0s autopkgtest [07:10:36]: starting date and time: 2025-01-08 07:10:36+0000 0s autopkgtest [07:10:36]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [07:10:36]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.u_gc1vju/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:jinja2 --apt-upgrade pycoqc --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=jinja2/3.1.3-2 -- lxd -r lxd-armhf-10.145.243.36 lxd-armhf-10.145.243.36:autopkgtest/ubuntu/plucky/armhf 54s autopkgtest [07:11:30]: testbed dpkg architecture: armhf 57s autopkgtest [07:11:33]: testbed apt version: 2.9.14ubuntu1 63s autopkgtest [07:11:39]: @@@@@@@@@@@@@@@@@@@@ test bed setup 66s autopkgtest [07:11:42]: testbed release detected to be: None 75s autopkgtest [07:11:51]: updating testbed package index (apt update) 78s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 78s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [213 kB] 78s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 78s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 78s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 78s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [830 kB] 78s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [18.0 kB] 78s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [129 kB] 78s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [227 kB] 78s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf Packages [756 B] 78s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [877 kB] 78s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [6036 B] 78s Get:13 http://ftpmaster.internal/ubuntu plucky/universe Sources [20.8 MB] 79s Get:14 http://ftpmaster.internal/ubuntu plucky/main Sources [1376 kB] 79s Get:15 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [297 kB] 79s Get:16 http://ftpmaster.internal/ubuntu plucky/restricted Sources [15.2 kB] 79s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1357 kB] 79s Get:18 http://ftpmaster.internal/ubuntu plucky/restricted armhf Packages [2544 B] 79s Get:19 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [14.9 MB] 80s Get:20 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [173 kB] 83s Fetched 41.3 MB in 5s (7900 kB/s) 84s Reading package lists... 90s autopkgtest [07:12:06]: upgrading testbed (apt dist-upgrade and autopurge) 92s Reading package lists... 93s Building dependency tree... 93s Reading state information... 93s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 94s Starting 2 pkgProblemResolver with broken count: 0 94s Done 95s Entering ResolveByKeep 95s 96s The following package was automatically installed and is no longer required: 96s libassuan0 96s Use 'apt autoremove' to remove it. 96s The following NEW packages will be installed: 96s openssl-provider-legacy python3-bcrypt 96s The following packages will be upgraded: 96s apport apport-core-dump-handler appstream apt apt-utils base-passwd bash 96s bash-completion binutils binutils-arm-linux-gnueabihf binutils-common 96s bsdextrautils bsdutils curl dirmngr dracut-install eject ethtool fdisk fwupd 96s gcc-14-base gettext-base gir1.2-girepository-2.0 gir1.2-glib-2.0 gnupg 96s gnupg-l10n gnupg-utils gpg gpg-agent gpg-wks-client gpgconf gpgsm gpgv 96s groff-base iputils-ping iputils-tracepath keyboxd libappstream5 96s libapt-pkg6.0t64 libatomic1 libbinutils libblkid1 libbpf1 libc-bin libc6 96s libcap-ng0 libctf-nobfd0 libctf0 libcurl3t64-gnutls libcurl4t64 96s libdebconfclient0 libfdisk1 libfribidi0 libftdi1-2 libfwupd3 libgcc-s1 96s libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-bin libglib2.0-data 96s libgpg-error-l10n libgpg-error0 libgstreamer1.0-0 libjson-glib-1.0-0 96s libjson-glib-1.0-common libmount1 libnewt0.52 libnpth0t64 libnss-systemd 96s libnss3 libpam-systemd libpng16-16t64 libpython3-stdlib 96s libpython3.12-minimal libpython3.12-stdlib libqmi-glib5 libqmi-proxy 96s libreadline8t64 libsframe1 libsmartcols1 libssl3t64 libstdc++6 96s libsystemd-shared libsystemd0 libtraceevent1 libtraceevent1-plugin libudev1 96s libunistring5 libuuid1 libwrap0 libxkbcommon0 libxml2 libyaml-0-2 locales 96s make mount nano openssl pci.ids publicsuffix python-apt-common python3 96s python3-apport python3-apt python3-attr python3-cryptography python3-gdbm 96s python3-jinja2 python3-json-pointer python3-jsonpatch python3-minimal 96s python3-newt python3-openssl python3-pkg-resources python3-problem-report 96s python3-rich python3-setuptools python3-software-properties python3-wadllib 96s python3.12 python3.12-gdbm python3.12-minimal python3.13-gdbm 96s readline-common rsync software-properties-common systemd systemd-cryptsetup 96s systemd-resolved systemd-sysv systemd-timesyncd tar tzdata ucf udev usb.ids 96s util-linux uuid-runtime whiptail xauth 96s 140 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 96s Need to get 58.6 MB of archives. 96s After this operation, 8867 kB of additional disk space will be used. 96s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf bash armhf 5.2.37-1ubuntu1 [677 kB] 96s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf bsdutils armhf 1:2.40.2-1ubuntu2 [108 kB] 96s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf tar armhf 1.35+dfsg-3.1 [240 kB] 96s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libatomic1 armhf 14.2.0-12ubuntu1 [7892 B] 96s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-base armhf 14.2.0-12ubuntu1 [52.6 kB] 96s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-s1 armhf 14.2.0-12ubuntu1 [40.6 kB] 96s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++6 armhf 14.2.0-12ubuntu1 [711 kB] 96s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libc6 armhf 2.40-4ubuntu1 [2866 kB] 97s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf openssl-provider-legacy armhf 3.4.0-1ubuntu2 [29.4 kB] 97s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libssl3t64 armhf 3.4.0-1ubuntu2 [1756 kB] 97s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf systemd-timesyncd armhf 257-2ubuntu1 [41.2 kB] 97s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf systemd-resolved armhf 257-2ubuntu1 [307 kB] 