0s autopkgtest [20:39:11]: starting date and time: 2024-11-23 20:39:11+0000
  0s autopkgtest [20:39:11]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [20:39:11]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.g285wvkc/out --timeout-copy=6000 -a i386 --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-20@bos03-12.secgroup --name adt-plucky-i386-augur-20241123-203911-juju-7f2275-prod-proposed-migration-environment-20-afb45bd3-69c3-4394-9b36-3fe7c04d8ec9 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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/
 45s autopkgtest [20:39:56]: testbed dpkg architecture: amd64
 45s autopkgtest [20:39:56]: testbed apt version: 2.9.8
 46s autopkgtest [20:39:57]: test architecture: i386
 46s autopkgtest [20:39:57]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 47s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
 47s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [54.8 kB]
 47s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.6 kB]
 47s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [930 kB]
 47s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9704 B]
 47s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [91.3 kB]
 47s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [43.4 kB]
 47s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2408 B]
 47s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [40.1 kB]
 47s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [295 kB]
 47s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [806 kB]
 47s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [20.0 kB]
 47s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [5528 B]
 47s Fetched 2386 kB in 1s (2854 kB/s)
 47s Reading package lists...
 50s Reading package lists...
 50s Building dependency tree...
 50s Reading state information...
 50s Calculating upgrade...
 50s The following package was automatically installed and is no longer required:
 50s   libsgutils2-1.46-2
 50s Use 'sudo apt autoremove' to remove it.
 51s The following NEW packages will be installed:
 51s   libsgutils2-1.48
 51s The following packages will be upgraded:
 51s   amd64-microcode bash bpftrace curl debconf debconf-i18n distro-info
 51s   fwupd-signed gir1.2-girepository-2.0 gir1.2-glib-2.0 hostname
 51s   intel-microcode libaudit-common libaudit1 libcurl3t64-gnutls libcurl4t64
 51s   libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-data libpam-modules
 51s   libpam-modules-bin libpam-runtime libpam0g libplymouth5 libpython3-stdlib
 51s   libselinux1 libsemanage-common libsemanage2 linux-base lxd-installer
 51s   openssh-client openssh-server openssh-sftp-server plymouth
 51s   plymouth-theme-ubuntu-text python3 python3-blinker python3-dbus
 51s   python3-debconf python3-gi python3-jsonschema-specifications python3-minimal
 51s   python3-rpds-py python3-yaml sg3-utils sg3-utils-udev vim-common vim-tiny
 51s   xxd
 51s 49 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
 51s Need to get 19.9 MB of archives.
 51s After this operation, 4441 kB of additional disk space will be used.
 51s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 bash amd64 5.2.32-1ubuntu2 [918 kB]
 51s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 hostname amd64 3.25 [11.1 kB]
 51s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu1 [6578 B]
 51s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu1 [53.9 kB]
 51s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 debconf-i18n all 1.5.87ubuntu1 [204 kB]
 51s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB]
 51s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB]
 51s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB]
 51s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-debconf all 1.5.87ubuntu1 [4156 B]
 51s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 debconf all 1.5.87ubuntu1 [124 kB]
 51s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam0g amd64 1.5.3-7ubuntu4 [69.6 kB]
 51s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu1 [86.9 kB]
 51s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-modules-bin amd64 1.5.3-7ubuntu4 [53.7 kB]
 51s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-modules amd64 1.5.3-7ubuntu4 [294 kB]
 51s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 openssh-sftp-server amd64 1:9.9p1-3ubuntu2 [41.2 kB]
 51s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 openssh-server amd64 1:9.9p1-3ubuntu2 [625 kB]
 51s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 openssh-client amd64 1:9.9p1-3ubuntu2 [1080 kB]
 51s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-runtime all 1.5.3-7ubuntu4 [40.8 kB]
 51s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage-common all 3.7-2build1 [7186 B]
 51s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage2 amd64 3.7-2build1 [105 kB]
 51s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 distro-info amd64 1.12 [20.0 kB]
 51s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.82.0-2 [25.3 kB]
 51s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.82.2-3 [182 kB]
 51s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.82.2-3 [1655 kB]
 51s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.82.0-2 [88.7 kB]
 51s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.82.2-3 [51.7 kB]
 51s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build4 [110 kB]
 51s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-3build1 [293 kB]
 51s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build1 [187 kB]
 51s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 vim-tiny amd64 2:9.1.0861-1ubuntu1 [1037 kB]
 51s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 vim-common all 2:9.1.0861-1ubuntu1 [395 kB]
 51s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 xxd amd64 2:9.1.0861-1ubuntu1 [67.8 kB]
 51s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libplymouth5 amd64 24.004.60-2ubuntu3 [145 kB]
 51s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 plymouth-theme-ubuntu-text amd64 24.004.60-2ubuntu3 [10.3 kB]
 51s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 plymouth amd64 24.004.60-2ubuntu3 [140 kB]
 51s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftrace amd64 0.21.2-2ubuntu3 [1787 kB]
 51s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.9.1-2ubuntu3 [243 kB]
 51s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.9.1-2ubuntu3 [420 kB]
 51s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd-signed amd64 1.55+1.7-1 [30.6 kB]
 51s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.9.1-2ubuntu3 [412 kB]
 51s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libsgutils2-1.48 amd64 1.48-0ubuntu1 [124 kB]
 51s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-base all 4.10.1ubuntu1 [34.8 kB]
 51s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 lxd-installer all 10 [5264 B]
 51s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-blinker all 1.9.0-1 [10.7 kB]
 51s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-rpds-py amd64 0.21.0-2ubuntu1 [323 kB]
 51s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jsonschema-specifications all 2023.12.1-2 [9116 B]
 51s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 sg3-utils amd64 1.48-0ubuntu1 [1042 kB]
 51s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 sg3-utils-udev all 1.48-0ubuntu1 [6608 B]
 51s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 amd64-microcode amd64 3.20240820.1ubuntu1 [187 kB]
 51s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 intel-microcode amd64 3.20241112.1ubuntu2 [7055 kB]
 52s Preconfiguring packages ...
 52s Fetched 19.9 MB in 2s (12.3 MB/s)
 52s (Reading database ... 
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 52s Preparing to unpack .../bash_5.2.32-1ubuntu2_amd64.deb ...
 52s Unpacking bash (5.2.32-1ubuntu2) over (5.2.32-1ubuntu1) ...
 52s Setting up bash (5.2.32-1ubuntu2) ...
 52s 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
 53s (Reading database ... 
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 53s Preparing to unpack .../hostname_3.25_amd64.deb ...
 53s Unpacking hostname (3.25) over (3.23+nmu2ubuntu2) ...
 53s Setting up hostname (3.25) ...
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 53s Preparing to unpack .../libaudit-common_1%3a4.0.2-2ubuntu1_all.deb ...
 53s Unpacking libaudit-common (1:4.0.2-2ubuntu1) over (1:4.0.1-1ubuntu2) ...
 53s Setting up libaudit-common (1:4.0.2-2ubuntu1) ...
 53s (Reading database ... 
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 53s Preparing to unpack .../libaudit1_1%3a4.0.2-2ubuntu1_amd64.deb ...
 53s Unpacking libaudit1:amd64 (1:4.0.2-2ubuntu1) over (1:4.0.1-1ubuntu2) ...
 53s Setting up libaudit1:amd64 (1:4.0.2-2ubuntu1) ...
 53s (Reading database ... 
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 53s Preparing to unpack .../debconf-i18n_1.5.87ubuntu1_all.deb ...
 53s Unpacking debconf-i18n (1.5.87ubuntu1) over (1.5.86ubuntu1) ...
 53s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ...
 53s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ...
 53s Setting up python3-minimal (3.12.7-1) ...
 53s (Reading database ... 
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 53s Preparing to unpack .../python3_3.12.7-1_amd64.deb ...
 53s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ...
 53s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ...
 53s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ...
 53s Preparing to unpack .../python3-debconf_1.5.87ubuntu1_all.deb ...
 53s Unpacking python3-debconf (1.5.87ubuntu1) over (1.5.86ubuntu1) ...
 53s Preparing to unpack .../debconf_1.5.87ubuntu1_all.deb ...
 53s Unpacking debconf (1.5.87ubuntu1) over (1.5.86ubuntu1) ...
 53s Setting up debconf (1.5.87ubuntu1) ...
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 53s Preparing to unpack .../libpam0g_1.5.3-7ubuntu4_amd64.deb ...
 53s Unpacking libpam0g:amd64 (1.5.3-7ubuntu4) over (1.5.3-7ubuntu2) ...
 53s Setting up libpam0g:amd64 (1.5.3-7ubuntu4) ...
 54s (Reading database ... 
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 54s Preparing to unpack .../libselinux1_3.7-3ubuntu1_amd64.deb ...
 54s Unpacking libselinux1:amd64 (3.7-3ubuntu1) over (3.5-2ubuntu5) ...
 54s Setting up libselinux1:amd64 (3.7-3ubuntu1) ...
 54s (Reading database ... 
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 54s Preparing to unpack .../libpam-modules-bin_1.5.3-7ubuntu4_amd64.deb ...
 54s Unpacking libpam-modules-bin (1.5.3-7ubuntu4) over (1.5.3-7ubuntu2) ...
 54s Setting up libpam-modules-bin (1.5.3-7ubuntu4) ...
 54s pam_namespace.service is a disabled or a static unit not running, not starting it.
 54s (Reading database ... 
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 54s Preparing to unpack .../libpam-modules_1.5.3-7ubuntu4_amd64.deb ...
 54s Unpacking libpam-modules:amd64 (1.5.3-7ubuntu4) over (1.5.3-7ubuntu2) ...
 54s Setting up libpam-modules:amd64 (1.5.3-7ubuntu4) ...
 54s (Reading database ... 
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 54s Preparing to unpack .../openssh-sftp-server_1%3a9.9p1-3ubuntu2_amd64.deb ...
 54s Unpacking openssh-sftp-server (1:9.9p1-3ubuntu2) over (1:9.7p1-7ubuntu5) ...
 54s Preparing to unpack .../openssh-server_1%3a9.9p1-3ubuntu2_amd64.deb ...
 54s Unpacking openssh-server (1:9.9p1-3ubuntu2) over (1:9.7p1-7ubuntu5) ...
 55s Preparing to unpack .../openssh-client_1%3a9.9p1-3ubuntu2_amd64.deb ...
 55s Unpacking openssh-client (1:9.9p1-3ubuntu2) over (1:9.7p1-7ubuntu5) ...
 55s Preparing to unpack .../libpam-runtime_1.5.3-7ubuntu4_all.deb ...
 55s Unpacking libpam-runtime (1.5.3-7ubuntu4) over (1.5.3-7ubuntu2) ...
 55s Setting up libpam-runtime (1.5.3-7ubuntu4) ...
 55s (Reading database ... 
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 55s Preparing to unpack .../libsemanage-common_3.7-2build1_all.deb ...
 55s Unpacking libsemanage-common (3.7-2build1) over (3.5-1build6) ...
 55s Setting up libsemanage-common (3.7-2build1) ...
 55s (Reading database ... 
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 55s Preparing to unpack .../libsemanage2_3.7-2build1_amd64.deb ...
 55s Unpacking libsemanage2:amd64 (3.7-2build1) over (3.5-1build6) ...
 55s Setting up libsemanage2:amd64 (3.7-2build1) ...
