0s autopkgtest [07:12:55]: starting date and time: 2024-11-14 07:12:55+0000 0s autopkgtest [07:12:55]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [07:12:55]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.nixi01rc/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\n" >> /etc/environment' --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade uncalled --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- lxd -r lxd-armhf-10.145.243.21 lxd-armhf-10.145.243.21:autopkgtest/ubuntu/plucky/armhf 55s autopkgtest [07:13:50]: testbed dpkg architecture: armhf 57s autopkgtest [07:13:52]: testbed apt version: 2.9.8 57s autopkgtest [07:13:52]: @@@@@@@@@@@@@@@@@@@@ test bed setup 65s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 65s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.4 kB] 65s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [98.0 kB] 65s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 65s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [985 kB] 65s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [103 kB] 65s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [686 kB] 65s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [5040 B] 66s Fetched 1974 kB in 1s (1868 kB/s) 66s Reading package lists... 84s tee: /proc/self/fd/2: Permission denied 107s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 107s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 107s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 107s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 108s Reading package lists... 108s Reading package lists... 109s Building dependency tree... 109s Reading state information... 110s Calculating upgrade... 111s The following packages were automatically installed and are no longer required: 111s libperl5.38t64 perl-modules-5.38 python3-netifaces 111s Use 'apt autoremove' to remove them. 111s The following NEW packages will be installed: 111s libperl5.40 perl-modules-5.40 python3.13-gdbm systemd-cryptsetup 111s The following packages will be upgraded: 111s apport apport-core-dump-handler base-files base-passwd bash-completion 111s dhcpcd-base distro-info-data dpkg dpkg-dev fwupd gcc-14-base info 111s install-info iproute2 libarchive13t64 libatomic1 libattr1 111s libblockdev-crypto3 libblockdev-fs3 libblockdev-loop3 libblockdev-mdraid3 111s libblockdev-nvme3 libblockdev-part3 libblockdev-swap3 libblockdev-utils3 111s libblockdev3 libbpf1 libbsd0 libbytesize-common libbytesize1 libdb5.3t64 111s libdpkg-perl libdrm-common libdrm2 libdw1t64 libedit2 libelf1t64 libevdev2 111s libfastjson4 libflashrom1 libftdi1-2 libfwupd2 libgcc-s1 libgnutls30t64 111s libgpgme11t64 libinih1 libjson-c5 libjson-glib-1.0-0 libjson-glib-1.0-common 111s libkeyutils1 libldap-common libldap2 liblocale-gettext-perl libmaxminddb0 111s libmnl0 libnetfilter-conntrack3 libnetplan1 libnewt0.52 libnghttp2-14 111s libnspr4 libnss-systemd libnvme1t64 libpam-systemd libpipeline1 libplymouth5 111s libpng16-16t64 libpopt0 libpython3-stdlib libpython3.12-minimal 111s libpython3.12-stdlib libsgutils2-1.46-2 libssh2-1t64 libstdc++6 111s libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl 111s libtraceevent1 libtraceevent1-plugin libudev1 libudisks2-0 liburcu8t64 111s libutempter0 libuv1t64 libx11-6 libx11-data libxau6 libxmlb2 mawk 111s motd-news-config nano netplan-generator netplan.io openssh-client 111s openssh-server openssh-sftp-server pci.ids perl perl-base plymouth 111s plymouth-theme-ubuntu-text python3 python3-apport python3-certifi 111s python3-cffi-backend python3-configobj python3-gdbm python3-gi python3-idna 111s python3-jaraco.functools python3-json-pointer python3-jsonpatch 111s python3-lazr.restfulclient python3-lazr.uri python3-minimal 111s python3-more-itertools python3-netplan python3-newt python3-oauthlib 111s python3-problem-report python3-typeguard python3-urllib3 python3-wadllib 111s python3-zipp python3.12 python3.12-gdbm python3.12-minimal sg3-utils 111s sg3-utils-udev ssh-import-id systemd systemd-resolved systemd-sysv 111s systemd-timesyncd tzdata udev udisks2 ufw usbutils vim-common vim-tiny 111s whiptail xxd 111s 143 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 111s Need to get 45.5 MB of archives. 