97s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf systemd-cryptsetup armhf 257-2ubuntu1 [122 kB] 97s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf eject armhf 2.40.2-1ubuntu2 [62.3 kB] 97s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf bsdextrautils armhf 2.40.2-1ubuntu2 [99.4 kB] 97s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf fdisk armhf 2.40.2-1ubuntu2 [155 kB] 97s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libblkid1 armhf 2.40.2-1ubuntu2 [167 kB] 97s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libmount1 armhf 2.40.2-1ubuntu2 [189 kB] 97s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libsmartcols1 armhf 2.40.2-1ubuntu2 [135 kB] 97s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libuuid1 armhf 2.40.2-1ubuntu2 [39.5 kB] 97s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf util-linux armhf 2.40.2-1ubuntu2 [1195 kB] 97s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf uuid-runtime armhf 2.40.2-1ubuntu2 [62.7 kB] 97s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf libfdisk1 armhf 2.40.2-1ubuntu2 [211 kB] 97s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf mount armhf 2.40.2-1ubuntu2 [156 kB] 97s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf readline-common all 8.2-6 [56.5 kB] 97s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libreadline8t64 armhf 8.2-6 [131 kB] 97s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libnss-systemd armhf 257-2ubuntu1 [160 kB] 97s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf systemd armhf 257-2ubuntu1 [3489 kB] 97s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf udev armhf 257-2ubuntu1 [1974 kB] 97s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf systemd-sysv armhf 257-2ubuntu1 [11.8 kB] 97s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf libpam-systemd armhf 257-2ubuntu1 [233 kB] 97s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libsystemd-shared armhf 257-2ubuntu1 [2156 kB] 97s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libudev1 armhf 257-2ubuntu1 [190 kB] 97s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libsystemd0 armhf 257-2ubuntu1 [483 kB] 97s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libdebconfclient0 armhf 0.274ubuntu1 [11.2 kB] 97s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf base-passwd armhf 3.6.6 [53.4 kB] 97s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libc-bin armhf 2.40-4ubuntu1 [542 kB] 97s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libapt-pkg6.0t64 armhf 2.9.18 [1085 kB] 97s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf apt armhf 2.9.18 [1349 kB] 97s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf apt-utils armhf 2.9.18 [216 kB] 97s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libgpg-error-l10n all 1.51-3 [8800 B] 97s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf libgpg-error0 armhf 1.51-3 [64.8 kB] 97s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf libnpth0t64 armhf 1.8-2 [7572 B] 97s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf gpg-wks-client armhf 2.4.4-2ubuntu21 [88.9 kB] 97s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf dirmngr armhf 2.4.4-2ubuntu21 [351 kB] 97s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf gpgsm armhf 2.4.4-2ubuntu21 [246 kB] 97s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf gnupg-utils armhf 2.4.4-2ubuntu21 [160 kB] 97s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf gpg-agent armhf 2.4.4-2ubuntu21 [238 kB] 97s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf gpg armhf 2.4.4-2ubuntu21 [536 kB] 97s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf gpgconf armhf 2.4.4-2ubuntu21 [118 kB] 97s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf gnupg all 2.4.4-2ubuntu21 [359 kB] 97s Get:52 http://ftpmaster.internal/ubuntu plucky/main armhf keyboxd armhf 2.4.4-2ubuntu21 [113 kB] 97s Get:53 http://ftpmaster.internal/ubuntu plucky/main armhf gpgv armhf 2.4.4-2ubuntu21 [228 kB] 97s Get:54 http://ftpmaster.internal/ubuntu plucky/main armhf python3-minimal armhf 3.12.8-1 [27.5 kB] 97s Get:55 http://ftpmaster.internal/ubuntu plucky/main armhf python3 armhf 3.12.8-1 [23.9 kB] 97s Get:56 http://ftpmaster.internal/ubuntu plucky/main armhf tzdata all 2024b-4ubuntu1 [196 kB] 97s Get:57 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12 armhf 3.12.8-3 [667 kB] 97s Get:58 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12-stdlib armhf 3.12.8-3 [1939 kB] 97s Get:59 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-minimal armhf 3.12.8-3 [2029 kB] 97s Get:60 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12-minimal armhf 3.12.8-3 [825 kB] 97s Get:61 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3-stdlib armhf 3.12.8-1 [10.1 kB] 97s Get:62 http://ftpmaster.internal/ubuntu plucky/main armhf rsync armhf 3.3.0+ds1-2 [422 kB] 97s Get:63 http://ftpmaster.internal/ubuntu plucky/main armhf python-apt-common all 2.9.6build1 [21.0 kB] 97s Get:64 http://ftpmaster.internal/ubuntu plucky/main armhf python3-apt armhf 2.9.6build1 [174 kB] 97s Get:65 http://ftpmaster.internal/ubuntu plucky/main armhf python3-problem-report all 2.31.0-0ubuntu2 [25.3 kB] 97s Get:66 http://ftpmaster.internal/ubuntu plucky/main armhf python3-apport all 2.31.0-0ubuntu2 [93.1 kB] 97s Get:67 http://ftpmaster.internal/ubuntu plucky/main armhf libglib2.0-data all 2.82.4-1 [52.2 kB] 97s Get:68 http://ftpmaster.internal/ubuntu plucky/main armhf libglib2.0-bin armhf 2.82.4-1 [93.0 kB] 98s Get:69 http://ftpmaster.internal/ubuntu plucky/main armhf gir1.2-girepository-2.0 armhf 1.82.0-3 [25.3 kB] 98s Get:70 http://ftpmaster.internal/ubuntu plucky/main armhf gir1.2-glib-2.0 armhf 2.82.4-1 [182 kB] 98s Get:71 http://ftpmaster.internal/ubuntu plucky/main armhf libglib2.0-0t64 armhf 2.82.4-1 [1421 kB] 98s Get:72 http://ftpmaster.internal/ubuntu plucky/main armhf libgirepository-1.0-1 armhf 1.82.0-3 [108 kB] 98s Get:73 http://ftpmaster.internal/ubuntu plucky/main armhf apport-core-dump-handler all 2.31.0-0ubuntu2 [18.2 kB] 98s Get:74 http://ftpmaster.internal/ubuntu plucky/main armhf apport all 