 55s (Reading database ... 
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 55s Preparing to unpack .../00-distro-info_1.12_amd64.deb ...
 55s Unpacking distro-info (1.12) over (1.9) ...
 55s Preparing to unpack .../01-gir1.2-girepository-2.0_1.82.0-2_amd64.deb ...
 55s Unpacking gir1.2-girepository-2.0:amd64 (1.82.0-2) over (1.80.1-4) ...
 55s Preparing to unpack .../02-gir1.2-glib-2.0_2.82.2-3_amd64.deb ...
 55s Unpacking gir1.2-glib-2.0:amd64 (2.82.2-3) over (2.82.1-0ubuntu1) ...
 55s Preparing to unpack .../03-libglib2.0-0t64_2.82.2-3_amd64.deb ...
 55s Unpacking libglib2.0-0t64:amd64 (2.82.2-3) over (2.82.1-0ubuntu1) ...
 55s Preparing to unpack .../04-libgirepository-1.0-1_1.82.0-2_amd64.deb ...
 55s Unpacking libgirepository-1.0-1:amd64 (1.82.0-2) over (1.80.1-4) ...
 55s Preparing to unpack .../05-libglib2.0-data_2.82.2-3_all.deb ...
 55s Unpacking libglib2.0-data (2.82.2-3) over (2.82.1-0ubuntu1) ...
 55s Preparing to unpack .../06-python3-dbus_1.3.2-5build4_amd64.deb ...
 55s Unpacking python3-dbus (1.3.2-5build4) over (1.3.2-5build3) ...
 55s Preparing to unpack .../07-python3-gi_3.50.0-3build1_amd64.deb ...
 55s Unpacking python3-gi (3.50.0-3build1) over (3.50.0-3) ...
 55s Preparing to unpack .../08-python3-yaml_6.0.2-1build1_amd64.deb ...
 56s Unpacking python3-yaml (6.0.2-1build1) over (6.0.2-1) ...
 56s Preparing to unpack .../09-vim-tiny_2%3a9.1.0861-1ubuntu1_amd64.deb ...
 56s Unpacking vim-tiny (2:9.1.0861-1ubuntu1) over (2:9.1.0777-1ubuntu1) ...
 56s Preparing to unpack .../10-vim-common_2%3a9.1.0861-1ubuntu1_all.deb ...
 56s Unpacking vim-common (2:9.1.0861-1ubuntu1) over (2:9.1.0777-1ubuntu1) ...
 56s Preparing to unpack .../11-xxd_2%3a9.1.0861-1ubuntu1_amd64.deb ...
 56s Unpacking xxd (2:9.1.0861-1ubuntu1) over (2:9.1.0777-1ubuntu1) ...
 56s Preparing to unpack .../12-libplymouth5_24.004.60-2ubuntu3_amd64.deb ...
 56s Unpacking libplymouth5:amd64 (24.004.60-2ubuntu3) over (24.004.60-1ubuntu11) ...
 56s Preparing to unpack .../13-plymouth-theme-ubuntu-text_24.004.60-2ubuntu3_amd64.deb ...
 56s Unpacking plymouth-theme-ubuntu-text (24.004.60-2ubuntu3) over (24.004.60-1ubuntu11) ...
 56s Preparing to unpack .../14-plymouth_24.004.60-2ubuntu3_amd64.deb ...
 56s Unpacking plymouth (24.004.60-2ubuntu3) over (24.004.60-1ubuntu11) ...
 56s Preparing to unpack .../15-bpftrace_0.21.2-2ubuntu3_amd64.deb ...
 56s Unpacking bpftrace (0.21.2-2ubuntu3) over (0.21.2-2ubuntu2) ...
 56s Preparing to unpack .../16-curl_8.9.1-2ubuntu3_amd64.deb ...
 56s Unpacking curl (8.9.1-2ubuntu3) over (8.9.1-2ubuntu2) ...
 56s Preparing to unpack .../17-libcurl4t64_8.9.1-2ubuntu3_amd64.deb ...
 56s Unpacking libcurl4t64:amd64 (8.9.1-2ubuntu3) over (8.9.1-2ubuntu2) ...
 56s Preparing to unpack .../18-fwupd-signed_1.55+1.7-1_amd64.deb ...
 56s Unpacking fwupd-signed (1.55+1.7-1) over (1.54+1.6-1build1) ...
 56s Preparing to unpack .../19-libcurl3t64-gnutls_8.9.1-2ubuntu3_amd64.deb ...
 56s Unpacking libcurl3t64-gnutls:amd64 (8.9.1-2ubuntu3) over (8.9.1-2ubuntu2) ...
 56s Selecting previously unselected package libsgutils2-1.48:amd64.
 56s Preparing to unpack .../20-libsgutils2-1.48_1.48-0ubuntu1_amd64.deb ...
 56s Unpacking libsgutils2-1.48:amd64 (1.48-0ubuntu1) ...
 56s Preparing to unpack .../21-linux-base_4.10.1ubuntu1_all.deb ...
 56s Unpacking linux-base (4.10.1ubuntu1) over (4.5ubuntu9) ...
 56s Preparing to unpack .../22-lxd-installer_10_all.deb ...
 56s Unpacking lxd-installer (10) over (9) ...
 56s Preparing to unpack .../23-python3-blinker_1.9.0-1_all.deb ...
 56s Unpacking python3-blinker (1.9.0-1) over (1.8.2-1) ...
 56s Preparing to unpack .../24-python3-rpds-py_0.21.0-2ubuntu1_amd64.deb ...
 56s Unpacking python3-rpds-py (0.21.0-2ubuntu1) over (0.20.0-0ubuntu3) ...
 56s Preparing to unpack .../25-python3-jsonschema-specifications_2023.12.1-2_all.deb ...
 57s Unpacking python3-jsonschema-specifications (2023.12.1-2) over (2023.12.1-1ubuntu1) ...
 57s Preparing to unpack .../26-sg3-utils_1.48-0ubuntu1_amd64.deb ...
 57s Unpacking sg3-utils (1.48-0ubuntu1) over (1.46-3ubuntu5) ...
 57s Preparing to unpack .../27-sg3-utils-udev_1.48-0ubuntu1_all.deb ...
 57s Unpacking sg3-utils-udev (1.48-0ubuntu1) over (1.46-3ubuntu5) ...
 57s Preparing to unpack .../28-amd64-microcode_3.20240820.1ubuntu1_amd64.deb ...
 57s Unpacking amd64-microcode (3.20240820.1ubuntu1) over (3.20240116.2+nmu1ubuntu1.1) ...
 57s Preparing to unpack .../29-intel-microcode_3.20241112.1ubuntu2_amd64.deb ...
 57s Unpacking intel-microcode (3.20241112.1ubuntu2) over (3.20240910.0ubuntu1) ...
 57s Setting up distro-info (1.12) ...
 57s Setting up linux-base (4.10.1ubuntu1) ...
 57s Setting up libcurl4t64:amd64 (8.9.1-2ubuntu3) ...
 57s Setting up bpftrace (0.21.2-2ubuntu3) ...
 57s Setting up openssh-client (1:9.9p1-3ubuntu2) ...
 57s Setting up intel-microcode (3.20241112.1ubuntu2) ...
 57s intel-microcode: microcode will be updated at next boot
 57s Setting up libcurl3t64-gnutls:amd64 (8.9.1-2ubuntu3) ...
 57s Setting up fwupd-signed (1.55+1.7-1) ...
 57s Setting up libsgutils2-1.48:amd64 (1.48-0ubuntu1) ...
 57s Setting up debconf-i18n (1.5.87ubuntu1) ...
 57s Setting up amd64-microcode (3.20240820.1ubuntu1) ...
 57s amd64-microcode: microcode will be updated at next boot
 57s Setting up xxd (2:9.1.0861-1ubuntu1) ...
 57s Setting up libglib2.0-0t64:amd64 (2.82.2-3) ...
 57s No schema files found: doing nothing.
 57s Setting up libglib2.0-data (2.82.2-3) ...
 57s Setting up vim-common (2:9.1.0861-1ubuntu1) ...
 57s Setting up gir1.2-glib-2.0:amd64 (2.82.2-3) ...
 57s Setting up lxd-installer (10) ...
 57s Setting up libplymouth5:amd64 (24.004.60-2ubuntu3) ...
 57s Setting up libgirepository-1.0-1:amd64 (1.82.0-2) ...
 57s Setting up curl (8.9.1-2ubuntu3) ...
 57s Setting up libpython3-stdlib:amd64 (3.12.7-1) ...
 57s Setting up sg3-utils (1.48-0ubuntu1) ...
 57s Setting up openssh-sftp-server (1:9.9p1-3ubuntu2) ...
 57s Setting up openssh-server (1:9.9p1-3ubuntu2) ...
 57s Installing new version of config file /etc/ssh/moduli ...
 58s Replacing config file /etc/ssh/sshd_config with new version
 58s Setting up plymouth (24.004.60-2ubuntu3) ...
 58s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic
 58s W: No lz4 in /usr/bin:/sbin:/bin, using gzip
 67s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
 67s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
 67s Setting up python3 (3.12.7-1) ...
 67s Setting up vim-tiny (2:9.1.0861-1ubuntu1) ...
 67s Setting up sg3-utils-udev (1.48-0ubuntu1) ...
 67s update-initramfs: deferring update (trigger activated)
 67s Setting up plymouth-theme-ubuntu-text (24.004.60-2ubuntu3) ...
 67s update-initramfs: deferring update (trigger activated)
 67s Setting up gir1.2-girepository-2.0:amd64 (1.82.0-2) ...
 67s Setting up python3-gi (3.50.0-3build1) ...
 68s Setting up python3-rpds-py (0.21.0-2ubuntu1) ...
 68s Setting up python3-jsonschema-specifications (2023.12.1-2) ...
 68s Setting up python3-blinker (1.9.0-1) ...
 68s Setting up python3-dbus (1.3.2-5build4) ...
 68s Setting up python3-debconf (1.5.87ubuntu1) ...
 68s Setting up python3-yaml (6.0.2-1build1) ...
 68s Processing triggers for man-db (2.13.0-1) ...
 69s Processing triggers for debianutils (5.21) ...
 69s Processing triggers for install-info (7.1.1-1) ...
 69s Processing triggers for initramfs-tools (0.142ubuntu35) ...
 69s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic
 69s W: No lz4 in /usr/bin:/sbin:/bin, using gzip
 76s Processing triggers for libc-bin (2.40-1ubuntu3) ...
 76s Processing triggers for ufw (0.36.2-8) ...
 77s Reading package lists...
 77s Building dependency tree...
 77s Reading state information...
 77s The following packages will be REMOVED:
 77s   libsgutils2-1.46-2*
 77s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded.
 77s After this operation, 294 kB disk space will be freed.
 77s (Reading database ... 
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(Reading database ... 75656 files and directories currently installed.)
 77s Removing libsgutils2-1.46-2:amd64 (1.46-3ubuntu5) ...
 77s Processing triggers for libc-bin (2.40-1ubuntu3) ...
 78s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
 78s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
 78s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
 78s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
 79s Reading package lists...
 79s Reading package lists...
 79s Building dependency tree...
 79s Reading state information...
 79s Calculating upgrade...
 79s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 79s Reading package lists...
 80s Building dependency tree...
 80s Reading state information...
