootdir: /tmp/autopkgtest.qYTrYA/build.5Qk/src 209s plugins: mock-3.14.0, typeguard-4.4.1 211s collecting ... collected 12 items / 25 errors 211s 211s ==================================== ERRORS ==================================== 211s _____________ ERROR collecting tests/dates/test_ambiguous_date.py ______________ 211s ImportError while importing test module '/tmp/autopkgtest.qYTrYA/build.5Qk/src/tests/dates/test_ambiguous_date.py'. 211s Hint: make sure your test modules/packages have valid Python names. 211s Traceback: 211s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 211s return _bootstrap._gcd_import(name[level:], package, level) 211s tests/dates/test_ambiguous_date.py:3: in 211s from augur.dates import ambiguous_date 211s augur/__init__.py:15: in 211s from .io.print import print_err 211s augur/io/__init__.py:6: in 211s from .metadata import read_metadata # noqa: F401 211s augur/io/metadata.py:5: in 211s import pyfastx 211s E ModuleNotFoundError: No module named 'pyfastx' 211s __________________ ERROR collecting tests/dates/test_dates.py __________________ 211s ImportError while importing test module '/tmp/autopkgtest.qYTrYA/build.5Qk/src/tests/dates/test_dates.py'. 211s Hint: make sure your test modules/packages have valid Python names. 211s Traceback: 211s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 211s return _bootstrap._gcd_import(name[level:], package, level) 211s tests/dates/test_dates.py:4: in 211s from augur import dates 211s augur/__init__.py:15: in 211s from .io.print import print_err 211s augur/io/__init__.py:6: in 211s from .metadata import read_metadata # noqa: F401 211s augur/io/metadata.py:5: in 211s import pyfastx 211s E ModuleNotFoundError: No module named 'pyfastx' 211s _____________ ERROR collecting tests/filter/test_relative_dates.py _____________ 211s ImportError while importing test module '/tmp/autopkgtest.qYTrYA/build.5Qk/src/tests/filter/test_relative_dates.py'. 211s Hint: make sure your test modules/packages have valid Python names. 211s Traceback: 211s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 211s return _bootstrap._gcd_import(name[level:], package, level) 211s tests/filter/test_relative_dates.py:12: in 211s from augur.filter import register_arguments 211s augur/__init__.py:15: in 211s from .io.print import print_err 211s augur/io/__init__.py:6: in 211s from .metadata import read_metadata # noqa: F401 211s augur/io/metadata.py:5: in 211s import pyfastx 211s E ModuleNotFoundError: No module named 'pyfastx' 211s _______________ ERROR collecting tests/filter/test_subsample.py ________________ 211s ImportError while importing test module '/tmp/autopkgtest.qYTrYA/build.5Qk/src/tests/filter/test_subsample.py'. 211s Hint: make sure your test modules/packages have valid Python names. 211s Traceback: 211s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 211s return _bootstrap._gcd_import(name[level:], package, level) 211s tests/filter/test_subsample.py:4: in 211s import augur.filter.subsample 211s augur/__init__.py:15: in 211s from .io.print import print_err 211s augur/io/__init__.py:6: in 211s from .metadata import read_metadata # noqa: F401 211s augur/io/metadata.py:5: in 211s import pyfastx 211s E ModuleNotFoundError: No module named 'pyfastx' 211s ____________________ ERROR collecting tests/io/test_file.py ____________________ 211s ImportError while importing test module '/tmp/autopkgtest.qYTrYA/build.5Qk/src/tests/io/test_file.py'. 211s Hint: make sure your test modules/packages have valid Python names. 211s Traceback: 211s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 211s return _bootstrap._gcd_import(name[level:], package, level) 211s tests/io/test_file.py:2: in 211s import augur.io.file 211s augur/__init__.py:15: in 211s from .io.print import print_err 211s augur/io/__init__.py:6: in 211s from .metadata import read_metadata # noqa: F401 211s augur/io/metadata.py:5: in 211s import pyfastx 211s E ModuleNotFoundError: No module named 'pyfastx' 211s __________________ ERROR collecting tests/io/test_metadata.py __________________ 211s ImportError while importing test module '/tmp/autopkgtest.qYTrYA/build.5Qk/src/tests/io/test_metadata.py'. 