111s After this operation, 43.2 MB of additional disk space will be used. 111s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf motd-news-config all 13.5ubuntu3 [5190 B] 111s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf base-files armhf 13.5ubuntu3 [75.1 kB] 111s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf dpkg armhf 1.22.11ubuntu3 [1247 kB] 112s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf perl-modules-5.40 all 5.40.0-7 [3214 kB] 112s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf libperl5.40 armhf 5.40.0-7 [4139 kB] 112s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf perl armhf 5.40.0-7 [263 kB] 112s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf perl-base armhf 5.40.0-7 [1674 kB] 112s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf liblocale-gettext-perl armhf 1.07-7build1 [15.0 kB] 112s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libtext-iconv-perl armhf 1.7-8build4 [12.8 kB] 112s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libtext-charwidth-perl armhf 0.04-11build4 [9128 B] 112s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libdb5.3t64 armhf 5.3.28+dfsg2-9 [655 kB] 112s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf base-passwd armhf 3.6.5 [53.2 kB] 112s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-minimal armhf 3.12.7-1 [27.4 kB] 112s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3 armhf 3.12.7-1 [24.0 kB] 112s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf tzdata all 2024b-1ubuntu2 [274 kB] 112s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12 armhf 3.12.7-3 [661 kB] 112s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12-stdlib armhf 3.12.7-3 [1934 kB] 112s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-minimal armhf 3.12.7-3 [2012 kB] 112s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12-minimal armhf 3.12.7-3 [822 kB] 112s Get:20 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libpython3-stdlib armhf 3.12.7-1 [10.0 kB] 112s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libnss-systemd armhf 256.5-2ubuntu4 [155 kB] 112s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf systemd-timesyncd armhf 256.5-2ubuntu4 [40.7 kB] 112s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf systemd-resolved armhf 256.5-2ubuntu4 [309 kB] 112s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf libsystemd-shared armhf 256.5-2ubuntu4 [2129 kB] 112s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf libsystemd0 armhf 256.5-2ubuntu4 [428 kB] 112s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf systemd-sysv armhf 256.5-2ubuntu4 [11.9 kB] 112s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libpam-systemd armhf 256.5-2ubuntu4 [226 kB] 112s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf systemd armhf 256.5-2ubuntu4 [3442 kB] 112s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf udev armhf 256.5-2ubuntu4 [1949 kB] 112s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libudev1 armhf 256.5-2ubuntu4 [188 kB] 112s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf python3-problem-report all 2.30.0-0ubuntu5 [25.0 kB] 112s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf python3-apport all 2.30.0-0ubuntu5 [93.2 kB] 112s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf python3-gi armhf 3.50.0-3 [227 kB] 112s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf apport-core-dump-handler all 2.30.0-0ubuntu5 [17.9 kB] 112s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf apport all 2.30.0-0ubuntu5 [83.0 kB] 112s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libbsd0 armhf 0.12.2-2 [36.8 kB] 112s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libedit2 armhf 3.1-20240808-1 [79.0 kB] 112s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf openssh-sftp-server armhf 1:9.7p1-7ubuntu5 [35.4 kB] 112s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf openssh-server armhf 1:9.7p1-7ubuntu5 [505 kB] 113s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf openssh-client armhf 1:9.7p1-7ubuntu5 [889 kB] 113s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libatomic1 armhf 14.2.0-8ubuntu1 [7846 B] 113s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-base armhf 14.2.0-8ubuntu1 [51.5 kB] 113s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++6 armhf 14.2.0-8ubuntu1 [711 kB] 113s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-s1 armhf 14.2.0-8ubuntu1 [40.8 kB] 113s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf libattr1 armhf 1:2.5.2-2 [10.5 kB] 113s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls30t64 armhf 3.8.8-2ubuntu1 [955 kB] 113s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf install-info armhf 7.1.1-1 [61.4 kB] 113s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf mawk armhf 1.3.4.20240905-1 [116 kB] 113s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf dhcpcd-base armhf 1:10.1.0-2 [188 kB] 113s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf distro-info-data all 0.63 [6588 B] 113s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf libdw1t64 armhf 0.192-4 [243 kB] 113s Get:52 http://ftpmaster.internal/ubuntu plucky/main armhf libelf1t64 armhf 0.192-4 [50.2 kB] 113s Get:53 http://ftpmaster.internal/ubuntu plucky/main armhf libbpf1 armhf 1:1.5.0-1 [158 kB] 113s Get:54 http://ftpmaster.internal/ubuntu plucky/main armhf libmnl0 armhf 1.0.5-3 [10.7 kB] 113s Get:55 http://ftpmaster.internal/ubuntu plucky/main armhf iproute2 armhf 6.10.0-2ubuntu1 [1082 kB] 113s Get:56 http://ftpmaster.internal/ubuntu plucky/main armhf libfastjson4 armhf 1.2304.0-2 [20.2 kB] 113s Get:57 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-c5 armhf 0.18+ds-1 [33.2 kB] 113s Get:58 http://ftpmaster.internal/ubuntu plucky/main armhf libkeyutils1 armhf 1.6.3-4ubuntu2 [8712 B] 113s Get:59 http://ftpmaster.internal/ubuntu plucky/main armhf netplan-generator armhf 1.1.1-1 [60.4 kB] 113s Get:60 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cffi-backend armhf 1.17.1-2 [68.7 kB] 113s Get:61 http://ftpmaster.internal/ubuntu plucky/main armhf python3-netplan armhf 1.1.1-1 [24.1 kB] 113s Get:62 http://ftpmaster.internal/ubuntu plucky/main armhf netplan.io armhf 1.1.1-1 [66.4 kB] 113s Get:63 http://ftpmaster.internal/ubuntu plucky/main armhf libnetplan1 armhf 1.1.1-1 [122 kB] 113s Get:64 http://ftpmaster.internal/ubuntu plucky/main armhf python3-newt armhf 0.52.24-2ubuntu4 [19.7 kB] 113s Get:65 http://ftpmaster.internal/ubuntu plucky/main armhf libnewt0.52 armhf 0.52.24-2ubuntu4 [39.2 kB] 113s Get:66 http://ftpmaster.internal/ubuntu plucky/main armhf libpopt0 armhf 1.19+dfsg-2 [25.4 kB] 113s Get:67 http://ftpmaster.internal/ubuntu plucky/main armhf vim-tiny armhf 2:9.1.0777-1ubuntu1 [693 kB] 113s Get:68 http://ftpmaster.internal/ubuntu plucky/main armhf vim-common all 2:9.1.0777-1ubuntu1 [394 kB] 113s Get:69 http://ftpmaster.internal/ubuntu plucky/main armhf whiptail armhf 