 80s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 80s autopkgtest [20:40:31]: rebooting testbed after setup commands that affected boot
 97s autopkgtest [20:40:48]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024
 99s autopkgtest [20:40:50]: @@@@@@@@@@@@@@@@@@@@ apt-source augur
101s Get:1 http://ftpmaster.internal/ubuntu plucky/universe augur 24.4.0-1 (dsc) [2754 B]
101s Get:2 http://ftpmaster.internal/ubuntu plucky/universe augur 24.4.0-1 (tar) [6802 kB]
101s Get:3 http://ftpmaster.internal/ubuntu plucky/universe augur 24.4.0-1 (diff) [16.5 kB]
101s gpgv: Signature made Wed May 22 16:59:51 2024 UTC
101s gpgv:                using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
101s gpgv:                issuer "emollier@debian.org"
101s gpgv: Can't check signature: No public key
101s dpkg-source: warning: cannot verify inline signature for ./augur_24.4.0-1.dsc: no acceptable signature found
102s autopkgtest [20:40:53]: testing package augur version 24.4.0-1
102s autopkgtest [20:40:53]: build not needed
103s autopkgtest [20:40:54]: test run-unit-test: preparing testbed
106s Note, using file '/tmp/autopkgtest.oTGnkF/1-autopkgtest-satdep.dsc' to get the build dependencies
106s Reading package lists...
106s Building dependency tree...
106s Reading state information...
106s Starting pkgProblemResolver with broken count: 0
106s Starting 2 pkgProblemResolver with broken count: 0
106s Done
107s The following NEW packages will be installed:
107s   augur blt build-essential cpp cpp-14 cpp-14-x86-64-linux-gnu
107s   cpp-x86-64-linux-gnu fasttree flake8 fontconfig-config fonts-dejavu-core
107s   fonts-dejavu-mono fonts-lyx fonts-urw-base35 g++ g++-14
107s   g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14
107s   gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu libamd3 libasan8 libblas3
107s   libcairo2 libcamd3 libcc1-0 libccolamd3 libcholmod5 libcolamd3 libdeflate0
107s   libdsdp-5.8t64 libfftw3-double3 libfontconfig1 libfontenc1 libgcc-14-dev
107s   libgfortran5 libglpk40 libgomp1 libgraphite2-3 libgsl28 libgslcblas0
107s   libharfbuzz0b libhwasan0 libimagequant0 libisl23 libitm1 libjbig0
107s   libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0
107s   liblcms2-2 liblerc4 liblsan0 libltdl7 libmpc3 libopenjp2-7 libpixman-1-0
107s   libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libquadmath0
107s   libraqm0 libsharpyuv0 libstdc++-14-dev libsuitesparseconfig7 libtcl8.6
107s   libtiff6 libtk8.6 libtsan2 libubsan1 libumfpack6 libwebp7 libwebpdemux2
107s   libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1
107s   libxss1 mafft mypy pigz python-matplotlib-data python3-all python3-appdirs
107s   python3-asttokens python3-bcbio-gff python3-biopython python3-boto3
107s   python3-botocore python3-brotli python3-cairo python3-contourpy
107s   python3-cvxopt python3-cycler python3-dateutil python3-decorator
107s   python3-dendropy python3-executing python3-flake8 python3-fonttools
107s   python3-freetype python3-freezegun python3-fs python3-importlib-metadata
107s   python3-iniconfig python3-ipdb python3-ipython python3-isodate python3-jedi
107s   python3-jmespath python3-kiwisolver python3-lxml python3-lz4
107s   python3-matplotlib python3-matplotlib-inline python3-mccabe python3-mpmath
107s   python3-mypy python3-mypy-extensions python3-networkx python3-numpy
107s   python3-packaging python3-pandas python3-pandas-lib python3-parso
107s   python3-pexpect python3-pil python3-pil.imagetk python3-pluggy
107s   python3-prompt-toolkit python3-psutil python3-ptyprocess python3-pure-eval
107s   python3-pycodestyle python3-pyfaidx python3-pyfastx python3-pyflakes
107s   python3-pygtrie python3-pytest python3-pytest-mock python3-reportlab
107s   python3-rlpycairo python3-s3transfer python3-schedule python3-scipy
107s   python3-seaborn python3-six python3-stack-data python3-sympy python3-tk
107s   python3-traitlets python3-treetime python3-typeshed python3-tz
107s   python3-ufolib2 python3-unicodedata2 python3-wcwidth python3-xopen
107s   python3-zstandard python3.12-tk python3.13 python3.13-minimal python3.13-tk
107s   raxml seqmagick sgml-base tk8.6-blt2.5 unicode-data vcftools w3c-sgml-lib
107s   x11-common xfonts-encodings xfonts-utils xml-core
107s 0 upgraded, 181 newly installed, 0 to remove and 0 not upgraded.
107s Need to get 211 MB of archives.
107s After this operation, 979 MB of additional disk space will be used.
107s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB]
107s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB]
107s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB]
107s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 pigz amd64 2.8-1 [65.6 kB]
107s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB]
107s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB]
108s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB]
108s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11ubuntu1 [5319 kB]
108s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1085 kB]
108s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB]
108s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB]
108s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB]
108s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
108s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB]
108s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB]
108s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB]
108s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB]
108s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB]
108s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB]
108s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB]
108s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B]
108s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.15-1 [862 kB]
108s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.7-3 [116 kB]
108s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.0-2 [106 kB]
108s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB]
108s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B]
108s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tk amd64 3.12.7-1 [9752 B]
108s Get:28 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 10.4.0-1ubuntu2 [9568 B]
108s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB]
108s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB]
108s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB]
108s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B]
108s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB]
108s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB]
108s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB]
109s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB]
109s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB]
109s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB]
109s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB]
109s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB]
109s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB]
109s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB]
109s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB]
109s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB]
109s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB]
109s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu2 [580 kB]
109s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB]
109s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB]
109s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B]
109s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB]
109s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2build1 [143 kB]
109s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB]
109s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B]
109s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB]
109s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB]
109s Get:56 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB]
109s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.84+dfsg-4build1 [1719 kB]
109s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB]
109s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-bcbio-gff all 0.7.1-2 [33.9 kB]
109s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libsuitesparseconfig7 amd64 1:7.8.3+dfsg-2 [13.4 kB]
109s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamd3 amd64 1:7.8.3+dfsg-2 [31.1 kB]
109s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcamd3 amd64 1:7.8.3+dfsg-2 [27.6 kB]
109s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 libccolamd3 amd64 1:7.8.3+dfsg-2 [27.5 kB]
109s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 libcolamd3 amd64 1:7.8.3+dfsg-2 [19.5 kB]
109s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcholmod5 amd64 1:7.8.3+dfsg-2 [876 kB]
109s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 libdsdp-5.8t64 amd64 5.8-10.1build1 [199 kB]
109s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 libfftw3-double3 amd64 3.3.10-1ubuntu4 [839 kB]
109s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libltdl7 amd64 2.4.7-8 [43.9 kB]
109s Get:69 http://ftpmaster.internal/ubuntu plucky/universe amd64 libglpk40 amd64 5.0-1build2 [369 kB]
109s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgslcblas0 amd64 2.8+dfsg-5 [290 kB]
109s Get:71 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgsl28 amd64 2.8+dfsg-5 [1285 kB]
109s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 libumfpack6 amd64 1:7.8.3+dfsg-2 [337 kB]
109s Get:73 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cvxopt amd64 1.3.0+dfsg-1build8 [296 kB]
109s Get:74 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-isodate all 0.7.0-1 [18.6 kB]
109s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB]
109s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB]
109s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-3 [80.2 kB]
109s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB]
109s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5ubuntu1 [8271 kB]
110s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5ubuntu1 [3112 kB]
110s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-importlib-metadata all 8.5.0-1 [20.7 kB]
110s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyfaidx all 0.8.1.3-1 [29.7 kB]
110s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyfastx amd64 2.1.0-2 [56.7 kB]
110s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB]
110s Get:85 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB]
110s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5ubuntu1 [21.7 MB]
111s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
111s Get:88 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB]
111s Get:89 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.2.1-1 [171 kB]
111s Get:90 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3ubuntu1 [2928 kB]
111s Get:91 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.0-2build1 [271 kB]
111s Get:92 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B]
111s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build3 [368 kB]
111s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB]
111s Get:95 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-4 [91.3 kB]
111s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu1 [169 kB]
111s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.0-1build1 [1834 kB]
111s Get:98 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build5 [27.5 kB]
111s Get:99 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB]
111s Get:100 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB]
111s Get:101 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB]
111s Get:102 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build2 [360 kB]
112s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB]
112s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB]
112s Get:105 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B]
112s Get:106 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB]
112s Get:107 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.55.0-3 [1759 kB]
112s Get:108 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-2build1 [70.3 kB]
112s Get:109 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB]
112s Get:110 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3ubuntu1 [4691 kB]
112s Get:111 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-treetime all 0.11.4-1 [941 kB]
112s Get:112 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-xopen all 1.7.0-2 [17.0 kB]
112s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jmespath all 1.0.1-1 [21.3 kB]
112s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-botocore all 1.34.46+repack-1ubuntu1 [6211 kB]
113s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-s3transfer all 0.10.1-1ubuntu2 [54.3 kB]
113s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-boto3 all 1.34.46+dfsg-1ubuntu1 [72.5 kB]
113s Get:117 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-dendropy all 4.6.1-1 [278 kB]
113s Get:118 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-schedule all 1.2.2-1 [12.2 kB]
113s Get:119 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-seaborn all 0.13.2-4 [225 kB]
113s Get:120 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-zstandard amd64 0.23.0-2build1 [419 kB]
113s Get:121 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pygtrie all 2.2-2 [16.0 kB]
113s Get:122 http://ftpmaster.internal/ubuntu plucky/universe amd64 seqmagick all 0.8.6-3 [38.6 kB]
113s Get:123 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-parso all 0.8.3-1 [67.2 kB]
113s Get:124 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-typeshed all 0.0~git20231111.6764465-3 [1274 kB]
113s Get:125 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-jedi all 0.19.1+ds1-1 [693 kB]
113s Get:126 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB]
113s Get:127 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib-inline all 0.1.6-2 [8784 B]
113s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-wcwidth all 0.2.13+dfsg1-1 [26.3 kB]
113s Get:129 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-prompt-toolkit all 3.0.48-1 [256 kB]
113s Get:130 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-asttokens all 2.4.1-2 [20.8 kB]
113s Get:131 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-executing all 2.1.0-0.1 [24.4 kB]
113s Get:132 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pure-eval all 0.2.3-1 [11.4 kB]
113s Get:133 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-stack-data all 0.6.3-1 [22.0 kB]
113s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-ptyprocess all 0.7.0-6 [14.8 kB]
113s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pexpect all 4.9-3 [48.1 kB]
113s Get:136 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ipython all 8.29.0-1 [569 kB]
113s Get:137 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ipdb all 0.13.13-2 [15.4 kB]
113s Get:138 http://ftpmaster.internal/ubuntu plucky/universe amd64 mafft amd64 7.505-1 [795 kB]
113s Get:139 http://ftpmaster.internal/ubuntu plucky/universe amd64 raxml amd64 8.2.13+dfsg-1 [1640 kB]
113s Get:140 http://ftpmaster.internal/ubuntu plucky/universe amd64 fasttree amd64 2.1.11-2 [174 kB]
113s Get:141 http://ftpmaster.internal/ubuntu plucky/universe amd64 vcftools amd64 0.1.16-3 [393 kB]
113s Get:142 http://ftpmaster.internal/ubuntu plucky/universe amd64 augur all 24.4.0-1 [238 kB]
113s Get:143 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB]
113s Get:144 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB]
113s Get:145 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [11.9 MB]
114s Get:146 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-8ubuntu1 [1030 B]
114s Get:147 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [5452 B]
114s Get:148 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.1.0-2ubuntu1 [22.4 kB]
114s Get:149 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 14.2.0-8ubuntu1 [47.6 kB]
114s Get:150 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 14.2.0-8ubuntu1 [29.1 kB]
114s Get:151 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 14.2.0-8ubuntu1 [2998 kB]
114s Get:152 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 14.2.0-8ubuntu1 [1317 kB]
114s Get:153 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 14.2.0-8ubuntu1 [2732 kB]
114s Get:154 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 14.2.0-8ubuntu1 [1177 kB]
114s Get:155 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 14.2.0-8ubuntu1 [1634 kB]
114s Get:156 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 14.2.0-8ubuntu1 [153 kB]
114s Get:157 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-8ubuntu1 [2814 kB]
114s Get:158 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [23.3 MB]
115s Get:159 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-8ubuntu1 [528 kB]
115s Get:160 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [1214 B]
115s Get:161 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.1.0-2ubuntu1 [5000 B]
115s Get:162 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-8ubuntu1 [2504 kB]
115s Get:163 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [13.3 MB]
115s Get:164 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-8ubuntu1 [19.9 kB]
115s Get:165 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [966 B]
115s Get:166 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.1.0-2ubuntu1 [1100 B]
115s Get:167 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B]
115s Get:168 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mccabe all 0.7.0-1 [8678 B]
115s Get:169 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pycodestyle all 2.12.1-1 [30.1 kB]
115s Get:170 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyflakes all 3.2.0-2 [52.9 kB]
115s Get:171 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-flake8 all 7.1.1-2 [44.1 kB]
115s Get:172 http://ftpmaster.internal/ubuntu plucky/universe amd64 flake8 all 7.1.1-2 [6444 B]
115s Get:173 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mypy-extensions all 1.0.0-1 [6148 B]
115s Get:174 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-psutil amd64 5.9.8-2build3 [196 kB]
115s Get:175 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mypy amd64 1.13.0-1build1 [15.7 MB]
116s Get:176 http://ftpmaster.internal/ubuntu plucky/universe amd64 mypy all 1.13.0-1build1 [24.9 kB]
116s Get:177 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freezegun all 1.5.1-1.1 [15.9 kB]
116s Get:178 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B]
116s Get:179 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB]
116s Get:180 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.3-1 [251 kB]
116s Get:181 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest-mock all 3.14.0-2 [11.7 kB]
116s Fetched 211 MB in 9s (22.9 MB/s)
116s Selecting previously unselected package libpython3.13-minimal:amd64.