211s Hint: make sure your test modules/packages have valid Python names. 211s Traceback: 211s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 211s return _bootstrap._gcd_import(name[level:], package, level) 211s tests/io/test_metadata.py:7: in 211s from augur.io.metadata import InvalidDelimiter, read_table_to_dict, read_metadata_with_sequences, write_records_to_tsv, Metadata 211s augur/__init__.py:15: in 211s from .io.print import print_err 211s augur/io/__init__.py:6: in 211s from .metadata import read_metadata # noqa: F401 211s augur/io/metadata.py:5: in 211s import pyfastx 211s E ModuleNotFoundError: No module named 'pyfastx' 211s _________________ ERROR collecting tests/io/test_sequences.py __________________ 211s ImportError while importing test module '/tmp/autopkgtest.qYTrYA/build.5Qk/src/tests/io/test_sequences.py'. 211s Hint: make sure your test modules/packages have valid Python names. 211s Traceback: 211s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 211s return _bootstrap._gcd_import(name[level:], package, level) 211s tests/io/test_sequences.py:13: in 211s import augur.io.sequences 211s augur/__init__.py:15: in 211s from .io.print import print_err 211s augur/io/__init__.py:6: in 211s from .metadata import read_metadata # noqa: F401 211s augur/io/metadata.py:5: in 211s import pyfastx 211s E ModuleNotFoundError: No module named 'pyfastx' 211s ____________ ERROR collecting tests/io/test_shell_command_runner.py ____________ 211s ImportError while importing test module '/tmp/autopkgtest.qYTrYA/build.5Qk/src/tests/io/test_shell_command_runner.py'. 211s Hint: make sure your test modules/packages have valid Python names. 211s Traceback: 211s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 211s return _bootstrap._gcd_import(name[level:], package, level) 211s tests/io/test_shell_command_runner.py:5: in 211s from augur.io.shell_command_runner import ShellCommandRunner 211s augur/__init__.py:15: in 211s from .io.print import print_err 211s augur/io/__init__.py:6: in 211s from .metadata import read_metadata # noqa: F401 211s augur/io/metadata.py:5: in 211s import pyfastx 211s E ModuleNotFoundError: No module named 'pyfastx' 211s __________________ ERROR collecting tests/io/test_strains.py ___________________ 211s ImportError while importing test module '/tmp/autopkgtest.qYTrYA/build.5Qk/src/tests/io/test_strains.py'. 211s Hint: make sure your test modules/packages have valid Python names. 211s Traceback: 211s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 211s return _bootstrap._gcd_import(name[level:], package, level) 211s tests/io/test_strains.py:3: in 211s from augur.io.strains import read_strains 211s augur/__init__.py:15: in 211s from .io.print import print_err 211s augur/io/__init__.py:6: in 211s from .metadata import read_metadata # noqa: F401 211s augur/io/metadata.py:5: in 211s import pyfastx 211s E ModuleNotFoundError: No module named 'pyfastx' 211s ____________________ ERROR collecting tests/io/test_vcf.py _____________________ 211s ImportError while importing test module '/tmp/autopkgtest.qYTrYA/build.5Qk/src/tests/io/test_vcf.py'. 211s Hint: make sure your test modules/packages have valid Python names. 211s Traceback: 211s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 211s return _bootstrap._gcd_import(name[level:], package, level) 211s tests/io/test_vcf.py:2: in 211s import augur.io.vcf 211s augur/__init__.py:15: in 211s from .io.print import print_err 211s augur/io/__init__.py:6: in 211s from .metadata import read_metadata # noqa: F401 211s augur/io/metadata.py:5: in 211s import pyfastx 211s E ModuleNotFoundError: No module named 'pyfastx' 211s _____________________ ERROR collecting tests/test_align.py _____________________ 211s ImportError while importing test module '/tmp/autopkgtest.qYTrYA/build.5Qk/src/tests/test_align.py'. 211s Hint: make sure your test modules/packages have valid Python names. 