0.52.24-2ubuntu4 [17.2 kB] 113s Get:70 http://ftpmaster.internal/ubuntu plucky/main armhf xxd armhf 2:9.1.0777-1ubuntu1 [66.8 kB] 113s Get:71 http://ftpmaster.internal/ubuntu plucky/main armhf bash-completion all 1:2.14.0-2 [210 kB] 113s Get:72 http://ftpmaster.internal/ubuntu plucky/main armhf info armhf 7.1.1-1 [126 kB] 113s Get:73 http://ftpmaster.internal/ubuntu plucky/main armhf libdrm-common all 2.4.123-1 [8436 B] 113s Get:74 http://ftpmaster.internal/ubuntu plucky/main armhf libdrm2 armhf 2.4.123-1 [36.5 kB] 113s Get:75 http://ftpmaster.internal/ubuntu plucky/main armhf libevdev2 armhf 1.13.3+dfsg-1 [29.7 kB] 113s Get:76 http://ftpmaster.internal/ubuntu plucky/main armhf libmaxminddb0 armhf 1.11.0-1 [16.8 kB] 113s Get:77 http://ftpmaster.internal/ubuntu plucky/main armhf libnetfilter-conntrack3 armhf 1.1.0-1 [38.4 kB] 113s Get:78 http://ftpmaster.internal/ubuntu plucky/main armhf libnghttp2-14 armhf 1.64.0-1 [68.9 kB] 113s Get:79 http://ftpmaster.internal/ubuntu plucky/main armhf libpipeline1 armhf 1.5.8-1 [26.9 kB] 113s Get:80 http://ftpmaster.internal/ubuntu plucky/main armhf libpng16-16t64 armhf 1.6.44-2 [168 kB] 113s Get:81 http://ftpmaster.internal/ubuntu plucky/main armhf libplymouth5 armhf 24.004.60-1ubuntu11 [140 kB] 113s Get:82 http://ftpmaster.internal/ubuntu plucky/main armhf libtraceevent1-plugin armhf 1:1.8.3-1ubuntu1 [18.1 kB] 113s Get:83 http://ftpmaster.internal/ubuntu plucky/main armhf libtraceevent1 armhf 1:1.8.3-1ubuntu1 [52.1 kB] 113s Get:84 http://ftpmaster.internal/ubuntu plucky/main armhf liburcu8t64 armhf 0.14.1-1 [56.6 kB] 113s Get:85 http://ftpmaster.internal/ubuntu plucky/main armhf libuv1t64 armhf 1.48.0-7 [83.3 kB] 113s Get:86 http://ftpmaster.internal/ubuntu plucky/main armhf libx11-data all 2:1.8.10-2 [116 kB] 113s Get:87 http://ftpmaster.internal/ubuntu plucky/main armhf libx11-6 armhf 2:1.8.10-2 [587 kB] 113s Get:88 http://ftpmaster.internal/ubuntu plucky/main armhf libxau6 armhf 1:1.0.11-1 [6558 B] 113s Get:89 http://ftpmaster.internal/ubuntu plucky/main armhf nano armhf 8.2-1 [276 kB] 113s Get:90 http://ftpmaster.internal/ubuntu plucky/main armhf pci.ids all 0.0~2024.10.24-1 [279 kB] 113s Get:91 http://ftpmaster.internal/ubuntu plucky/main armhf plymouth-theme-ubuntu-text armhf 24.004.60-1ubuntu11 [9920 B] 113s Get:92 http://ftpmaster.internal/ubuntu plucky/main armhf plymouth armhf 24.004.60-1ubuntu11 [142 kB] 113s Get:93 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-gdbm armhf 3.12.7-3 [28.7 kB] 113s Get:94 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-gdbm armhf 3.13.0-2 [29.5 kB] 113s Get:95 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-gdbm armhf 3.12.7-1 [8642 B] 113s Get:96 http://ftpmaster.internal/ubuntu plucky/main armhf ufw all 0.36.2-8 [170 kB] 113s Get:97 http://ftpmaster.internal/ubuntu plucky/main armhf usbutils armhf 1:018-1 [76.1 kB] 113s Get:98 http://ftpmaster.internal/ubuntu plucky/main armhf dpkg-dev all 1.22.11ubuntu3 [1088 kB] 113s Get:99 http://ftpmaster.internal/ubuntu plucky/main armhf libdpkg-perl all 1.22.11ubuntu3 [279 kB] 113s Get:100 http://ftpmaster.internal/ubuntu plucky/main armhf libarchive13t64 armhf 3.7.4-1.1 [331 kB] 113s Get:101 http://ftpmaster.internal/ubuntu plucky/main armhf libftdi1-2 armhf 1.5-7 [25.7 kB] 113s Get:102 http://ftpmaster.internal/ubuntu plucky/main armhf libflashrom1 armhf 1.4.0-3ubuntu1 [141 kB] 114s Get:103 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 114s Get:104 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-0 armhf 1.10.0+ds-3 [61.7 kB] 114s Get:105 http://ftpmaster.internal/ubuntu plucky/main armhf libfwupd2 armhf 1.9.26-2 [125 kB] 114s Get:106 http://ftpmaster.internal/ubuntu plucky/main armhf libxmlb2 armhf 