117s (Reading database ... 
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(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) ...
117s Selecting previously unselected package libtcl8.6:amd64.
117s Preparing to unpack .../008-libtcl8.6_8.6.15+dfsg-2_amd64.deb ...
117s Unpacking libtcl8.6:amd64 (8.6.15+dfsg-2) ...
117s Selecting previously unselected package fonts-dejavu-mono.
117s Preparing to unpack .../009-fonts-dejavu-mono_2.37-8_all.deb ...
117s Unpacking fonts-dejavu-mono (2.37-8) ...
117s Selecting previously unselected package fonts-dejavu-core.
117s Preparing to unpack .../010-fonts-dejavu-core_2.37-8_all.deb ...
117s Unpacking fonts-dejavu-core (2.37-8) ...
117s Selecting previously unselected package libfontenc1:amd64.
117s Preparing to unpack .../011-libfontenc1_1%3a1.1.8-1build1_amd64.deb ...
117s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ...
117s Selecting previously unselected package x11-common.
117s Preparing to unpack .../012-x11-common_1%3a7.7+23ubuntu3_all.deb ...
117s Unpacking x11-common (1:7.7+23ubuntu3) ...
117s Selecting previously unselected package xfonts-encodings.
117s Preparing to unpack .../013-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ...
117s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ...
117s Selecting previously unselected package xfonts-utils.
117s Preparing to unpack .../014-xfonts-utils_1%3a7.7+7_amd64.deb ...
117s Unpacking xfonts-utils (1:7.7+7) ...
117s Selecting previously unselected package fonts-urw-base35.
117s Preparing to unpack .../015-fonts-urw-base35_20200910-8_all.deb ...
117s Unpacking fonts-urw-base35 (20200910-8) ...
117s Selecting previously unselected package fontconfig-config.
117s 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 ...
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118s Selecting previously unselected package libimagequant0:amd64.
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118s Selecting previously unselected package libjpeg-turbo8:amd64.
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118s Selecting previously unselected package libjpeg8:amd64.
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118s Selecting previously unselected package liblcms2-2:amd64.
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118s Selecting previously unselected package libopenjp2-7:amd64.
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118s Selecting previously unselected package libgraphite2-3:amd64.
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118s Selecting previously unselected package libharfbuzz0b:amd64.
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118s Selecting previously unselected package libdeflate0:amd64.
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118s Selecting previously unselected package libjbig0:amd64.
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118s Selecting previously unselected package liblerc4:amd64.
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118s Selecting previously unselected package libsharpyuv0:amd64.
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118s Selecting previously unselected package libwebp7:amd64.
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118s Selecting previously unselected package libtiff6:amd64.
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118s Selecting previously unselected package libwebpdemux2:amd64.
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118s Selecting previously unselected package libwebpmux3:amd64.
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118s Selecting previously unselected package python3-pil:amd64.
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118s Selecting previously unselected package libpixman-1-0:amd64.
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118s Selecting previously unselected package libxcb-render0:amd64.
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118s Selecting previously unselected package libxcb-shm0:amd64.
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118s Selecting previously unselected package libcairo2:amd64.
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118s Selecting previously unselected package python3-cairo.
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118s Selecting previously unselected package python3-freetype.
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118s Selecting previously unselected package python3-rlpycairo.
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118s Selecting previously unselected package python3-reportlab.
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118s Selecting previously unselected package xml-core.
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119s Selecting previously unselected package w3c-sgml-lib.
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119s Selecting previously unselected package python3-biopython.
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119s Selecting previously unselected package python3-six.
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119s Selecting previously unselected package python3-bcbio-gff.
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119s Selecting previously unselected package libsuitesparseconfig7:amd64.
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119s Selecting previously unselected package libamd3:amd64.
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119s Unpacking libamd3:amd64 (1:7.8.3+dfsg-2) ...
119s Selecting previously unselected package libcamd3:amd64.
119s Preparing to unpack .../061-libcamd3_1%3a7.8.3+dfsg-2_amd64.deb ...
119s Unpacking libcamd3:amd64 (1:7.8.3+dfsg-2) ...
119s Selecting previously unselected package libccolamd3:amd64.
119s Preparing to unpack .../062-libccolamd3_1%3a7.8.3+dfsg-2_amd64.deb ...
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119s Selecting previously unselected package libcolamd3:amd64.
119s Preparing to unpack .../063-libcolamd3_1%3a7.8.3+dfsg-2_amd64.deb ...
119s Unpacking libcolamd3:amd64 (1:7.8.3+dfsg-2) ...
119s Selecting previously unselected package libcholmod5:amd64.
119s Preparing to unpack .../064-libcholmod5_1%3a7.8.3+dfsg-2_amd64.deb ...
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119s Selecting previously unselected package libdsdp-5.8t64.
119s Preparing to unpack .../065-libdsdp-5.8t64_5.8-10.1build1_amd64.deb ...
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119s Selecting previously unselected package libfftw3-double3:amd64.
119s Preparing to unpack .../066-libfftw3-double3_3.3.10-1ubuntu4_amd64.deb ...
119s Unpacking libfftw3-double3:amd64 (3.3.10-1ubuntu4) ...
119s Selecting previously unselected package libltdl7:amd64.
119s Preparing to unpack .../067-libltdl7_2.4.7-8_amd64.deb ...
119s Unpacking libltdl7:amd64 (2.4.7-8) ...
119s Selecting previously unselected package libglpk40:amd64.
119s Preparing to unpack .../068-libglpk40_5.0-1build2_amd64.deb ...
119s Unpacking libglpk40:amd64 (5.0-1build2) ...
119s Selecting previously unselected package libgslcblas0:amd64.
119s Preparing to unpack .../069-libgslcblas0_2.8+dfsg-5_amd64.deb ...
119s Unpacking libgslcblas0:amd64 (2.8+dfsg-5) ...
119s Selecting previously unselected package libgsl28:amd64.
119s Preparing to unpack .../070-libgsl28_2.8+dfsg-5_amd64.deb ...
119s Unpacking libgsl28:amd64 (2.8+dfsg-5) ...
119s Selecting previously unselected package libumfpack6:amd64.
119s Preparing to unpack .../071-libumfpack6_1%3a7.8.3+dfsg-2_amd64.deb ...
119s Unpacking libumfpack6:amd64 (1:7.8.3+dfsg-2) ...
119s Selecting previously unselected package python3-cvxopt.
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119s Unpacking python3-cvxopt (1.3.0+dfsg-1build8) ...
119s Selecting previously unselected package python3-isodate.
119s Preparing to unpack .../073-python3-isodate_0.7.0-1_all.deb ...
119s Unpacking python3-isodate (0.7.0-1) ...
119s Selecting previously unselected package python3-networkx.
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119s 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) ...
120s Selecting previously unselected package python3-pandas.
120s Preparing to unpack .../079-python3-pandas_2.2.3+dfsg-5ubuntu1_all.deb ...
120s Unpacking python3-pandas (2.2.3+dfsg-5ubuntu1) ...
120s Selecting previously unselected package python3-importlib-metadata.
120s Preparing to unpack .../080-python3-importlib-metadata_8.5.0-1_all.deb ...
120s Unpacking python3-importlib-metadata (8.5.0-1) ...
120s Selecting previously unselected package python3-pyfaidx.
120s Preparing to unpack .../081-python3-pyfaidx_0.8.1.3-1_all.deb ...
120s Unpacking python3-pyfaidx (0.8.1.3-1) ...
120s Selecting previously unselected package python3-pyfastx.
120s Preparing to unpack .../082-python3-pyfastx_2.1.0-2_amd64.deb ...
120s Unpacking python3-pyfastx (2.1.0-2) ...
120s Selecting previously unselected package python3-decorator.
120s Preparing to unpack .../083-python3-decorator_5.1.1-5_all.deb ...
120s Unpacking python3-decorator (5.1.1-5) ...
120s Selecting previously unselected package liblbfgsb0:amd64.
120s Preparing to unpack .../084-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ...
120s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ...
120s Selecting previously unselected package python3-scipy.
120s Preparing to unpack .../085-python3-scipy_1.13.1-5ubuntu1_amd64.deb ...
120s Unpacking python3-scipy (1.13.1-5ubuntu1) ...
121s Selecting previously unselected package libjs-jquery.
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121s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
121s Selecting previously unselected package libjs-jquery-ui.
121s Preparing to unpack .../087-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ...