211s Traceback: 211s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 211s return _bootstrap._gcd_import(name[level:], package, level) 211s tests/test_align.py:16: in 211s from augur import align 211s augur/__init__.py:15: in 211s from .io.print import print_err 211s augur/io/__init__.py:6: in 211s from .metadata import read_metadata # noqa: F401 211s augur/io/metadata.py:5: in 211s import pyfastx 211s E ModuleNotFoundError: No module named 'pyfastx' 211s ___________________ ERROR collecting tests/test_ancestral.py ___________________ 211s ImportError while importing test module '/tmp/autopkgtest.qYTrYA/build.5Qk/src/tests/test_ancestral.py'. 211s Hint: make sure your test modules/packages have valid Python names. 211s Traceback: 211s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 211s return _bootstrap._gcd_import(name[level:], package, level) 211s tests/test_ancestral.py:1: in 211s from augur.ancestral import run_ancestral 211s augur/__init__.py:15: in 211s from .io.print import print_err 211s augur/io/__init__.py:6: in 211s from .metadata import read_metadata # noqa: F401 211s augur/io/metadata.py:5: in 211s import pyfastx 211s E ModuleNotFoundError: No module named 'pyfastx' 211s ____________________ ERROR collecting tests/test_clades.py _____________________ 211s ImportError while importing test module '/tmp/autopkgtest.qYTrYA/build.5Qk/src/tests/test_clades.py'. 211s Hint: make sure your test modules/packages have valid Python names. 211s Traceback: 211s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 211s return _bootstrap._gcd_import(name[level:], package, level) 211s tests/test_clades.py:4: in 211s from augur.clades import read_in_clade_definitions 211s augur/__init__.py:15: in 211s from .io.print import print_err 211s augur/io/__init__.py:6: in 211s from .metadata import read_metadata # noqa: F401 211s augur/io/metadata.py:5: in 211s import pyfastx 211s E ModuleNotFoundError: No module named 'pyfastx' 211s __________________ ERROR collecting tests/test_frequencies.py __________________ 211s ImportError while importing test module '/tmp/autopkgtest.qYTrYA/build.5Qk/src/tests/test_frequencies.py'. 211s Hint: make sure your test modules/packages have valid Python names. 211s Traceback: 211s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 211s return _bootstrap._gcd_import(name[level:], package, level) 211s tests/test_frequencies.py:14: in 211s from augur.dates import numeric_date 211s augur/__init__.py:15: in 211s from .io.print import print_err 211s augur/io/__init__.py:6: in 211s from .metadata import read_metadata # noqa: F401 211s augur/io/metadata.py:5: in 211s import pyfastx 211s E ModuleNotFoundError: No module named 'pyfastx' 211s _____________________ ERROR collecting tests/test_mask.py ______________________ 211s ImportError while importing test module '/tmp/autopkgtest.qYTrYA/build.5Qk/src/tests/test_mask.py'. 211s Hint: make sure your test modules/packages have valid Python names. 211s Traceback: 211s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 211s return _bootstrap._gcd_import(name[level:], package, level) 211s tests/test_mask.py:15: in 211s from augur import mask 211s augur/__init__.py:15: in 211s from .io.print import print_err 211s augur/io/__init__.py:6: in 211s from .metadata import read_metadata # noqa: F401 211s augur/io/metadata.py:5: in 211s import pyfastx 211s E ModuleNotFoundError: No module named 'pyfastx' 211s _____________________ ERROR collecting tests/test_parse.py _____________________ 211s ImportError while importing test module '/tmp/autopkgtest.qYTrYA/build.5Qk/src/tests/test_parse.py'. 211s Hint: make sure your test modules/packages have valid Python names. 211s Traceback: 211s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 211s return _bootstrap._gcd_import(name[level:], package, level) 211s tests/test_parse.py:8: in 211s from augur import parse 211s augur/__init__.py:15: in 211s from .io.print import print_err 211s augur/io/__init__.py:6: in 211s from .metadata import read_metadata # noqa: F401 211s augur/io/metadata.py:5: in 211s import pyfastx 211s E ModuleNotFoundError: No module named 'pyfastx' 211s _________________ ERROR collecting tests/test_titer_models.py __________________ 211s ImportError while importing test module '/tmp/autopkgtest.qYTrYA/build.5Qk/src/tests/test_titer_models.py'. 211s Hint: make sure your test modules/packages have valid Python names. 