0.3.21-1 [57.7 kB] 114s Get:107 http://ftpmaster.internal/ubuntu plucky/main armhf fwupd armhf 1.9.26-2 [4404 kB] 114s Get:108 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-utils3 armhf 3.2.1-1 [17.4 kB] 114s Get:109 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-crypto3 armhf 3.2.1-1 [22.4 kB] 114s Get:110 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-fs3 armhf 3.2.1-1 [34.3 kB] 114s Get:111 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-loop3 armhf 3.2.1-1 [6552 B] 114s Get:112 http://ftpmaster.internal/ubuntu plucky/main armhf libbytesize1 armhf 2.11-1ubuntu1 [12.0 kB] 114s Get:113 http://ftpmaster.internal/ubuntu plucky/main armhf libbytesize-common all 2.11-1ubuntu1 [3584 B] 114s Get:114 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-mdraid3 armhf 3.2.1-1 [13.4 kB] 114s Get:115 http://ftpmaster.internal/ubuntu plucky/main armhf libnvme1t64 armhf 1.11-1 [73.8 kB] 114s Get:116 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-nvme3 armhf 3.2.1-1 [17.6 kB] 114s Get:117 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-part3 armhf 3.2.1-1 [16.5 kB] 114s Get:118 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-swap3 armhf 3.2.1-1 [8952 B] 114s Get:119 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev3 armhf 3.2.1-1 [44.2 kB] 114s Get:120 http://ftpmaster.internal/ubuntu plucky/main armhf libgpgme11t64 armhf 1.23.2-5ubuntu4 [123 kB] 114s Get:121 http://ftpmaster.internal/ubuntu plucky/main armhf libinih1 armhf 58-1ubuntu1 [6750 B] 114s Get:122 http://ftpmaster.internal/ubuntu plucky/main armhf libldap-common all 2.6.8+dfsg-1~exp4ubuntu3 [32.3 kB] 114s Get:123 http://ftpmaster.internal/ubuntu plucky/main armhf libldap2 armhf 2.6.8+dfsg-1~exp4ubuntu3 [173 kB] 114s Get:124 http://ftpmaster.internal/ubuntu plucky/main armhf libnspr4 armhf 2:4.35-1.1ubuntu2 [94.1 kB] 114s Get:125 http://ftpmaster.internal/ubuntu plucky/main armhf libsgutils2-1.46-2 armhf 1.46-3ubuntu5 [82.5 kB] 114s Get:126 http://ftpmaster.internal/ubuntu plucky/main armhf libssh2-1t64 armhf 1.11.1-1 [116 kB] 114s Get:127 http://ftpmaster.internal/ubuntu plucky/main armhf udisks2 armhf 2.10.1-11ubuntu1 [278 kB] 114s Get:128 http://ftpmaster.internal/ubuntu plucky/main armhf libudisks2-0 armhf 2.10.1-11ubuntu1 [142 kB] 114s Get:129 http://ftpmaster.internal/ubuntu plucky/main armhf libutempter0 armhf 1.2.1-4 [9062 B] 114s Get:130 http://ftpmaster.internal/ubuntu plucky/main armhf python3-certifi all 2024.8.30+dfsg-1 [9742 B] 114s Get:131 http://ftpmaster.internal/ubuntu plucky/main armhf python3-configobj all 5.0.9-1 [33.9 kB] 114s Get:132 http://ftpmaster.internal/ubuntu plucky/main armhf python3-idna all 3.8-2 [47.0 kB] 114s Get:133 http://ftpmaster.internal/ubuntu plucky/main armhf python3-more-itertools all 10.5.0-1 [56.2 kB] 114s Get:134 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jaraco.functools all 4.1.0-1 [11.8 kB] 114s Get:135 http://ftpmaster.internal/ubuntu plucky/main armhf python3-json-pointer all 2.4-2 [8396 B] 114s Get:136 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jsonpatch all 1.32-4 [12.2 kB] 114s Get:137 http://ftpmaster.internal/ubuntu plucky/main armhf python3-lazr.uri all 1.0.6-4 [13.6 kB] 114s Get:138 http://ftpmaster.internal/ubuntu plucky/main armhf python3-wadllib all 2.0.0-1 [36.7 kB] 114s Get:139 http://ftpmaster.internal/ubuntu plucky/main armhf python3-oauthlib all 3.2.2-2 [89.8 kB] 114s Get:140 http://ftpmaster.internal/ubuntu plucky/main armhf python3-lazr.restfulclient all 0.14.6-2 [50.9 kB] 114s Get:141 http://ftpmaster.internal/ubuntu plucky/main armhf python3-typeguard all 4.4.1-1 [29.0 kB] 114s Get:142 http://ftpmaster.internal/ubuntu plucky/main armhf python3-urllib3 all 