2.31.0-0ubuntu2 [82.9 kB] 98s Get:75 http://ftpmaster.internal/ubuntu plucky/main armhf libcap-ng0 armhf 0.8.5-4 [13.8 kB] 98s Get:76 http://ftpmaster.internal/ubuntu plucky/main armhf libunistring5 armhf 1.3-1 [583 kB] 98s Get:77 http://ftpmaster.internal/ubuntu plucky/main armhf iputils-ping armhf 3:20240905-1ubuntu1 [45.0 kB] 98s Get:78 http://ftpmaster.internal/ubuntu plucky/main armhf libbpf1 armhf 1:1.5.0-2 [158 kB] 98s Get:79 http://ftpmaster.internal/ubuntu plucky/main armhf libfribidi0 armhf 1.0.16-1 [24.3 kB] 98s Get:80 http://ftpmaster.internal/ubuntu plucky/main armhf python3-newt armhf 0.52.24-4ubuntu1 [20.1 kB] 98s Get:81 http://ftpmaster.internal/ubuntu plucky/main armhf libnewt0.52 armhf 0.52.24-4ubuntu1 [39.7 kB] 98s Get:82 http://ftpmaster.internal/ubuntu plucky/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2build1 [599 kB] 98s Get:83 http://ftpmaster.internal/ubuntu plucky/main armhf libyaml-0-2 armhf 0.2.5-2 [45.3 kB] 98s Get:84 http://ftpmaster.internal/ubuntu plucky/main armhf locales all 2.40-4ubuntu1 [4224 kB] 98s Get:85 http://ftpmaster.internal/ubuntu plucky/main armhf openssl armhf 3.4.0-1ubuntu2 [1159 kB] 98s Get:86 http://ftpmaster.internal/ubuntu plucky/main armhf python3-rich all 13.9.4-1 [190 kB] 98s Get:87 http://ftpmaster.internal/ubuntu plucky/main armhf ucf all 3.0046 [41.9 kB] 98s Get:88 http://ftpmaster.internal/ubuntu plucky/main armhf whiptail armhf 0.52.24-4ubuntu1 [17.3 kB] 98s Get:89 http://ftpmaster.internal/ubuntu plucky/main armhf bash-completion all 1:2.16.0-1 [214 kB] 98s Get:90 http://ftpmaster.internal/ubuntu plucky/main armhf ethtool armhf 1:6.11-1 [222 kB] 98s Get:91 http://ftpmaster.internal/ubuntu plucky/main armhf gettext-base armhf 0.22.5-3 [40.7 kB] 98s Get:92 http://ftpmaster.internal/ubuntu plucky/main armhf groff-base armhf 1.23.0-7 [949 kB] 98s Get:93 http://ftpmaster.internal/ubuntu plucky/main armhf iputils-tracepath armhf 3:20240905-1ubuntu1 [13.3 kB] 98s Get:94 http://ftpmaster.internal/ubuntu plucky/main armhf libpng16-16t64 armhf 1.6.44-3 [169 kB] 98s Get:95 http://ftpmaster.internal/ubuntu plucky/main armhf libtraceevent1-plugin armhf 1:1.8.4-2 [19.0 kB] 98s Get:96 http://ftpmaster.internal/ubuntu plucky/main armhf libtraceevent1 armhf 1:1.8.4-2 [53.8 kB] 98s Get:97 http://ftpmaster.internal/ubuntu plucky/main armhf libxkbcommon0 armhf 1.7.0-2 [113 kB] 98s Get:98 http://ftpmaster.internal/ubuntu plucky/main armhf nano armhf 8.3-1 [277 kB] 98s Get:99 http://ftpmaster.internal/ubuntu plucky/main armhf pci.ids all 0.0~2024.11.25-1 [282 kB] 98s Get:100 http://ftpmaster.internal/ubuntu plucky/main armhf publicsuffix all 20241206.1516-0.1 [135 kB] 98s Get:101 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-gdbm armhf 3.13.1-2 [29.8 kB] 98s Get:102 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-gdbm armhf 3.12.8-3 [28.9 kB] 98s Get:103 http://ftpmaster.internal/ubuntu plucky/main armhf python3-gdbm armhf 3.13.1-1 [8668 B] 98s Get:104 http://ftpmaster.internal/ubuntu plucky/main armhf usb.ids all 2024.12.04-1 [223 kB] 99s Get:105 http://ftpmaster.internal/ubuntu plucky/main armhf xauth armhf 1:1.1.2-1.1 [23.0 kB] 99s Get:106 http://ftpmaster.internal/ubuntu plucky/main armhf libcurl3t64-gnutls armhf 8.11.1-1ubuntu1 [333 kB] 99s Get:107 http://ftpmaster.internal/ubuntu plucky/main armhf libappstream5 armhf 1.0.4-1 [211 kB] 99s Get:108 http://ftpmaster.internal/ubuntu plucky/main armhf appstream armhf 1.0.4-1 [67.3 kB] 99s Get:109 http://ftpmaster.internal/ubuntu plucky/main armhf libctf0 armhf 2.43.50.20241230-1ubuntu1 [74.5 kB] 99s Get:110 http://ftpmaster.internal/ubuntu plucky/main armhf libctf-nobfd0 armhf 2.43.50.20241230-1ubuntu1 [77.3 kB] 99s Get:111 http://ftpmaster.internal/ubuntu plucky/main armhf binutils-arm-linux-gnueabihf armhf 2.43.50.20241230-1ubuntu1 [2960 kB] 99s Get:112 http://ftpmaster.internal/ubuntu plucky/main armhf libbinutils armhf 2.43.50.20241230-1ubuntu1 [403 kB] 99s Get:113 http://ftpmaster.internal/ubuntu plucky/main armhf binutils armhf 2.43.50.20241230-1ubuntu1 [3086 B] 99s Get:114 http://ftpmaster.internal/ubuntu plucky/main armhf binutils-common armhf 2.43.50.20241230-1ubuntu1 [222 kB] 99s Get:115 http://ftpmaster.internal/ubuntu plucky/main armhf libsframe1 armhf 2.43.50.20241230-1ubuntu1 [12.1 kB] 99s Get:116 http://ftpmaster.internal/ubuntu plucky/main armhf curl armhf 8.11.1-1ubuntu1 [244 kB] 99s Get:117 http://ftpmaster.internal/ubuntu plucky/main armhf libcurl4t64 armhf 8.11.1-1ubuntu1 [337 kB] 99s Get:118 http://ftpmaster.internal/ubuntu plucky/main armhf dracut-install armhf 105-2ubuntu5 [37.3 kB] 99s Get:119 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-common all 1.10.6+ds-1 [5636 B] 99s Get:120 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-0 armhf 1.10.6+ds-1 [59.5 kB] 99s Get:121 http://ftpmaster.internal/ubuntu plucky/main armhf fwupd armhf 2.0.3-3 [5028 kB] 99s Get:122 http://ftpmaster.internal/ubuntu plucky/main armhf libfwupd3 armhf 2.0.3-3 [121 kB] 99s Get:123 http://ftpmaster.internal/ubuntu plucky/main armhf libqmi-proxy armhf 1.35.6-1 [5878 B] 99s Get:124 http://ftpmaster.internal/ubuntu plucky/main armhf libqmi-glib5 armhf 1.35.6-1 [928 kB] 99s Get:125 http://ftpmaster.internal/ubuntu plucky/main armhf gnupg-l10n all 2.4.4-2ubuntu21 [66.3 kB] 99s Get:126 http://ftpmaster.internal/ubuntu plucky/main armhf libftdi1-2 armhf 1.5-8 [26.3 kB] 99s Get:127 http://ftpmaster.internal/ubuntu plucky/main armhf libgstreamer1.0-0 armhf 1.24.10-2 [1109 kB] 99s Get:128 http://ftpmaster.internal/ubuntu plucky/main armhf libnss3 armhf 2:3.106-1ubuntu1 [1321 kB] 99s Get:129 http://ftpmaster.internal/ubuntu plucky/main armhf libwrap0 armhf 7.6.q-34 [45.7 kB] 99s Get:130 http://ftpmaster.internal/ubuntu plucky/main armhf make armhf 4.4.1-1 [180 kB] 99s Get:131 http://ftpmaster.internal/ubuntu plucky/main armhf python3-attr all 24.2.0-1 [50.2 kB] 99s Get:132 http://ftpmaster.internal/ubuntu plucky/main armhf python3-bcrypt armhf 4.2.0-2.1 [239 kB] 99s Get:133 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cryptography armhf 43.0.0-1 [925 kB] 