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121s Selecting previously unselected package fonts-lyx.
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121s Selecting previously unselected package python-matplotlib-data.
121s Preparing to unpack .../089-python-matplotlib-data_3.8.3-3ubuntu1_all.deb ...
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121s Selecting previously unselected package python3-contourpy.
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121s Selecting previously unselected package python3-cycler.
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121s Unpacking python3-cycler (0.12.1-1) ...
121s Selecting previously unselected package python3-brotli.
121s Preparing to unpack .../092-python3-brotli_1.1.0-2build3_amd64.deb ...
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121s Selecting previously unselected package python3-appdirs.
121s Preparing to unpack .../093-python3-appdirs_1.4.4-4_all.deb ...
121s Unpacking python3-appdirs (1.4.4-4) ...
121s Selecting previously unselected package python3-fs.
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121s Unpacking python3-fs (2.4.16-4) ...
121s Selecting previously unselected package libxslt1.1:amd64.
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121s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ...
121s Selecting previously unselected package python3-lxml:amd64.
121s Preparing to unpack .../096-python3-lxml_5.3.0-1build1_amd64.deb ...
121s Unpacking python3-lxml:amd64 (5.3.0-1build1) ...
121s Selecting previously unselected package python3-lz4.
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121s Unpacking python3-lz4 (4.0.2+dfsg-1build5) ...
121s Selecting previously unselected package python3-mpmath.
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121s Unpacking python3-mpmath (1.3.0-1) ...
121s Selecting previously unselected package python3-sympy.
121s Preparing to unpack .../099-python3-sympy_1.13.3-1_all.deb ...
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122s Selecting previously unselected package python3-ufolib2.
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122s Selecting previously unselected package python3-unicodedata2.
122s Preparing to unpack .../101-python3-unicodedata2_15.1.0+ds-1build2_amd64.deb ...
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122s Selecting previously unselected package libpython3.13-stdlib:amd64.
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122s Selecting previously unselected package python3.13.
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122s Unpacking python3.13 (3.13.0-2) ...
122s Selecting previously unselected package python3-all.
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122s Unpacking python3-all (3.12.7-1) ...
122s Selecting previously unselected package unicode-data.
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122s Unpacking unicode-data (15.1.0-1) ...
122s Selecting previously unselected package python3-fonttools.
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122s Selecting previously unselected package python3-kiwisolver.
122s Preparing to unpack .../107-python3-kiwisolver_1.4.7-2build1_amd64.deb ...
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122s Selecting previously unselected package libqhull-r8.0:amd64.
122s Preparing to unpack .../108-libqhull-r8.0_2020.2-6build1_amd64.deb ...
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122s Selecting previously unselected package python3-matplotlib.
122s Preparing to unpack .../109-python3-matplotlib_3.8.3-3ubuntu1_amd64.deb ...
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122s Selecting previously unselected package python3-treetime.
122s Preparing to unpack .../110-python3-treetime_0.11.4-1_all.deb ...
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122s Selecting previously unselected package python3-xopen.
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122s Selecting previously unselected package python3-jmespath.
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122s Selecting previously unselected package python3-botocore.
122s Preparing to unpack .../113-python3-botocore_1.34.46+repack-1ubuntu1_all.deb ...
122s Unpacking python3-botocore (1.34.46+repack-1ubuntu1) ...
123s Selecting previously unselected package python3-s3transfer.
123s Preparing to unpack .../114-python3-s3transfer_0.10.1-1ubuntu2_all.deb ...
123s Unpacking python3-s3transfer (0.10.1-1ubuntu2) ...
123s Selecting previously unselected package python3-boto3.
123s Preparing to unpack .../115-python3-boto3_1.34.46+dfsg-1ubuntu1_all.deb ...
123s Unpacking python3-boto3 (1.34.46+dfsg-1ubuntu1) ...
123s Selecting previously unselected package python3-dendropy.
123s Preparing to unpack .../116-python3-dendropy_4.6.1-1_all.deb ...
123s Unpacking python3-dendropy (4.6.1-1) ...
123s Selecting previously unselected package python3-schedule.
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123s Unpacking python3-schedule (1.2.2-1) ...
123s Selecting previously unselected package python3-seaborn.
123s Preparing to unpack .../118-python3-seaborn_0.13.2-4_all.deb ...
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123s Selecting previously unselected package python3-zstandard.
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123s Unpacking python3-zstandard (0.23.0-2build1) ...
123s Selecting previously unselected package python3-pygtrie.
123s Preparing to unpack .../120-python3-pygtrie_2.2-2_all.deb ...
123s Unpacking python3-pygtrie (2.2-2) ...
123s Selecting previously unselected package seqmagick.
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123s Unpacking seqmagick (0.8.6-3) ...
123s Selecting previously unselected package python3-parso.
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123s Unpacking python3-parso (0.8.3-1) ...
123s Selecting previously unselected package python3-typeshed.
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123s Unpacking python3-typeshed (0.0~git20231111.6764465-3) ...
124s Selecting previously unselected package python3-jedi.
124s Preparing to unpack .../124-python3-jedi_0.19.1+ds1-1_all.deb ...
124s Unpacking python3-jedi (0.19.1+ds1-1) ...
124s Selecting previously unselected package python3-traitlets.
124s Preparing to unpack .../125-python3-traitlets_5.14.3+really5.14.3-1_all.deb ...
124s Unpacking python3-traitlets (5.14.3+really5.14.3-1) ...
124s Selecting previously unselected package python3-matplotlib-inline.
124s Preparing to unpack .../126-python3-matplotlib-inline_0.1.6-2_all.deb ...
124s Unpacking python3-matplotlib-inline (0.1.6-2) ...
124s Selecting previously unselected package python3-wcwidth.
124s Preparing to unpack .../127-python3-wcwidth_0.2.13+dfsg1-1_all.deb ...
124s Unpacking python3-wcwidth (0.2.13+dfsg1-1) ...
124s Selecting previously unselected package python3-prompt-toolkit.
124s Preparing to unpack .../128-python3-prompt-toolkit_3.0.48-1_all.deb ...
124s Unpacking python3-prompt-toolkit (3.0.48-1) ...
124s Selecting previously unselected package python3-asttokens.
124s Preparing to unpack .../129-python3-asttokens_2.4.1-2_all.deb ...
124s Unpacking python3-asttokens (2.4.1-2) ...
124s Selecting previously unselected package python3-executing.
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124s Unpacking python3-executing (2.1.0-0.1) ...
124s Selecting previously unselected package python3-pure-eval.
124s Preparing to unpack .../131-python3-pure-eval_0.2.3-1_all.deb ...
124s Unpacking python3-pure-eval (0.2.3-1) ...
124s Selecting previously unselected package python3-stack-data.
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124s Unpacking python3-stack-data (0.6.3-1) ...
124s Selecting previously unselected package python3-ptyprocess.
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124s Unpacking python3-ptyprocess (0.7.0-6) ...
124s Selecting previously unselected package python3-pexpect.
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124s Unpacking python3-pexpect (4.9-3) ...
124s Selecting previously unselected package python3-ipython.
124s Preparing to unpack .../135-python3-ipython_8.29.0-1_all.deb ...
124s Unpacking python3-ipython (8.29.0-1) ...
124s Selecting previously unselected package python3-ipdb.
124s Preparing to unpack .../136-python3-ipdb_0.13.13-2_all.deb ...
124s Unpacking python3-ipdb (0.13.13-2) ...
124s Selecting previously unselected package mafft.
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124s Unpacking mafft (7.505-1) ...
124s Selecting previously unselected package raxml.
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124s Unpacking raxml (8.2.13+dfsg-1) ...
124s Selecting previously unselected package fasttree.
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124s Selecting previously unselected package vcftools.
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124s Unpacking vcftools (0.1.16-3) ...
124s Selecting previously unselected package augur.
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124s Unpacking augur (24.4.0-1) ...
124s Selecting previously unselected package libisl23:amd64.
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124s Unpacking libisl23:amd64 (0.27-1) ...
124s Selecting previously unselected package libmpc3:amd64.
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124s Unpacking libmpc3:amd64 (1.3.1-1build2) ...
124s Selecting previously unselected package cpp-14-x86-64-linux-gnu.
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124s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ...
125s Selecting previously unselected package cpp-14.
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125s Unpacking cpp-14 (14.2.0-8ubuntu1) ...
125s Selecting previously unselected package cpp-x86-64-linux-gnu.
125s Preparing to unpack .../146-cpp-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ...
125s Unpacking cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ...
125s Selecting previously unselected package cpp.
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125s Unpacking cpp (4:14.1.0-2ubuntu1) ...
125s Selecting previously unselected package libcc1-0:amd64.
125s Preparing to unpack .../148-libcc1-0_14.2.0-8ubuntu1_amd64.deb ...
125s Unpacking libcc1-0:amd64 (14.2.0-8ubuntu1) ...
125s Selecting previously unselected package libitm1:amd64.
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125s Unpacking libitm1:amd64 (14.2.0-8ubuntu1) ...
125s Selecting previously unselected package libasan8:amd64.
125s Preparing to unpack .../150-libasan8_14.2.0-8ubuntu1_amd64.deb ...
125s Unpacking libasan8:amd64 (14.2.0-8ubuntu1) ...
125s Selecting previously unselected package liblsan0:amd64.
125s Preparing to unpack .../151-liblsan0_14.2.0-8ubuntu1_amd64.deb ...
125s Unpacking liblsan0:amd64 (14.2.0-8ubuntu1) ...
125s Selecting previously unselected package libtsan2:amd64.
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125s Unpacking libtsan2:amd64 (14.2.0-8ubuntu1) ...
125s Selecting previously unselected package libubsan1:amd64.
125s Preparing to unpack .../153-libubsan1_14.2.0-8ubuntu1_amd64.deb ...
125s Unpacking libubsan1:amd64 (14.2.0-8ubuntu1) ...
125s Selecting previously unselected package libhwasan0:amd64.
125s Preparing to unpack .../154-libhwasan0_14.2.0-8ubuntu1_amd64.deb ...
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125s Selecting previously unselected package libquadmath0:amd64.
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125s Unpacking libquadmath0:amd64 (14.2.0-8ubuntu1) ...
125s Selecting previously unselected package libgcc-14-dev:amd64.
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125s Selecting previously unselected package gcc-14-x86-64-linux-gnu.
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125s Selecting previously unselected package gcc-14.
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125s Unpacking gcc-14 (14.2.0-8ubuntu1) ...
125s Selecting previously unselected package gcc-x86-64-linux-gnu.
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125s Unpacking gcc-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ...
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125s Unpacking gcc (4:14.1.0-2ubuntu1) ...
125s Selecting previously unselected package libstdc++-14-dev:amd64.
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126s Selecting previously unselected package g++-14-x86-64-linux-gnu.
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126s Selecting previously unselected package g++-14.
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127s Selecting previously unselected package python3-pytest.
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127s Unpacking python3-pytest-mock (3.14.0-2) ...
127s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ...
127s Setting up python3-schedule (1.2.2-1) ...
127s Setting up liblcms2-2:amd64 (2.16-2) ...
127s Setting up python3-iniconfig (1.1.1-2) ...
127s Setting up libpixman-1-0:amd64 (0.44.0-3) ...
127s Setting up vcftools (0.1.16-3) ...
127s Setting up libsharpyuv0:amd64 (1.4.0-0.1) ...