2.0.7-2ubuntu0.1 [93.1 kB] 114s Get:143 http://ftpmaster.internal/ubuntu plucky/main armhf python3-zipp all 3.21.0-1 [10.2 kB] 114s Get:144 http://ftpmaster.internal/ubuntu plucky/main armhf sg3-utils armhf 1.46-3ubuntu5 [816 kB] 114s Get:145 http://ftpmaster.internal/ubuntu plucky/main armhf sg3-utils-udev all 1.46-3ubuntu5 [5916 B] 114s Get:146 http://ftpmaster.internal/ubuntu plucky/main armhf systemd-cryptsetup armhf 256.5-2ubuntu4 [122 kB] 114s Get:147 http://ftpmaster.internal/ubuntu plucky/main armhf ssh-import-id all 5.11-0ubuntu3 [10.1 kB] 115s Preconfiguring packages ... 115s Fetched 45.5 MB in 3s (13.0 MB/s) 116s (Reading database ... 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(0.18+ds-1) ... 133s Setting up libevdev2:armhf (1.13.3+dfsg-1) ... 133s Setting up libldap2:armhf (2.6.8+dfsg-1~exp4ubuntu3) ... 133s Setting up info (7.1.1-1) ... 133s Setting up liblocale-gettext-perl (1.07-7build1) ... 133s Setting up libbpf1:armhf (1:1.5.0-1) ... 133s Setting up libudisks2-0:armhf (2.10.1-11ubuntu1) ... 133s Setting up python3.13-gdbm (3.13.0-2) ... 133s Setting up libpopt0:armhf (1.19+dfsg-2) ... 133s Setting up sg3-utils (1.46-3ubuntu5) ... 133s Setting up python3.12-minimal (3.12.7-3) ... 134s Setting up libpython3.12-stdlib:armhf (3.12.7-3) ... 134s Setting up libblockdev-mdraid3:armhf (3.2.1-1) ... 134s Setting up libblockdev-crypto3:armhf (3.2.1-1) ... 134s Setting up libblockdev-swap3:armhf (3.2.1-1) ... 134s Setting up iproute2 (6.10.0-2ubuntu1) ... 134s Setting up openssh-client (1:9.7p1-7ubuntu5) ... 134s Setting up python3.12 (3.12.7-3) ... 136s Setting up libblockdev-loop3:armhf (3.2.1-1) ... 136s Setting up systemd (256.5-2ubuntu4) ... 136s /usr/lib/tmpfiles.d/legacy.conf:13: Duplicate line for path "/run/lock", ignoring. 136s Created symlink '/run/systemd/system/tmp.mount' → '/dev/null'. 136s /usr/lib/tmpfiles.d/legacy.conf:13: Duplicate line for path "/run/lock", ignoring. 137s Setting up vim-tiny (2:9.1.0777-1ubuntu1) ... 137s Setting up libblockdev3:armhf (3.2.1-1) ... 137s Installing new version of config file /etc/libblockdev/3/conf.d/00-default.cfg ... 137s Setting up libjson-glib-1.0-0:armhf (1.10.0+ds-3) ... 137s Setting up libblockdev-part3:armhf (3.2.1-1) ... 137s Setting up sg3-utils-udev (1.46-3ubuntu5) ... 137s update-initramfs: deferring update (trigger activated) 137s Setting up libperl5.40:armhf (5.40.0-7) ... 137s Setting up perl (5.40.0-7) ... 137s Setting up systemd-cryptsetup (256.5-2ubuntu4) ... 137s Setting up libnvme1t64 (1.11-1) ... 137s Setting up systemd-timesyncd (256.5-2ubuntu4) ... 137s systemd-time-wait-sync.service is a disabled or a static unit not running, not starting it. 137s Setting up udev (256.5-2ubuntu4) ... 138s Setting up libdpkg-perl (1.22.11ubuntu3) ... 138s Setting up libblockdev-nvme3:armhf (3.2.1-1) ... 138s Setting up libdrm2:armhf (2.4.123-1) ... 138s Setting up whiptail (0.52.24-2ubuntu4) ... 138s Setting up libtraceevent1-plugin:armhf (1:1.8.3-1ubuntu1) ... 138s Setting up libplymouth5:armhf (24.004.60-1ubuntu11) ... 138s Setting up netplan-generator (1.1.1-1) ... 138s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 138s Setting up libpython3-stdlib:armhf (3.12.7-1) ... 138s Setting up systemd-resolved (256.5-2ubuntu4) ... 139s Setting up openssh-sftp-server (1:9.7p1-7ubuntu5) ... 139s Setting up udisks2 (2.10.1-11ubuntu1) ... 