99s Get:134 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-jinja2 all 3.1.3-2 [108 kB] 99s Get:135 http://ftpmaster.internal/ubuntu plucky/main armhf python3-json-pointer all 2.4-3 [8444 B] 99s Get:136 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jsonpatch all 1.32-5 [12.3 kB] 99s Get:137 http://ftpmaster.internal/ubuntu plucky/main armhf python3-openssl all 24.3.0-1 [45.8 kB] 99s Get:138 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pkg-resources all 75.6.0-1 [144 kB] 99s Get:139 http://ftpmaster.internal/ubuntu plucky/main armhf python3-setuptools all 75.6.0-1 [645 kB] 99s Get:140 http://ftpmaster.internal/ubuntu plucky/main armhf software-properties-common all 0.108 [16.5 kB] 99s Get:141 http://ftpmaster.internal/ubuntu plucky/main armhf python3-software-properties all 0.108 [30.9 kB] 99s Get:142 http://ftpmaster.internal/ubuntu plucky/main armhf python3-wadllib all 2.0.0-2 [36.2 kB] 100s Preconfiguring packages ... 100s Fetched 58.6 MB in 4s (16.7 MB/s) 100s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59970 files and directories currently installed.) 100s Preparing to unpack .../bash_5.2.37-1ubuntu1_armhf.deb ... 100s Unpacking bash (5.2.37-1ubuntu1) over (5.2.32-1ubuntu2) ... 100s Setting up bash (5.2.37-1ubuntu1) ... 100s 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 101s (Reading database ... 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... 116s Unpacking python3-wadllib (2.0.0-2) over (2.0.0-1) ... 117s Setting up systemd-sysv (257-2ubuntu1) ... 117s Setting up pci.ids (0.0~2024.11.25-1) ... 117s Setting up libnewt0.52:armhf (0.52.24-4ubuntu1) ... 117s Setting up apt-utils (2.9.18) ... 117s Setting up bsdextrautils (2.40.2-1ubuntu2) ... 117s Setting up libcurl4t64:armhf (8.11.1-1ubuntu1) ... 117s Setting up libyaml-0-2:armhf (0.2.5-2) ... 117s Setting up python3.12-gdbm (3.12.8-3) ... 117s Setting up libpython3.12-minimal:armhf (3.12.8-3) ... 117s Setting up binutils-common:armhf (2.43.50.20241230-1ubuntu1) ... 117s Setting up libcurl3t64-gnutls:armhf (8.11.1-1ubuntu1) ... 117s Setting up libctf-nobfd0:armhf (2.43.50.20241230-1ubuntu1) ... 117s Setting up gettext-base (0.22.5-3) ... 117s Setting up libnss-systemd:armhf (257-2ubuntu1) ... 117s Setting up libnss3:armhf (2:3.106-1ubuntu1) ... 117s Setting up locales (2.40-4ubuntu1) ... 118s Generating locales (this might take a while)... 120s en_US.UTF-8... done 120s Generation complete. 120s Setting up libsframe1:armhf (2.43.50.20241230-1ubuntu1) ... 120s Setting up tzdata (2024b-4ubuntu1) ... 120s 120s Current default time zone: 'Etc/UTC' 120s Local time is now: Wed Jan 8 07:12:36 UTC 2025. 120s Universal Time is now: Wed Jan 8 07:12:36 UTC 2025. 120s Run 'dpkg-reconfigure tzdata' if you wish to change it. 120s 120s Setting up eject (2.40.2-1ubuntu2) ... 120s Setting up libftdi1-2:armhf (1.5-8) ... 120s Setting up libglib2.0-data (2.82.4-1) ... 120s Setting up systemd-cryptsetup (257-2ubuntu1) ... 120s Setting up libwrap0:armhf (7.6.q-34) ... 120s Setting up make (4.4.1-1) ... 120s Setting up gnupg-l10n (2.4.4-2ubuntu21) ... 120s Setting up bash-completion (1:2.16.0-1) ... 120s Setting up libfribidi0:armhf (1.0.16-1) ... 120s Setting up libpng16-16t64:armhf (1.6.44-3) ... 120s Setting up systemd-timesyncd (257-2ubuntu1) ... 121s systemd-time-wait-sync.service is a disabled or a static unit not running, not starting it. 121s Setting up libatomic1:armhf (14.2.0-12ubuntu1) ... 121s Setting up udev (257-2ubuntu1) ... 122s Setting up usb.ids (2024.12.04-1) ... 122s Setting up ucf (3.0046) ... 122s Installing new version of config file /etc/ucf.conf ... 122s Setting up libfdisk1:armhf (2.40.2-1ubuntu2) ... 122s Setting up nano (8.3-1) ... 122s Installing new version of config file /etc/nanorc ... 122s Setting up whiptail (0.52.24-4ubuntu1) ... 122s Setting up python-apt-common (2.9.6build1) ... 122s Setting up dracut-install (105-2ubuntu5) ... 122s Setting up uuid-runtime (2.40.2-1ubuntu2) ... 123s uuidd.service is a disabled or a static unit not running, not starting it. 123s Setting up xauth (1:1.1.2-1.1) ... 123s Setting up groff-base (1.23.0-7) ... 123s Setting up libtraceevent1:armhf (1:1.8.4-2) ... 123s Setting up libpam-systemd:armhf (257-2ubuntu1) ... 123s Setting up libjson-glib-1.0-common (1.10.6+ds-1) ... 123s Setting up curl (8.11.1-1ubuntu1) ... 123s Setting up libbinutils:armhf (2.43.50.20241230-1ubuntu1) ... 123s Setting up openssl (3.4.0-1ubuntu2) ... 123s Installing new version of config file /etc/ssl/openssl.cnf ... 123s Setting up libgpg-error-l10n (1.51-3) ... 123s Setting up iputils-ping (3:20240905-1ubuntu1) ... 123s Setting up readline-common (8.2-6) ... 123s Setting up publicsuffix (20241206.1516-0.1) ... 123s Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2build1) ... 123s Setting up libbpf1:armhf (1:1.5.0-2) ... 123s Setting up iputils-tracepath (3:20240905-1ubuntu1) ... 123s Setting up rsync (3.3.0+ds1-2) ... 124s rsync.service is a disabled or a static unit not running, not starting it. 124s Setting up python3.13-gdbm (3.13.1-2) ... 124s Setting up ethtool (1:6.11-1) ... 124s Setting up gnupg-utils (2.4.4-2ubuntu21) ... 124s Setting up systemd-resolved (257-2ubuntu1) ... 125s Setting up libxkbcommon0:armhf (1.7.0-2) ... 125s Setting up libctf0:armhf (2.43.50.20241230-1ubuntu1) ... 125s Setting up python3.12-minimal (3.12.8-3) ... 126s Setting up libglib2.0-0t64:armhf (2.82.4-1) ... 126s No schema files found: doing nothing. 126s Setting up gir1.2-glib-2.0:armhf (2.82.4-1) ... 126s Setting up libreadline8t64:armhf (8.2-6) ... 126s Setting up libtraceevent1-plugin:armhf (1:1.8.4-2) ... 126s Setting up gpgconf (2.4.4-2ubuntu21) ... 126s Setting up libgirepository-1.0-1:armhf (1.82.0-3) ... 126s Setting up binutils-arm-linux-gnueabihf (2.43.50.20241230-1ubuntu1) ... 126s Setting up gpg (2.4.4-2ubuntu21) ... 126s Setting up libgstreamer1.0-0:armhf (1.24.10-2) ... 126s Setcap worked! gst-ptp-helper is not suid! 126s Setting up gpg-agent (2.4.4-2ubuntu21) ... 126s Setting up libpython3.12-stdlib:armhf (3.12.8-3) ... 126s Setting up python3.12 (3.12.8-3) ... 