127s Setting up python3-pure-eval (0.2.3-1) ...
127s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ...
127s Setting up python3-importlib-metadata (8.5.0-1) ...
127s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ...
127s Setting up libgslcblas0:amd64 (2.8+dfsg-5) ...
127s Setting up python3-parso (0.8.3-1) ...
127s Setting up python3-lz4 (4.0.2+dfsg-1build5) ...
128s Setting up libxcb-render0:amd64 (1.17.0-2) ...
128s Setting up mafft (7.505-1) ...
128s Setting up python3-asttokens (2.4.1-2) ...
128s Setting up python3-unicodedata2 (15.1.0+ds-1build2) ...
128s Setting up fonts-lyx (2.4.2.1-1) ...
128s Setting up python3-mypy-extensions (1.0.0-1) ...
128s Setting up python3-pyflakes (3.2.0-2) ...
128s Setting up x11-common (1:7.7+23ubuntu3) ...
128s Setting up libdeflate0:amd64 (1.22-1) ...
128s Setting up libqhull-r8.0:amd64 (2020.2-6build1) ...
128s Setting up libxcb-shm0:amd64 (1.17.0-2) ...
128s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ...
128s Setting up python3-freetype (2.5.1-1) ...
129s Setting up python3-networkx (3.2.1-4ubuntu1) ...
130s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ...
130s Setting up python3-psutil (5.9.8-2build3) ...
131s Setting up python3-tz (2024.1-2) ...
131s Setting up unicode-data (15.1.0-1) ...
131s Setting up python3-six (1.16.0-7) ...
131s Setting up libpython3.13-minimal:amd64 (3.13.0-2) ...
131s Setting up python3-isodate (0.7.0-1) ...
131s Setting up python3-decorator (5.1.1-5) ...
131s Setting up python3-pycodestyle (2.12.1-1) ...
132s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ...
132s Setting up python3-pygtrie (2.2-2) ...
132s Setting up libblas3:amd64 (3.12.0-3build2) ...
132s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
132s Setting up python3-zstandard (0.23.0-2build1) ...
132s Setting up python3-packaging (24.2-1) ...
132s Setting up python3-wcwidth (0.2.13+dfsg1-1) ...
132s Setting up python3-typeshed (0.0~git20231111.6764465-3) ...
132s Setting up python3-executing (2.1.0-0.1) ...
133s Setting up python3-jmespath (1.0.1-1) ...
133s Setting up python3-brotli (1.1.0-2build3) ...
133s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ...
133s Setting up libquadmath0:amd64 (14.2.0-8ubuntu1) ...
133s Setting up python3-cycler (0.12.1-1) ...
133s Setting up libimagequant0:amd64 (2.18.0-1build1) ...
133s Setting up fonts-dejavu-mono (2.37-8) ...
133s Setting up python3-kiwisolver (1.4.7-2build1) ...
133s Setting up libmpc3:amd64 (1.3.1-1build2) ...
133s Setting up python3-mypy (1.13.0-1build1) ...
135s Setting up libtcl8.6:amd64 (8.6.15+dfsg-2) ...
135s Setting up fonts-dejavu-core (2.37-8) ...
135s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ...
135s Setting up libltdl7:amd64 (2.4.7-8) ...
135s Setting up libfftw3-double3:amd64 (3.3.10-1ubuntu4) ...
135s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ...
135s Setting up python3-pluggy (1.5.0-1) ...
135s Setting up libwebp7:amd64 (1.4.0-0.1) ...
135s Setting up libubsan1:amd64 (14.2.0-8ubuntu1) ...
135s Setting up libhwasan0:amd64 (14.2.0-8ubuntu1) ...
135s Setting up pigz (2.8-1) ...
135s Setting up python3-traitlets (5.14.3+really5.14.3-1) ...
135s Setting up libasan8:amd64 (14.2.0-8ubuntu1) ...
135s Setting up libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ...
135s Setting up libsuitesparseconfig7:amd64 (1:7.8.3+dfsg-2) ...
135s Setting up mypy (1.13.0-1build1) ...
135s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu1) ...
135s Setting up python3.13-minimal (3.13.0-2) ...
136s Setting up libharfbuzz0b:amd64 (10.0.1-1) ...
136s Setting up python3-dateutil (2.9.0-3) ...
136s Setting up fasttree (2.1.11-2) ...
136s Setting up python3-mccabe (0.7.0-1) ...
136s Setting up sgml-base (1.31) ...
136s Setting up libxss1:amd64 (1:1.2.3-1build3) ...
136s Setting up libtsan2:amd64 (14.2.0-8ubuntu1) ...
136s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
136s Setting up python3-mpmath (1.3.0-1) ...
137s Setting up libisl23:amd64 (0.27-1) ...
137s Setting up libgsl28:amd64 (2.8+dfsg-5) ...
137s Setting up python-matplotlib-data (3.8.3-3ubuntu1) ...
137s Setting up libwebpmux3:amd64 (1.4.0-0.1) ...
137s Setting up python3-dendropy (4.6.1-1) ...
138s Setting up python3-appdirs (1.4.4-4) ...
138s Setting up libpython3.13-stdlib:amd64 (3.13.0-2) ...
138s Setting up python3-stack-data (0.6.3-1) ...
138s Setting up libcc1-0:amd64 (14.2.0-8ubuntu1) ...
138s Setting up python3-freezegun (1.5.1-1.1) ...
138s Setting up liblsan0:amd64 (14.2.0-8ubuntu1) ...
138s Setting up libitm1:amd64 (14.2.0-8ubuntu1) ...
138s Setting up raxml (8.2.13+dfsg-1) ...
138s Setting up python3-ptyprocess (0.7.0-6) ...
138s Setting up libjpeg8:amd64 (8c-2ubuntu11) ...
138s Setting up python3-prompt-toolkit (3.0.48-1) ...
139s Setting up python3-pyfaidx (0.8.1.3-1) ...
139s Setting up python3-sympy (1.13.3-1) ...
148s Setting up liblapack3:amd64 (3.12.0-3build2) ...
148s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
148s Setting up libamd3:amd64 (1:7.8.3+dfsg-2) ...
148s Setting up python3-jedi (0.19.1+ds1-1) ...
149s Setting up libcolamd3:amd64 (1:7.8.3+dfsg-2) ...
149s Setting up python3.13 (3.13.0-2) ...
149s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ...
149s Setting up python3-pytest (8.3.3-1) ...
150s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ...
150s Setting up python3-pyfastx (2.1.0-2) ...
150s Setting up python3-all (3.12.7-1) ...
150s Setting up xfonts-utils (1:7.7+7) ...
150s Setting up libcamd3:amd64 (1:7.8.3+dfsg-2) ...
150s Setting up python3-matplotlib-inline (0.1.6-2) ...
150s Setting up python3-flake8 (7.1.1-2) ...
150s Setting up python3-fs (2.4.16-4) ...
151s Setting up python3-xopen (1.7.0-2) ...
151s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
151s Setting up libglpk40:amd64 (5.0-1build2) ...
151s Setting up python3-pexpect (4.9-3) ...
151s Setting up libraqm0:amd64 (0.10.1-1build1) ...
151s Setting up python3-botocore (1.34.46+repack-1ubuntu1) ...
151s Setting up cpp-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ...
151s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ...
154s Setting up cpp-14 (14.2.0-8ubuntu1) ...
154s Setting up libccolamd3:amd64 (1:7.8.3+dfsg-2) ...
154s Setting up python3-pytest-mock (3.14.0-2) ...
154s Setting up python3-lxml:amd64 (5.3.0-1build1) ...
155s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ...
155s Setting up xml-core (0.19) ...
155s Setting up libdsdp-5.8t64 (5.8-10.1build1) ...
155s Setting up python3-contourpy (1.3.0-2build1) ...
155s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ...
155s Setting up libgcc-14-dev:amd64 (14.2.0-8ubuntu1) ...
155s Setting up libstdc++-14-dev:amd64 (14.2.0-8ubuntu1) ...
155s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ...
155s Setting up cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ...
155s Setting up libcholmod5:amd64 (1:7.8.3+dfsg-2) ...
155s Setting up libxft2:amd64 (2.3.6-1build1) ...
155s Setting up python3-scipy (1.13.1-5ubuntu1) ...
160s Setting up libtk8.6:amd64 (8.6.15-1) ...
160s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5ubuntu1) ...
160s Setting up python3-s3transfer (0.10.1-1ubuntu2) ...
160s Setting up python3.12-tk (3.12.7-3) ...
160s Setting up flake8 (7.1.1-2) ...
160s Setting up fonts-urw-base35 (20200910-8) ...
160s Setting up libcairo2:amd64 (1.18.2-2) ...
160s Setting up python3.13-tk (3.13.0-2) ...
160s Setting up python3-pil:amd64 (10.4.0-1ubuntu2) ...
161s Setting up python3-pandas (2.2.3+dfsg-5ubuntu1) ...
168s Setting up python3-ipython (8.29.0-1) ...
169s Setting up python3-boto3 (1.34.46+dfsg-1ubuntu1) ...
169s Setting up libumfpack6:amd64 (1:7.8.3+dfsg-2) ...
169s Setting up cpp (4:14.1.0-2ubuntu1) ...
169s Setting up python3-ipdb (0.13.13-2) ...
169s Setting up gcc-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ...
169s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ...
169s Setting up python3-cairo (1.26.1-2build1) ...
169s Setting up gcc-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ...
169s Setting up python3-cvxopt (1.3.0+dfsg-1build8) ...
169s Setting up blt (2.5.3+dfsg-7build1) ...
169s Setting up python3-tk:amd64 (3.12.7-1) ...
169s Setting up gcc-14 (14.2.0-8ubuntu1) ...
169s Setting up python3-pil.imagetk:amd64 (10.4.0-1ubuntu2) ...
170s Setting up python3-rlpycairo (0.3.0-3) ...
170s Setting up g++-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ...
170s Setting up python3-reportlab (4.2.5-1) ...
171s Setting up g++-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ...
171s Setting up g++-14 (14.2.0-8ubuntu1) ...
171s Setting up gcc (4:14.1.0-2ubuntu1) ...
171s Setting up g++ (4:14.1.0-2ubuntu1) ...
171s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
171s Setting up build-essential (12.10ubuntu1) ...
171s Setting up python3-fonttools (4.55.0-3) ...
172s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ...
172s Setting up python3-matplotlib (3.8.3-3ubuntu1) ...
175s Setting up python3-seaborn (0.13.2-4) ...
175s Processing triggers for systemd (256.5-2ubuntu4) ...
175s Processing triggers for man-db (2.13.0-1) ...
176s Processing triggers for libc-bin (2.40-1ubuntu3) ...
176s Processing triggers for sgml-base (1.31) ...
176s Setting up w3c-sgml-lib (1.3-3) ...
198s Setting up python3-biopython (1.84+dfsg-4build1) ...
200s Setting up python3-treetime (0.11.4-1) ...
200s Setting up seqmagick (0.8.6-3) ...
201s Setting up python3-bcbio-gff (0.7.1-2) ...
201s Setting up augur (24.4.0-1) ...
203s Reading package lists...
203s Building dependency tree...
203s Reading state information...
203s Starting pkgProblemResolver with broken count: 0
203s Starting 2 pkgProblemResolver with broken count: 0
203s Done
203s The following NEW packages will be installed:
203s   autopkgtest-satdep
203s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
203s Need to get 0 B/696 B of archives.