211s Traceback: 211s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 211s return _bootstrap._gcd_import(name[level:], package, level) 211s tests/test_titer_models.py:2: in 211s from augur.titer_model import TiterCollection 211s augur/__init__.py:15: in 211s from .io.print import print_err 211s augur/io/__init__.py:6: in 211s from .metadata import read_metadata # noqa: F401 211s augur/io/metadata.py:5: in 211s import pyfastx 211s E ModuleNotFoundError: No module named 'pyfastx' 211s ___________________ ERROR collecting tests/test_translate.py ___________________ 211s ImportError while importing test module '/tmp/autopkgtest.qYTrYA/build.5Qk/src/tests/test_translate.py'. 211s Hint: make sure your test modules/packages have valid Python names. 211s Traceback: 211s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 211s return _bootstrap._gcd_import(name[level:], package, level) 211s tests/test_translate.py:13: in 211s from augur import translate 211s augur/__init__.py:15: in 211s from .io.print import print_err 211s augur/io/__init__.py:6: in 211s from .metadata import read_metadata # noqa: F401 211s augur/io/metadata.py:5: in 211s import pyfastx 211s E ModuleNotFoundError: No module named 'pyfastx' 211s _____________________ ERROR collecting tests/test_utils.py _____________________ 211s ImportError while importing test module '/tmp/autopkgtest.qYTrYA/build.5Qk/src/tests/test_utils.py'. 211s Hint: make sure your test modules/packages have valid Python names. 211s Traceback: 211s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 211s return _bootstrap._gcd_import(name[level:], package, level) 211s tests/test_utils.py:9: in 211s from augur import utils 211s augur/__init__.py:15: in 211s from .io.print import print_err 211s augur/io/__init__.py:6: in 211s from .metadata import read_metadata # noqa: F401 211s augur/io/metadata.py:5: in 211s import pyfastx 211s E ModuleNotFoundError: No module named 'pyfastx' 211s ___________________ ERROR collecting tests/test_validate.py ____________________ 211s ImportError while importing test module '/tmp/autopkgtest.qYTrYA/build.5Qk/src/tests/test_validate.py'. 211s Hint: make sure your test modules/packages have valid Python names. 211s Traceback: 211s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 211s return _bootstrap._gcd_import(name[level:], package, level) 211s tests/test_validate.py:4: in 211s from augur.validate import ( 211s augur/__init__.py:15: in 211s from .io.print import print_err 211s augur/io/__init__.py:6: in 211s from .metadata import read_metadata # noqa: F401 211s augur/io/metadata.py:5: in 211s import pyfastx 211s E ModuleNotFoundError: No module named 'pyfastx' 211s ________________ ERROR collecting tests/test_validate_export.py ________________ 211s ImportError while importing test module '/tmp/autopkgtest.qYTrYA/build.5Qk/src/tests/test_validate_export.py'. 211s Hint: make sure your test modules/packages have valid Python names. 211s Traceback: 211s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 211s return _bootstrap._gcd_import(name[level:], package, level) 211s tests/test_validate_export.py:10: in 211s from augur.export_v2 import convert_tree_to_json_structure 211s augur/__init__.py:15: in 211s from .io.print import print_err 211s augur/io/__init__.py:6: in 211s from .metadata import read_metadata # noqa: F401 211s augur/io/metadata.py:5: in 211s import pyfastx 211s E ModuleNotFoundError: No module named 'pyfastx' 211s ___________ ERROR collecting tests/util_support/test_color_parser.py ___________ 211s ImportError while importing test module '/tmp/autopkgtest.qYTrYA/build.5Qk/src/tests/util_support/test_color_parser.py'. 211s Hint: make sure your test modules/packages have valid Python names. 211s Traceback: 211s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 211s return _bootstrap._gcd_import(name[level:], package, level) 211s tests/util_support/test_color_parser.py:1: in 211s from augur.util_support.color_parser import ColorParser 211s augur/__init__.py:15: in 211s from .io.print import print_err 211s augur/io/__init__.py:6: in 211s from .metadata import read_metadata # noqa: F401 211s augur/io/metadata.py:5: in 211s import pyfastx 211s E ModuleNotFoundError: No module named 'pyfastx' 211s ____________ ERROR collecting tests/util_support/test_node_data.py _____________ 211s ImportError while importing test module '/tmp/autopkgtest.qYTrYA/build.5Qk/src/tests/util_support/test_node_data.py'. 