127s Setting up gpgsm (2.4.4-2ubuntu21) ... 127s Setting up libglib2.0-bin (2.82.4-1) ... 127s Setting up libappstream5:armhf (1.0.4-1) ... 127s Setting up libqmi-glib5:armhf (1.35.6-1) ... 127s Setting up binutils (2.43.50.20241230-1ubuntu1) ... 127s Setting up fdisk (2.40.2-1ubuntu2) ... 127s Setting up libjson-glib-1.0-0:armhf (1.10.6+ds-1) ... 127s Setting up dirmngr (2.4.4-2ubuntu21) ... 128s Setting up appstream (1.0.4-1) ... 128s ✔ Metadata cache was updated successfully. 128s Setting up gir1.2-girepository-2.0:armhf (1.82.0-3) ... 128s Setting up keyboxd (2.4.4-2ubuntu21) ... 128s Setting up gnupg (2.4.4-2ubuntu21) ... 128s Setting up libpython3-stdlib:armhf (3.12.8-1) ... 128s Setting up gpg-wks-client (2.4.4-2ubuntu21) ... 128s Setting up libqmi-proxy (1.35.6-1) ... 128s Setting up libfwupd3:armhf (2.0.3-3) ... 128s Setting up python3 (3.12.8-1) ... 128s Setting up python3-newt:armhf (0.52.24-4ubuntu1) ... 128s Setting up python3-jinja2 (3.1.3-2) ... 129s Setting up python3-wadllib (2.0.0-2) ... 129s Setting up python3-json-pointer (2.4-3) ... 129s Setting up fwupd (2.0.3-3) ... 130s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 130s fwupd.service is a disabled or a static unit not running, not starting it. 130s Setting up python3-pkg-resources (75.6.0-1) ... 130s Setting up python3-attr (24.2.0-1) ... 130s Setting up python3-setuptools (75.6.0-1) ... 131s Setting up python3-rich (13.9.4-1) ... 131s Setting up python3-gdbm:armhf (3.13.1-1) ... 131s Setting up python3-problem-report (2.31.0-0ubuntu2) ... 132s Setting up python3-apt (2.9.6build1) ... 132s Setting up python3-jsonpatch (1.32-5) ... 132s Setting up python3-bcrypt (4.2.0-2.1) ... 132s Setting up python3-apport (2.31.0-0ubuntu2) ... 132s Setting up python3-software-properties (0.108) ... 132s Setting up python3-cryptography (43.0.0-1) ... 133s Setting up python3-openssl (24.3.0-1) ... 133s Setting up software-properties-common (0.108) ... 133s Setting up apport-core-dump-handler (2.31.0-0ubuntu2) ... 134s Setting up apport (2.31.0-0ubuntu2) ... 135s apport-autoreport.service is a disabled or a static unit not running, not starting it. 135s Processing triggers for dbus (1.14.10-4ubuntu5) ... 135s Processing triggers for shared-mime-info (2.4-5) ... 135s Warning: program compiled against libxml 212 using older 209 135s Processing triggers for debianutils (5.21) ... 135s Processing triggers for install-info (7.1.1-1) ... 135s Processing triggers for initramfs-tools (0.142ubuntu35) ... 135s Processing triggers for libc-bin (2.40-4ubuntu1) ... 135s Processing triggers for systemd (257-2ubuntu1) ... 135s Processing triggers for man-db (2.13.0-1) ... 140s Reading package lists... 141s Building dependency tree... 141s Reading state information... 141s Starting pkgProblemResolver with broken count: 0 141s Starting 2 pkgProblemResolver with broken count: 0 141s Done 143s The following packages will be REMOVED: 143s libassuan0* 143s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 143s After this operation, 68.6 kB disk space will be freed. 143s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 60003 files and directories currently installed.) 143s Removing libassuan0:armhf (2.5.6-1build1) ... 143s Processing triggers for libc-bin (2.40-4ubuntu1) ... 146s autopkgtest [07:13:02]: rebooting testbed after setup commands that affected boot 207s autopkgtest [07:14:02]: testbed running kernel: Linux 6.8.0-49-generic #49~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Nov 6 18:12:14 UTC 2 248s autopkgtest [07:14:44]: @@@@@@@@@@@@@@@@@@@@ apt-source pycoqc 264s Get:1 http://ftpmaster.internal/ubuntu plucky/universe pycoqc 2.5.2+dfsg-3 (dsc) [2051 B] 264s Get:2 http://ftpmaster.internal/ubuntu plucky/universe pycoqc 2.5.2+dfsg-3 (tar) [41.6 MB] 264s Get:3 http://ftpmaster.internal/ubuntu plucky/universe pycoqc 2.5.2+dfsg-3 (diff) [6764 B] 264s gpgv: Signature made Tue Dec 7 15:51:27 2021 UTC 264s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 264s gpgv: issuer "tille@debian.org" 264s gpgv: Can't check signature: No public key 264s dpkg-source: warning: cannot verify inline signature for ./pycoqc_2.5.2+dfsg-3.dsc: no acceptable signature found 266s autopkgtest [07:15:02]: testing package pycoqc version 2.5.2+dfsg-3 269s autopkgtest [07:15:05]: build not needed 277s autopkgtest [07:15:13]: test run-unit-test: preparing testbed 280s Reading package lists... 280s Building dependency tree... 280s Reading state information... 281s Starting pkgProblemResolver with broken count: 0 281s Starting 2 pkgProblemResolver with broken count: 0 281s Done 282s The following NEW packages will be installed: 282s libaec0 libblas3 libdeflate0 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 282s libhts3t64 libhtscodecs2 liblapack3 liblbfgsb0 liblzf1 libsz2 pycoqc 282s python3-dateutil python3-decorator python3-fastjsonschema python3-h5py 282s python3-h5py-serial python3-jupyter-core python3-nbformat python3-numpy 282s python3-pandas python3-pandas-lib python3-platformdirs python3-plotly 282s python3-pysam python3-scipy python3-tenacity python3-tqdm python3-traitlets 282s python3-tz 282s 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. 282s Need to get 47.7 MB of archives. 