203s After this operation, 0 B of additional disk space will be used.
203s Get:1 /tmp/autopkgtest.oTGnkF/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [696 B]
204s Selecting previously unselected package autopkgtest-satdep.
204s (Reading database ... 
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204s Preparing to unpack .../2-autopkgtest-satdep.deb ...
204s Unpacking autopkgtest-satdep (0) ...
204s Setting up autopkgtest-satdep (0) ...
205s (Reading database ... 104856 files and directories currently installed.)
205s Removing autopkgtest-satdep (0) ...
206s autopkgtest [20:42:37]: test run-unit-test: [-----------------------
207s ============================= test session starts ==============================
207s platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.13
207s cachedir: .pytest_cache
207s rootdir: /tmp/autopkgtest.oTGnkF/build.mdW/src
207s plugins: mock-3.14.0, typeguard-4.4.1
208s collecting ... collected 12 items / 25 errors
208s 
208s ==================================== ERRORS ====================================
208s _____________ ERROR collecting tests/dates/test_ambiguous_date.py ______________
208s ImportError while importing test module '/tmp/autopkgtest.oTGnkF/build.mdW/src/tests/dates/test_ambiguous_date.py'.
208s Hint: make sure your test modules/packages have valid Python names.
208s Traceback:
208s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
208s     return _bootstrap._gcd_import(name[level:], package, level)
208s tests/dates/test_ambiguous_date.py:3: in <module>
208s     from augur.dates import ambiguous_date
208s augur/__init__.py:15: in <module>
208s     from .io.print import print_err
208s augur/io/__init__.py:6: in <module>
208s     from .metadata import read_metadata  # noqa: F401
208s augur/io/metadata.py:5: in <module>
208s     import pyfastx
208s E   ModuleNotFoundError: No module named 'pyfastx'
208s __________________ ERROR collecting tests/dates/test_dates.py __________________
208s ImportError while importing test module '/tmp/autopkgtest.oTGnkF/build.mdW/src/tests/dates/test_dates.py'.
208s Hint: make sure your test modules/packages have valid Python names.
208s Traceback:
208s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
208s     return _bootstrap._gcd_import(name[level:], package, level)
208s tests/dates/test_dates.py:4: in <module>
208s     from augur import dates
208s augur/__init__.py:15: in <module>
208s     from .io.print import print_err
208s augur/io/__init__.py:6: in <module>
208s     from .metadata import read_metadata  # noqa: F401
208s augur/io/metadata.py:5: in <module>
208s     import pyfastx
208s E   ModuleNotFoundError: No module named 'pyfastx'
208s _____________ ERROR collecting tests/filter/test_relative_dates.py _____________
208s ImportError while importing test module '/tmp/autopkgtest.oTGnkF/build.mdW/src/tests/filter/test_relative_dates.py'.
208s Hint: make sure your test modules/packages have valid Python names.
208s Traceback:
208s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
208s     return _bootstrap._gcd_import(name[level:], package, level)
208s tests/filter/test_relative_dates.py:12: in <module>
208s     from augur.filter import register_arguments
208s augur/__init__.py:15: in <module>
208s     from .io.print import print_err
208s augur/io/__init__.py:6: in <module>
208s     from .metadata import read_metadata  # noqa: F401
208s augur/io/metadata.py:5: in <module>
208s     import pyfastx
208s E   ModuleNotFoundError: No module named 'pyfastx'
208s _______________ ERROR collecting tests/filter/test_subsample.py ________________
208s ImportError while importing test module '/tmp/autopkgtest.oTGnkF/build.mdW/src/tests/filter/test_subsample.py'.
208s Hint: make sure your test modules/packages have valid Python names.
208s Traceback:
208s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
208s     return _bootstrap._gcd_import(name[level:], package, level)
208s tests/filter/test_subsample.py:4: in <module>
208s     import augur.filter.subsample
208s augur/__init__.py:15: in <module>
208s     from .io.print import print_err
208s augur/io/__init__.py:6: in <module>
208s     from .metadata import read_metadata  # noqa: F401
208s augur/io/metadata.py:5: in <module>
208s     import pyfastx
208s E   ModuleNotFoundError: No module named 'pyfastx'
208s ____________________ ERROR collecting tests/io/test_file.py ____________________
208s ImportError while importing test module '/tmp/autopkgtest.oTGnkF/build.mdW/src/tests/io/test_file.py'.
208s Hint: make sure your test modules/packages have valid Python names.
208s Traceback:
208s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
208s     return _bootstrap._gcd_import(name[level:], package, level)
208s tests/io/test_file.py:2: in <module>
208s     import augur.io.file
208s augur/__init__.py:15: in <module>
208s     from .io.print import print_err
208s augur/io/__init__.py:6: in <module>
208s     from .metadata import read_metadata  # noqa: F401
208s augur/io/metadata.py:5: in <module>
208s     import pyfastx
208s E   ModuleNotFoundError: No module named 'pyfastx'
208s __________________ ERROR collecting tests/io/test_metadata.py __________________
208s ImportError while importing test module '/tmp/autopkgtest.oTGnkF/build.mdW/src/tests/io/test_metadata.py'.
208s Hint: make sure your test modules/packages have valid Python names.
208s Traceback:
208s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
208s     return _bootstrap._gcd_import(name[level:], package, level)
208s tests/io/test_metadata.py:7: in <module>
208s     from augur.io.metadata import InvalidDelimiter, read_table_to_dict, read_metadata_with_sequences, write_records_to_tsv, Metadata
208s augur/__init__.py:15: in <module>
208s     from .io.print import print_err
208s augur/io/__init__.py:6: in <module>
208s     from .metadata import read_metadata  # noqa: F401
208s augur/io/metadata.py:5: in <module>
208s     import pyfastx
208s E   ModuleNotFoundError: No module named 'pyfastx'
208s _________________ ERROR collecting tests/io/test_sequences.py __________________
208s ImportError while importing test module '/tmp/autopkgtest.oTGnkF/build.mdW/src/tests/io/test_sequences.py'.
208s Hint: make sure your test modules/packages have valid Python names.
208s Traceback:
208s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
208s     return _bootstrap._gcd_import(name[level:], package, level)
208s tests/io/test_sequences.py:13: in <module>
208s     import augur.io.sequences
208s augur/__init__.py:15: in <module>
208s     from .io.print import print_err
208s augur/io/__init__.py:6: in <module>
208s     from .metadata import read_metadata  # noqa: F401
208s augur/io/metadata.py:5: in <module>
208s     import pyfastx
208s E   ModuleNotFoundError: No module named 'pyfastx'
208s ____________ ERROR collecting tests/io/test_shell_command_runner.py ____________
208s ImportError while importing test module '/tmp/autopkgtest.oTGnkF/build.mdW/src/tests/io/test_shell_command_runner.py'.
208s Hint: make sure your test modules/packages have valid Python names.
208s Traceback:
208s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
208s     return _bootstrap._gcd_import(name[level:], package, level)
208s tests/io/test_shell_command_runner.py:5: in <module>
208s     from augur.io.shell_command_runner import ShellCommandRunner
208s augur/__init__.py:15: in <module>
208s     from .io.print import print_err
208s augur/io/__init__.py:6: in <module>
208s     from .metadata import read_metadata  # noqa: F401
208s augur/io/metadata.py:5: in <module>
208s     import pyfastx
208s E   ModuleNotFoundError: No module named 'pyfastx'
208s __________________ ERROR collecting tests/io/test_strains.py ___________________
208s ImportError while importing test module '/tmp/autopkgtest.oTGnkF/build.mdW/src/tests/io/test_strains.py'.
208s Hint: make sure your test modules/packages have valid Python names.
208s Traceback:
208s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
208s     return _bootstrap._gcd_import(name[level:], package, level)
208s tests/io/test_strains.py:3: in <module>
208s     from augur.io.strains import read_strains
208s augur/__init__.py:15: in <module>
208s     from .io.print import print_err
208s augur/io/__init__.py:6: in <module>
208s     from .metadata import read_metadata  # noqa: F401
208s augur/io/metadata.py:5: in <module>
208s     import pyfastx
208s E   ModuleNotFoundError: No module named 'pyfastx'
208s ____________________ ERROR collecting tests/io/test_vcf.py _____________________
208s ImportError while importing test module '/tmp/autopkgtest.oTGnkF/build.mdW/src/tests/io/test_vcf.py'.
208s Hint: make sure your test modules/packages have valid Python names.
208s Traceback:
208s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
208s     return _bootstrap._gcd_import(name[level:], package, level)
208s tests/io/test_vcf.py:2: in <module>
208s     import augur.io.vcf
208s augur/__init__.py:15: in <module>
208s     from .io.print import print_err
208s augur/io/__init__.py:6: in <module>
208s     from .metadata import read_metadata  # noqa: F401
208s augur/io/metadata.py:5: in <module>
208s     import pyfastx
208s E   ModuleNotFoundError: No module named 'pyfastx'
208s _____________________ ERROR collecting tests/test_align.py _____________________
208s ImportError while importing test module '/tmp/autopkgtest.oTGnkF/build.mdW/src/tests/test_align.py'.
208s Hint: make sure your test modules/packages have valid Python names.
208s Traceback:
208s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
208s     return _bootstrap._gcd_import(name[level:], package, level)
208s tests/test_align.py:16: in <module>
208s     from augur import align
208s augur/__init__.py:15: in <module>
208s     from .io.print import print_err
208s augur/io/__init__.py:6: in <module>
208s     from .metadata import read_metadata  # noqa: F401
208s augur/io/metadata.py:5: in <module>
208s     import pyfastx
208s E   ModuleNotFoundError: No module named 'pyfastx'
208s ___________________ ERROR collecting tests/test_ancestral.py ___________________
208s ImportError while importing test module '/tmp/autopkgtest.oTGnkF/build.mdW/src/tests/test_ancestral.py'.
208s Hint: make sure your test modules/packages have valid Python names.
208s Traceback:
208s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
208s     return _bootstrap._gcd_import(name[level:], package, level)
208s tests/test_ancestral.py:1: in <module>
208s     from augur.ancestral import run_ancestral
208s augur/__init__.py:15: in <module>
208s     from .io.print import print_err
208s augur/io/__init__.py:6: in <module>
208s     from .metadata import read_metadata  # noqa: F401
208s augur/io/metadata.py:5: in <module>
208s     import pyfastx
208s E   ModuleNotFoundError: No module named 'pyfastx'
208s ____________________ ERROR collecting tests/test_clades.py _____________________
208s ImportError while importing test module '/tmp/autopkgtest.oTGnkF/build.mdW/src/tests/test_clades.py'.
208s Hint: make sure your test modules/packages have valid Python names.
208s Traceback:
208s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
208s     return _bootstrap._gcd_import(name[level:], package, level)
208s tests/test_clades.py:4: in <module>
208s     from augur.clades import read_in_clade_definitions
208s augur/__init__.py:15: in <module>
208s     from .io.print import print_err
208s augur/io/__init__.py:6: in <module>
208s     from .metadata import read_metadata  # noqa: F401
208s augur/io/metadata.py:5: in <module>
208s     import pyfastx
208s E   ModuleNotFoundError: No module named 'pyfastx'
208s __________________ ERROR collecting tests/test_frequencies.py __________________
208s ImportError while importing test module '/tmp/autopkgtest.oTGnkF/build.mdW/src/tests/test_frequencies.py'.