211s Hint: make sure your test modules/packages have valid Python names. 211s Traceback: 211s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 211s return _bootstrap._gcd_import(name[level:], package, level) 211s tests/util_support/test_node_data.py:1: in 211s from augur.util_support.node_data import DuplicatedNonDictAttributeError 211s augur/__init__.py:15: in 211s from .io.print import print_err 211s augur/io/__init__.py:6: in 211s from .metadata import read_metadata # noqa: F401 211s augur/io/metadata.py:5: in 211s import pyfastx 211s E ModuleNotFoundError: No module named 'pyfastx' 211s __________ ERROR collecting tests/util_support/test_node_data_file.py __________ 211s ImportError while importing test module '/tmp/autopkgtest.qYTrYA/build.5Qk/src/tests/util_support/test_node_data_file.py'. 211s Hint: make sure your test modules/packages have valid Python names. 211s Traceback: 211s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 211s return _bootstrap._gcd_import(name[level:], package, level) 211s tests/util_support/test_node_data_file.py:3: in 211s from augur.__version__ import __version__ 211s augur/__init__.py:15: in 211s from .io.print import print_err 211s augur/io/__init__.py:6: in 211s from .metadata import read_metadata # noqa: F401 211s augur/io/metadata.py:5: in 211s import pyfastx 211s E ModuleNotFoundError: No module named 'pyfastx' 211s _________ ERROR collecting tests/util_support/test_node_data_reader.py _________ 211s ImportError while importing test module '/tmp/autopkgtest.qYTrYA/build.5Qk/src/tests/util_support/test_node_data_reader.py'. 211s Hint: make sure your test modules/packages have valid Python names. 211s Traceback: 211s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 211s return _bootstrap._gcd_import(name[level:], package, level) 211s tests/util_support/test_node_data_reader.py:1: in 211s from augur.util_support.node_data_reader import NodeDataReader 211s augur/__init__.py:15: in 211s from .io.print import print_err 211s augur/io/__init__.py:6: in 211s from .metadata import read_metadata # noqa: F401 211s augur/io/metadata.py:5: in 211s import pyfastx 211s E ModuleNotFoundError: No module named 'pyfastx' 211s =========================== short test summary info ============================ 211s ERROR tests/dates/test_ambiguous_date.py 211s ERROR tests/dates/test_dates.py 211s ERROR tests/filter/test_relative_dates.py 211s ERROR tests/filter/test_subsample.py 211s ERROR tests/io/test_file.py 211s ERROR tests/io/test_metadata.py 211s ERROR tests/io/test_sequences.py 211s ERROR tests/io/test_shell_command_runner.py 211s ERROR tests/io/test_strains.py 211s ERROR tests/io/test_vcf.py 211s ERROR tests/test_align.py 211s ERROR tests/test_ancestral.py 211s ERROR tests/test_clades.py 211s ERROR tests/test_frequencies.py 211s ERROR tests/test_mask.py 211s ERROR tests/test_parse.py 211s ERROR tests/test_titer_models.py 211s ERROR tests/test_translate.py 211s ERROR tests/test_utils.py 211s ERROR tests/test_validate.py 211s ERROR tests/test_validate_export.py 211s ERROR tests/util_support/test_color_parser.py 211s ERROR tests/util_support/test_node_data.py 211s ERROR tests/util_support/test_node_data_file.py 211s ERROR tests/util_support/test_node_data_reader.py 211s !!!!!!!!!!!!!!!!!!! Interrupted: 25 errors during collection !!!!!!!!!!!!!!!!!!! 211s ============================== 25 errors in 1.44s ============================== 211s autopkgtest [20:38:13]: test run-unit-test: -----------------------] 212s autopkgtest [20:38:14]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 212s run-unit-test FAIL non-zero exit status 2 212s autopkgtest [20:38:14]: @@@@@@@@@@@@@@@@@@@@ summary 212s run-unit-test FAIL non-zero exit status 2 224s virt: nova [W] Skipping flock for amd64 224s virt: Creating nova instance adt-plucky-amd64-augur-20241123-203441-juju-7f2275-prod-proposed-migration-environment-2-319e1b7b-1fdd-465f-bb1c-7707ec04bc09 from image adt/ubuntu-plucky-amd64-server-20241119.img (UUID 2e5306de-7efa-448c-bc27-5518979e66f0)...