282s After this operation, 271 MB of additional disk space will be used. 282s Get:1 http://ftpmaster.internal/ubuntu plucky/universe armhf libaec0 armhf 1.1.3-1 [20.8 kB] 282s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-4 [126 kB] 282s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.22-1 [38.9 kB] 282s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-12ubuntu1 [311 kB] 283s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf libsz2 armhf 1.1.3-1 [5302 B] 283s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-103-1t64 armhf 1.10.10+repack-5ubuntu1 [1266 kB] 283s Get:7 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-hl-100t64 armhf 1.10.10+repack-5ubuntu1 [56.2 kB] 283s Get:8 http://ftpmaster.internal/ubuntu plucky/universe armhf libhtscodecs2 armhf 1.6.1-1 [67.9 kB] 283s Get:9 http://ftpmaster.internal/ubuntu plucky/universe armhf libhts3t64 armhf 1.20+ds-2 [394 kB] 283s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-4 [2086 kB] 283s Get:11 http://ftpmaster.internal/ubuntu plucky/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1build1 [27.4 kB] 283s Get:12 http://ftpmaster.internal/ubuntu plucky/universe armhf liblzf1 armhf 3.6-4 [6554 B] 283s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-12 [4001 kB] 283s Get:14 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py-serial armhf 3.11.0-8ubuntu3 [1559 kB] 283s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf python3-dateutil all 2.9.0-3 [80.2 kB] 283s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tz all 2024.2-1 [31.5 kB] 283s Get:17 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas-lib armhf 2.2.3+dfsg-5ubuntu1 [7608 kB] 284s Get:18 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas all 2.2.3+dfsg-5ubuntu1 [3112 kB] 284s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf python3-decorator all 5.1.1-5 [10.1 kB] 284s Get:20 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-fastjsonschema all 2.21.1-1 [20.4 kB] 284s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf python3-platformdirs all 4.3.6-1 [16.8 kB] 284s Get:22 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 284s Get:23 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-jupyter-core all 5.7.2-5 [28.1 kB] 284s Get:24 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-nbformat all 5.9.1-1 [41.2 kB] 284s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tenacity all 8.5.0-0ubuntu1 [17.0 kB] 284s Get:26 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-plotly all 5.20.0+dfsg-1 [2766 kB] 284s Get:27 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pysam armhf 0.22.1+ds-2build1 [3965 kB] 284s Get:28 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-scipy armhf 1.14.1-3ubuntu1 [19.8 MB] 285s Get:29 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-tqdm all 4.67.1-1 [92.5 kB] 285s Get:30 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py all 3.11.0-8ubuntu3 [7982 B] 285s Get:31 http://ftpmaster.internal/ubuntu plucky/universe armhf pycoqc all 2.5.2+dfsg-3 [36.4 kB] 285s Fetched 47.7 MB in 3s (17.0 MB/s) 285s Selecting previously unselected package libaec0:armhf. 285s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59998 files and directories currently installed.) 285s Preparing to unpack .../00-libaec0_1.1.3-1_armhf.deb ... 285s Unpacking libaec0:armhf (1.1.3-1) ... 285s Selecting previously unselected package libblas3:armhf. 285s Preparing to unpack .../01-libblas3_3.12.0-4_armhf.deb ... 285s Unpacking libblas3:armhf (3.12.0-4) ... 285s Selecting previously unselected package libdeflate0:armhf. 285s Preparing to unpack .../02-libdeflate0_1.22-1_armhf.deb ... 285s Unpacking libdeflate0:armhf (1.22-1) ... 285s Selecting previously unselected package libgfortran5:armhf. 285s Preparing to unpack .../03-libgfortran5_14.2.0-12ubuntu1_armhf.deb ... 285s Unpacking libgfortran5:armhf (14.2.0-12ubuntu1) ... 286s Selecting previously unselected package libsz2:armhf. 286s Preparing to unpack .../04-libsz2_1.1.3-1_armhf.deb ... 286s Unpacking libsz2:armhf (1.1.3-1) ... 286s Selecting previously unselected package libhdf5-103-1t64:armhf. 286s Preparing to unpack .../05-libhdf5-103-1t64_1.10.10+repack-5ubuntu1_armhf.deb ... 286s Unpacking libhdf5-103-1t64:armhf (1.10.10+repack-5ubuntu1) ... 286s Selecting previously unselected package libhdf5-hl-100t64:armhf. 286s Preparing to unpack .../06-libhdf5-hl-100t64_1.10.10+repack-5ubuntu1_armhf.deb ... 286s Unpacking libhdf5-hl-100t64:armhf (1.10.10+repack-5ubuntu1) ... 286s Selecting previously unselected package libhtscodecs2:armhf. 286s Preparing to unpack .../07-libhtscodecs2_1.6.1-1_armhf.deb ... 286s Unpacking libhtscodecs2:armhf (1.6.1-1) ... 286s Selecting previously unselected package libhts3t64:armhf. 286s Preparing to unpack .../08-libhts3t64_1.20+ds-2_armhf.deb ... 286s Unpacking libhts3t64:armhf (1.20+ds-2) ... 286s Selecting previously unselected package liblapack3:armhf. 286s Preparing to unpack .../09-liblapack3_3.12.0-4_armhf.deb ... 286s Unpacking liblapack3:armhf (3.12.0-4) ... 286s Selecting previously unselected package liblbfgsb0:armhf. 286s Preparing to unpack .../10-liblbfgsb0_3.0+dfsg.4-1build1_armhf.deb ... 286s Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 286s Selecting previously unselected package liblzf1:armhf. 286s Preparing to unpack .../11-liblzf1_3.6-4_armhf.deb ... 286s Unpacking liblzf1:armhf (3.6-4) ... 286s Selecting previously unselected package python3-numpy. 286s Preparing to unpack .../12-python3-numpy_1%3a1.26.4+ds-12_armhf.deb ... 286s Unpacking python3-numpy (1:1.26.4+ds-12) ... 286s Selecting previously unselected package python3-h5py-serial. 286s Preparing to unpack .../13-python3-h5py-serial_3.11.0-8ubuntu3_armhf.deb ... 286s Unpacking python3-h5py-serial (3.11.0-8ubuntu3) ... 286s Selecting previously unselected package python3-dateutil. 286s Preparing to unpack .../14-python3-dateutil_2.9.0-3_all.deb ... 286s Unpacking python3-dateutil (2.9.0-3) ... 286s Selecting previously unselected package python3-tz. 286s Preparing to unpack .../15-python3-tz_2024.2-1_all.deb ... 286s Unpacking python3-tz (2024.2-1) ... 286s Selecting previously unselected package python3-pandas-lib:armhf. 286s Preparing to unpack .../16-python3-pandas-lib_2.2.3+dfsg-5ubuntu1_armhf.deb ... 286s Unpacking python3-pandas-lib:armhf (2.2.3+dfsg-5ubuntu1) ... 287s Selecting previously unselected package python3-pandas. 287s Preparing to unpack .../17-python3-pandas_2.2.3+dfsg-5ubuntu1_all.deb ... 287s Unpacking python3-pandas (2.2.3+dfsg-5ubuntu1) ... 287s Selecting previously unselected package python3-decorator. 287s Preparing to unpack .../18-python3-decorator_5.1.1-5_all.deb ... 287s Unpacking python3-decorator (5.1.1-5) ... 287s Selecting previously unselected package python3-fastjsonschema. 287s Preparing to unpack .../19-python3-fastjsonschema_2.21.1-1_all.deb ... 287s Unpacking python3-fastjsonschema (2.21.1-1) ... 