208s Hint: make sure your test modules/packages have valid Python names.
208s Traceback:
208s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
208s     return _bootstrap._gcd_import(name[level:], package, level)
208s tests/test_frequencies.py:14: in <module>
208s     from augur.dates import numeric_date
208s augur/__init__.py:15: in <module>
208s     from .io.print import print_err
208s augur/io/__init__.py:6: in <module>
208s     from .metadata import read_metadata  # noqa: F401
208s augur/io/metadata.py:5: in <module>
208s     import pyfastx
208s E   ModuleNotFoundError: No module named 'pyfastx'
208s _____________________ ERROR collecting tests/test_mask.py ______________________
208s ImportError while importing test module '/tmp/autopkgtest.oTGnkF/build.mdW/src/tests/test_mask.py'.
208s Hint: make sure your test modules/packages have valid Python names.
208s Traceback:
208s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
208s     return _bootstrap._gcd_import(name[level:], package, level)
208s tests/test_mask.py:15: in <module>
208s     from augur import mask
208s augur/__init__.py:15: in <module>
208s     from .io.print import print_err
208s augur/io/__init__.py:6: in <module>
208s     from .metadata import read_metadata  # noqa: F401
208s augur/io/metadata.py:5: in <module>
208s     import pyfastx
208s E   ModuleNotFoundError: No module named 'pyfastx'
208s _____________________ ERROR collecting tests/test_parse.py _____________________
208s ImportError while importing test module '/tmp/autopkgtest.oTGnkF/build.mdW/src/tests/test_parse.py'.
208s Hint: make sure your test modules/packages have valid Python names.
208s Traceback:
208s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
208s     return _bootstrap._gcd_import(name[level:], package, level)
208s tests/test_parse.py:8: in <module>
208s     from augur import parse
208s augur/__init__.py:15: in <module>
208s     from .io.print import print_err
208s augur/io/__init__.py:6: in <module>
208s     from .metadata import read_metadata  # noqa: F401
208s augur/io/metadata.py:5: in <module>
208s     import pyfastx
208s E   ModuleNotFoundError: No module named 'pyfastx'
208s _________________ ERROR collecting tests/test_titer_models.py __________________
208s ImportError while importing test module '/tmp/autopkgtest.oTGnkF/build.mdW/src/tests/test_titer_models.py'.
208s Hint: make sure your test modules/packages have valid Python names.
208s Traceback:
208s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
208s     return _bootstrap._gcd_import(name[level:], package, level)
208s tests/test_titer_models.py:2: in <module>
208s     from augur.titer_model import TiterCollection
208s augur/__init__.py:15: in <module>
208s     from .io.print import print_err
208s augur/io/__init__.py:6: in <module>
208s     from .metadata import read_metadata  # noqa: F401
208s augur/io/metadata.py:5: in <module>
208s     import pyfastx
208s E   ModuleNotFoundError: No module named 'pyfastx'
208s ___________________ ERROR collecting tests/test_translate.py ___________________
208s ImportError while importing test module '/tmp/autopkgtest.oTGnkF/build.mdW/src/tests/test_translate.py'.
208s Hint: make sure your test modules/packages have valid Python names.
208s Traceback:
208s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
208s     return _bootstrap._gcd_import(name[level:], package, level)
208s tests/test_translate.py:13: in <module>
208s     from augur import translate
208s augur/__init__.py:15: in <module>
208s     from .io.print import print_err
208s augur/io/__init__.py:6: in <module>
208s     from .metadata import read_metadata  # noqa: F401
208s augur/io/metadata.py:5: in <module>
208s     import pyfastx
208s E   ModuleNotFoundError: No module named 'pyfastx'
208s _____________________ ERROR collecting tests/test_utils.py _____________________
208s ImportError while importing test module '/tmp/autopkgtest.oTGnkF/build.mdW/src/tests/test_utils.py'.
208s Hint: make sure your test modules/packages have valid Python names.
208s Traceback:
208s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
208s     return _bootstrap._gcd_import(name[level:], package, level)
208s tests/test_utils.py:9: in <module>
208s     from augur import utils
208s augur/__init__.py:15: in <module>
208s     from .io.print import print_err
208s augur/io/__init__.py:6: in <module>
208s     from .metadata import read_metadata  # noqa: F401
208s augur/io/metadata.py:5: in <module>
208s     import pyfastx
208s E   ModuleNotFoundError: No module named 'pyfastx'
208s ___________________ ERROR collecting tests/test_validate.py ____________________
208s ImportError while importing test module '/tmp/autopkgtest.oTGnkF/build.mdW/src/tests/test_validate.py'.
208s Hint: make sure your test modules/packages have valid Python names.
208s Traceback:
208s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
208s     return _bootstrap._gcd_import(name[level:], package, level)
208s tests/test_validate.py:4: in <module>
208s     from augur.validate import (
208s augur/__init__.py:15: in <module>
208s     from .io.print import print_err
208s augur/io/__init__.py:6: in <module>
208s     from .metadata import read_metadata  # noqa: F401
208s augur/io/metadata.py:5: in <module>
208s     import pyfastx
208s E   ModuleNotFoundError: No module named 'pyfastx'
208s ________________ ERROR collecting tests/test_validate_export.py ________________
208s ImportError while importing test module '/tmp/autopkgtest.oTGnkF/build.mdW/src/tests/test_validate_export.py'.
208s Hint: make sure your test modules/packages have valid Python names.
208s Traceback:
208s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
208s     return _bootstrap._gcd_import(name[level:], package, level)
208s tests/test_validate_export.py:10: in <module>
208s     from augur.export_v2 import convert_tree_to_json_structure
208s augur/__init__.py:15: in <module>
208s     from .io.print import print_err
208s augur/io/__init__.py:6: in <module>
208s     from .metadata import read_metadata  # noqa: F401
208s augur/io/metadata.py:5: in <module>
208s     import pyfastx
208s E   ModuleNotFoundError: No module named 'pyfastx'
208s ___________ ERROR collecting tests/util_support/test_color_parser.py ___________
208s ImportError while importing test module '/tmp/autopkgtest.oTGnkF/build.mdW/src/tests/util_support/test_color_parser.py'.
208s Hint: make sure your test modules/packages have valid Python names.
208s Traceback:
208s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
208s     return _bootstrap._gcd_import(name[level:], package, level)
208s tests/util_support/test_color_parser.py:1: in <module>
208s     from augur.util_support.color_parser import ColorParser
208s augur/__init__.py:15: in <module>
208s     from .io.print import print_err
208s augur/io/__init__.py:6: in <module>
208s     from .metadata import read_metadata  # noqa: F401
208s augur/io/metadata.py:5: in <module>
208s     import pyfastx
208s E   ModuleNotFoundError: No module named 'pyfastx'
208s ____________ ERROR collecting tests/util_support/test_node_data.py _____________
208s ImportError while importing test module '/tmp/autopkgtest.oTGnkF/build.mdW/src/tests/util_support/test_node_data.py'.
208s Hint: make sure your test modules/packages have valid Python names.
208s Traceback:
208s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
208s     return _bootstrap._gcd_import(name[level:], package, level)
208s tests/util_support/test_node_data.py:1: in <module>
208s     from augur.util_support.node_data import DuplicatedNonDictAttributeError
208s augur/__init__.py:15: in <module>
208s     from .io.print import print_err
208s augur/io/__init__.py:6: in <module>
208s     from .metadata import read_metadata  # noqa: F401
208s augur/io/metadata.py:5: in <module>
208s     import pyfastx
208s E   ModuleNotFoundError: No module named 'pyfastx'
208s __________ ERROR collecting tests/util_support/test_node_data_file.py __________
208s ImportError while importing test module '/tmp/autopkgtest.oTGnkF/build.mdW/src/tests/util_support/test_node_data_file.py'.
208s Hint: make sure your test modules/packages have valid Python names.
208s Traceback:
208s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
208s     return _bootstrap._gcd_import(name[level:], package, level)
208s tests/util_support/test_node_data_file.py:3: in <module>
208s     from augur.__version__ import __version__
208s augur/__init__.py:15: in <module>
208s     from .io.print import print_err
208s augur/io/__init__.py:6: in <module>
208s     from .metadata import read_metadata  # noqa: F401
208s augur/io/metadata.py:5: in <module>
208s     import pyfastx
208s E   ModuleNotFoundError: No module named 'pyfastx'
208s _________ ERROR collecting tests/util_support/test_node_data_reader.py _________
208s ImportError while importing test module '/tmp/autopkgtest.oTGnkF/build.mdW/src/tests/util_support/test_node_data_reader.py'.
208s Hint: make sure your test modules/packages have valid Python names.
208s Traceback:
208s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
208s     return _bootstrap._gcd_import(name[level:], package, level)
208s tests/util_support/test_node_data_reader.py:1: in <module>
208s     from augur.util_support.node_data_reader import NodeDataReader
208s augur/__init__.py:15: in <module>
208s     from .io.print import print_err
208s augur/io/__init__.py:6: in <module>
208s     from .metadata import read_metadata  # noqa: F401
208s augur/io/metadata.py:5: in <module>
208s     import pyfastx
208s E   ModuleNotFoundError: No module named 'pyfastx'
208s =========================== short test summary info ============================
208s ERROR tests/dates/test_ambiguous_date.py
208s ERROR tests/dates/test_dates.py
208s ERROR tests/filter/test_relative_dates.py
208s ERROR tests/filter/test_subsample.py
208s ERROR tests/io/test_file.py
208s ERROR tests/io/test_metadata.py
208s ERROR tests/io/test_sequences.py
208s ERROR tests/io/test_shell_command_runner.py
208s ERROR tests/io/test_strains.py
208s ERROR tests/io/test_vcf.py
208s ERROR tests/test_align.py
208s ERROR tests/test_ancestral.py
208s ERROR tests/test_clades.py
208s ERROR tests/test_frequencies.py
208s ERROR tests/test_mask.py
208s ERROR tests/test_parse.py
208s ERROR tests/test_titer_models.py
208s ERROR tests/test_translate.py
208s ERROR tests/test_utils.py
208s ERROR tests/test_validate.py
208s ERROR tests/test_validate_export.py
208s ERROR tests/util_support/test_color_parser.py
208s ERROR tests/util_support/test_node_data.py
208s ERROR tests/util_support/test_node_data_file.py
208s ERROR tests/util_support/test_node_data_reader.py
208s !!!!!!!!!!!!!!!!!!! Interrupted: 25 errors during collection !!!!!!!!!!!!!!!!!!!
208s ============================== 25 errors in 1.39s ==============================
208s autopkgtest [20:42:39]: test run-unit-test: -----------------------]
209s autopkgtest [20:42:40]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
209s run-unit-test        FAIL non-zero exit status 2
209s autopkgtest [20:42:40]: @@@@@@@@@@@@@@@@@@@@ summary
209s run-unit-test        FAIL non-zero exit status 2
221s nova [W] Skipping flock for amd64
221s Creating nova instance adt-plucky-i386-augur-20241123-203911-juju-7f2275-prod-proposed-migration-environment-20-afb45bd3-69c3-4394-9b36-3fe7c04d8ec9 from image adt/ubuntu-plucky-amd64-server-20241119.img (UUID 2e5306de-7efa-448c-bc27-5518979e66f0)...