287s Selecting previously unselected package python3-platformdirs. 287s Preparing to unpack .../20-python3-platformdirs_4.3.6-1_all.deb ... 287s Unpacking python3-platformdirs (4.3.6-1) ... 287s Selecting previously unselected package python3-traitlets. 287s Preparing to unpack .../21-python3-traitlets_5.14.3+really5.14.3-1_all.deb ... 287s Unpacking python3-traitlets (5.14.3+really5.14.3-1) ... 287s Selecting previously unselected package python3-jupyter-core. 287s Preparing to unpack .../22-python3-jupyter-core_5.7.2-5_all.deb ... 287s Unpacking python3-jupyter-core (5.7.2-5) ... 287s Selecting previously unselected package python3-nbformat. 287s Preparing to unpack .../23-python3-nbformat_5.9.1-1_all.deb ... 287s Unpacking python3-nbformat (5.9.1-1) ... 287s Selecting previously unselected package python3-tenacity. 287s Preparing to unpack .../24-python3-tenacity_8.5.0-0ubuntu1_all.deb ... 287s Unpacking python3-tenacity (8.5.0-0ubuntu1) ... 287s Selecting previously unselected package python3-plotly. 287s Preparing to unpack .../25-python3-plotly_5.20.0+dfsg-1_all.deb ... 287s Unpacking python3-plotly (5.20.0+dfsg-1) ... 289s Selecting previously unselected package python3-pysam. 289s Preparing to unpack .../26-python3-pysam_0.22.1+ds-2build1_armhf.deb ... 289s Unpacking python3-pysam (0.22.1+ds-2build1) ... 289s Selecting previously unselected package python3-scipy. 289s Preparing to unpack .../27-python3-scipy_1.14.1-3ubuntu1_armhf.deb ... 289s Unpacking python3-scipy (1.14.1-3ubuntu1) ... 290s Selecting previously unselected package python3-tqdm. 290s Preparing to unpack .../28-python3-tqdm_4.67.1-1_all.deb ... 290s Unpacking python3-tqdm (4.67.1-1) ... 290s Selecting previously unselected package python3-h5py. 290s Preparing to unpack .../29-python3-h5py_3.11.0-8ubuntu3_all.deb ... 290s Unpacking python3-h5py (3.11.0-8ubuntu3) ... 290s Selecting previously unselected package pycoqc. 290s Preparing to unpack .../30-pycoqc_2.5.2+dfsg-3_all.deb ... 290s Unpacking pycoqc (2.5.2+dfsg-3) ... 290s Setting up libhtscodecs2:armhf (1.6.1-1) ... 290s Setting up python3-tenacity (8.5.0-0ubuntu1) ... 291s Setting up python3-tqdm (4.67.1-1) ... 291s Setting up libdeflate0:armhf (1.22-1) ... 291s Setting up libaec0:armhf (1.1.3-1) ... 291s Setting up python3-platformdirs (4.3.6-1) ... 291s Setting up python3-tz (2024.2-1) ... 291s Setting up python3-decorator (5.1.1-5) ... 291s Setting up libblas3:armhf (3.12.0-4) ... 291s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 291s Setting up liblzf1:armhf (3.6-4) ... 291s Setting up libgfortran5:armhf (14.2.0-12ubuntu1) ... 291s Setting up python3-fastjsonschema (2.21.1-1) ... 291s Setting up python3-traitlets (5.14.3+really5.14.3-1) ... 292s Setting up libhts3t64:armhf (1.20+ds-2) ... 292s Setting up python3-dateutil (2.9.0-3) ... 292s Setting up python3-jupyter-core (5.7.2-5) ... 292s Setting up libsz2:armhf (1.1.3-1) ... 292s Setting up liblapack3:armhf (3.12.0-4) ... 292s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 292s Setting up python3-pysam (0.22.1+ds-2build1) ... 292s Setting up python3-nbformat (5.9.1-1) ... 292s Setting up python3-plotly (5.20.0+dfsg-1) ... 301s Setting up python3-numpy (1:1.26.4+ds-12) ... 303s Setting up libhdf5-103-1t64:armhf (1.10.10+repack-5ubuntu1) ... 303s Setting up liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 303s Setting up libhdf5-hl-100t64:armhf (1.10.10+repack-5ubuntu1) ... 303s Setting up python3-scipy (1.14.1-3ubuntu1) ... 307s Setting up python3-pandas-lib:armhf (2.2.3+dfsg-5ubuntu1) ... 307s Setting up python3-h5py-serial (3.11.0-8ubuntu3) ... 308s Setting up python3-pandas (2.2.3+dfsg-5ubuntu1) ... 314s Setting up python3-h5py (3.11.0-8ubuntu3) ... 314s Setting up pycoqc (2.5.2+dfsg-3) ... 314s Processing triggers for libc-bin (2.40-4ubuntu1) ... 315s Processing triggers for man-db (2.13.0-1) ... 324s autopkgtest [07:16:00]: test run-unit-test: [----------------------- 327s Test 1 328s Checking arguments values 328s Check input data files 328s Parse data files 328s Merge data 328s Cleaning data 328s Loading plotting interface 329s PASS 329s 329s Test 2 329s Checking arguments values 329s Check input data files 329s Parse data files 330s Merge data 330s Cleaning data 330s Loading plotting interface 331s PASS 331s 331s Test 3 332s Checking arguments values 332s Check input data files 332s Parse data files 332s Merge data 332s Cleaning data 332s Loading plotting interface 333s PASS 333s 333s Test 4 333s Checking arguments values 333s Check input data files 333s Parse data files 334s Merge data 334s Cleaning data 334s Loading plotting interface 335s PASS 335s 335s Test 5 336s Checking arguments values 336s Check input data files 336s Parse data files 336s Merge data 336s Cleaning data 336s Loading plotting interface 337s PASS 337s 337s Test 6 338s PASS 338s 338s Test 7 339s Checking arguments values 339s Check input data files 339s Parse data files 339s Merge data 339s Cleaning data 339s Loading plotting interface 340s PASS 340s 340s Test 8 341s 0 reads [00:00, ? reads/s] 22 reads [00:00, 338.15 reads/s] 341s Total reads: 22 / Average speed: 280.1 reads/s 341s 341s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template 341s 61e799eb-5571-4cc4-bbf6-b3929b197459 40ebe55356ada6c830fa793745ef4c498d896c73 103 26 844 8.56 filtered_out 341s 0ef36fa0-7c3f-47f5-8410-027f50724701 40ebe55356ada6c830fa793745ef4c498d896c73 108 26 915 9.407 filtered_out 341s c38cbad9-d91e-4208-9317-832f4e2cc289 40ebe55356ada6c830fa793745ef4c498d896c73 113 30 824 8.693 filtered_out 341s 08642be5-5cf7-4c4c-8c45-e4d569b9a482 40ebe55356ada6c830fa793745ef4c498d896c73 121 28 450 7.805 filtered_out 341s 5b7fadd0-c646-4c7b-9800-66ee658a5ca8 40ebe55356ada6c830fa793745ef4c498d896c73 150 37 468 7.608 filtered_out 341s 151757ea-53de-44b1-b86e-f823511af02a 40ebe55356ada6c830fa793745ef4c498d896c73 191 13 568 8.23 filtered_out 341s bcb20156-a5fe-4daa-aad9-b62c286e468d 40ebe55356ada6c830fa793745ef4c498d896c73 192 21 306 7.337 filtered_out 341s ed05c5e6-7aab-4970-a431-3411047764a6 40ebe55356ada6c830fa793745ef4c498d896c73 224 34 880 8.891 filtered_out 341s 3784283c-47cc-48ac-8d7b-7efd32123b56 40ebe55356ada6c830fa793745ef4c498d896c73 243 20 893 8.54 filtered_out 341s PASS 341s 341s Test 9 342s Check input data and options 342s Start processing fast5 files 342s 0 reads [00:00, ? reads/s] 22 reads [00:00, 1511.98 reads/s] 342s Overall counts valid files: 22 342s 342s fields found mean_qscore_template: 22 342s called_events: 22 342s duration: 22 342s strand_score: 22 342s 342s fields not found 342s Total reads: 22 / Average speed: 761.86 reads/s 342s 342s mean_qscore_template called_events duration strand_score 342s 8.56 5838 87570 -0.0003 342s 8.693 2383 35752 -0.0005 342s 7.805 1438 21583 -0.0006 342s 9.407 2848 42730 -0.0003 342s 7.608 1615 24233 -0.0007 342s 8.23 2778 51387 -0.0007 342s 7.337 1972 29589 -0.0009 342s 8.891 2774 41612 -0.0006 342s 8.544 3740 56107 -0.0003 342s PASS 342s 342s Test 10 343s Check input data and options 343s Start processing fast5 files 343s 0 reads [00:00, ? reads/s] 22 reads [00:00, 910.96 reads/s] 343s Overall counts valid files: 22 343s 343s fields found read_id: 22 343s run_id: 22 343s channel: 22 343s start_time: 22 343s sequence_length_template: 22 343s mean_qscore_template: 22 343s calibration_strand_genome_template: 22 343s 343s fields not found barcode_arrangement: 22 343s 343s Total reads: 22 / Average speed: 515.76 reads/s 343s 343s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template path 343s 61e799eb-5571-4cc4-bbf6-b3929b197459 40ebe55356ada6c830fa793745ef4c498d896c73 103 26 844 8.56 filtered_out /tmp/autopkgtest.pJ0hYv/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_103_strand.fast5 343s 0ef36fa0-7c3f-47f5-8410-027f50724701 40ebe55356ada6c830fa793745ef4c498d896c73 108 26 915 9.407 filtered_out /tmp/autopkgtest.pJ0hYv/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_108_strand.fast5 343s c38cbad9-d91e-4208-9317-832f4e2cc289 40ebe55356ada6c830fa793745ef4c498d896c73 113 30 824 8.693 filtered_out /tmp/autopkgtest.pJ0hYv/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_113_strand.fast5 343s 5b7fadd0-c646-4c7b-9800-66ee658a5ca8 40ebe55356ada6c830fa793745ef4c498d896c73 150 37 468 7.608 filtered_out /tmp/autopkgtest.pJ0hYv/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_150_strand.fast5 343s 08642be5-5cf7-4c4c-8c45-e4d569b9a482 40ebe55356ada6c830fa793745ef4c498d896c73 121 28 450 7.805 filtered_out /tmp/autopkgtest.pJ0hYv/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_121_strand.fast5 343s 151757ea-53de-44b1-b86e-f823511af02a 40ebe55356ada6c830fa793745ef4c498d896c73 191 13 568 8.23 filtered_out /tmp/autopkgtest.pJ0hYv/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_191_strand.fast5 343s bcb20156-a5fe-4daa-aad9-b62c286e468d 40ebe55356ada6c830fa793745ef4c498d896c73 192 21 306 7.337 filtered_out /tmp/autopkgtest.pJ0hYv/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_192_strand.fast5 343s ed05c5e6-7aab-4970-a431-3411047764a6 40ebe55356ada6c830fa793745ef4c498d896c73 224 34 880 8.891 filtered_out /tmp/autopkgtest.pJ0hYv/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_224_strand.fast5 343s 2c32553e-62c6-4c7a-bf05-249771364f04 40ebe55356ada6c830fa793745ef4c498d896c73 237 11 1151 8.544 filtered_out /tmp/autopkgtest.pJ0hYv/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_237_strand.fast5 343s PASS 343s 343s Test 11 344s Import data from sequencing summary file(s) and cleanup 344s Read files and import in a dataframe 344s Check input data files 344s Parse data files 344s Merge data 344s Cleanup missing barcodes values 344s Cleaning up low frequency barcodes 345s Split data per barcode 345s Processing data for Barcode barcode02 345s Processing data for Barcode barcode07 345s Processing data for Barcode barcode08 345s Processing data for Barcode barcode09 345s Processing data for Barcode barcode10 345s Processing data for Barcode barcode11 345s Processing data for Barcode barcode12 345s Processing data for Barcode unclassified 345s Barcode Counts 345s Counts Write 345s barcode02 2 False 345s barcode07 1 False 345s barcode08 30 False 345s barcode09 9945 True 345s barcode10 12644 True 345s barcode11 13594 True 345s barcode12 9813 True 345s unclassified 3971 False 346s PASS 346s 346s Test 12 346s General info 346s package_name: pycoQC 346s package_version: 2.5.2 346s timestamp: 2025-01-08 07:16:22.924020 346s 346s Runtime options 346s summary_file: ['Guppy-basecall-1D-DNA_sequencing_summary.txt'] 346s barcode_file: ['Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt'] 346s output_dir: results/ 346s output_unclassified: False 346s min_barcode_percent: 0.1 346s verbose: True 346s quiet: False 346s 346s Import data from sequencing summary file(s) and cleanup 346s Read files and import in a dataframe 346s Check input data files 346s Sequencing summary files found: Guppy-basecall-1D-DNA_sequencing_summary.txt 346s Barcode files found: Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt 346s Parse data files 346s Parse summary files 346s 3,999 reads found in initial file 346s Parse barcode files 346s Found valid Deepbinner barcode file 346s 3,775 reads with barcodes assigned 346s Merge data 346s Cleanup missing barcodes values 346s Cleaning up low frequency barcodes 347s Split data per barcode 347s Processing data for Barcode 1 347s Processing data for Barcode 2 347s Processing data for Barcode 3 347s Processing data for Barcode 4 347s Processing data for Barcode 5 347s Processing data for Barcode 6 347s Processing data for Barcode 7 347s Processing data for Barcode 8 347s Processing data for Barcode unclassified 347s Barcode Counts 347s Counts Write 347s 1 534 True 347s 2 206 True 347s 3 562 True 347s 4 579 True 347s 5 590 True 347s 6 655 True 347s 7 271 True 347s 8 378 True 347s unclassified 224 False 347s PASS 347s 347s Check if files really exist 347s PASS 347s 347s autopkgtest [07:16:23]: test run-unit-test: -----------------------] 351s autopkgtest [07:16:27]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 351s run-unit-test PASS 355s autopkgtest [07:16:31]: @@@@@@@@@@@@@@@@@@@@ summary 355s run-unit-test PASS