139s vda: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/uevent': Permission denied 139s vda1: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/vda1/uevent': Permission denied 139s vda15: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/vda15/uevent': Permission denied 139s vda2: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/vda2/uevent': Permission denied 139s loop0: Failed to write 'change' to '/sys/devices/virtual/block/loop0/uevent': Permission denied 139s loop1: Failed to write 'change' to '/sys/devices/virtual/block/loop1/uevent': Permission denied 139s loop2: Failed to write 'change' to '/sys/devices/virtual/block/loop2/uevent': Permission denied 139s loop3: Failed to write 'change' to '/sys/devices/virtual/block/loop3/uevent': Permission denied 139s loop4: Failed to write 'change' to '/sys/devices/virtual/block/loop4/uevent': Permission denied 139s loop5: Failed to write 'change' to '/sys/devices/virtual/block/loop5/uevent': Permission denied 139s loop6: Failed to write 'change' to '/sys/devices/virtual/block/loop6/uevent': Permission denied 139s loop7: Failed to write 'change' to '/sys/devices/virtual/block/loop7/uevent': Permission denied 139s loop8: Failed to write 'change' to '/sys/devices/virtual/block/loop8/uevent': Permission denied 141s Setting up systemd-sysv (256.5-2ubuntu4) ... 141s Setting up openssh-server (1:9.7p1-7ubuntu5) ... 141s Setting up plymouth (24.004.60-1ubuntu11) ... 141s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 141s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 142s Setting up libfwupd2:armhf (1.9.26-2) ... 142s Setting up libnss-systemd:armhf (256.5-2ubuntu4) ... 142s Setting up python3 (3.12.7-1) ... 142s Setting up python3-zipp (3.21.0-1) ... 142s Setting up python3-newt:armhf (0.52.24-2ubuntu4) ... 142s Setting up dpkg-dev (1.22.11ubuntu3) ... 142s Setting up plymouth-theme-ubuntu-text (24.004.60-1ubuntu11) ... 142s update-initramfs: deferring update (trigger activated) 142s Setting up python3-oauthlib (3.2.2-2) ... 142s Setting up python3-configobj (5.0.9-1) ... 143s Setting up python3-certifi (2024.8.30+dfsg-1) ... 143s Setting up python3-gi (3.50.0-3) ... 143s Setting up python3-idna (3.8-2) ... 143s Setting up python3-urllib3 (2.0.7-2ubuntu0.1) ... 144s Setting up python3-json-pointer (2.4-2) ... 144s Setting up libpam-systemd:armhf (256.5-2ubuntu4) ... 144s Setting up fwupd (1.9.26-2) ... 145s fwupd-offline-update.service is a disabled or a static unit not running, not starting it. 145s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 145s fwupd.service is a disabled or a static unit not running, not starting it. 145s Setting up python3-cffi-backend:armhf (1.17.1-2) ... 145s Setting up python3-more-itertools (10.5.0-1) ... 145s Setting up python3-jaraco.functools (4.1.0-1) ... 145s Setting up python3-gdbm:armhf (3.12.7-1) ... 145s Setting up python3-problem-report (2.30.0-0ubuntu5) ... 145s Setting up ssh-import-id (5.11-0ubuntu3) ... 145s Setting up python3-jsonpatch (1.32-4) ... 146s Setting up python3-typeguard (4.4.1-1) ... 146s Setting up ufw (0.36.2-8) ... 147s Setting up python3-lazr.uri (1.0.6-4) ... 147s Setting up python3-apport (2.30.0-0ubuntu5) ... 147s Setting up python3-wadllib (2.0.0-1) ... 147s Setting up python3-netplan (1.1.1-1) ... 148s Setting up python3-lazr.restfulclient (0.14.6-2) ... 148s Setting up netplan.io (1.1.1-1) ... 148s Setting up apport-core-dump-handler (2.30.0-0ubuntu5) ... 148s Setting up apport (2.30.0-0ubuntu5) ... 148s Installing new version of config file /etc/apport/crashdb.conf ... 149s apport-autoreport.service is a disabled or a static unit not running, not starting it. 149s Processing triggers for dbus (1.14.10-4ubuntu5) ... 149s Processing triggers for shared-mime-info (2.4-5) ... 150s Processing triggers for install-info (7.1.1-1) ... 150s Processing triggers for initramfs-tools (0.142ubuntu34) ... 150s Processing triggers for libc-bin (2.40-1ubuntu3) ... 150s Processing triggers for rsyslog (8.2406.0-1ubuntu2) ... 152s Processing triggers for man-db (2.12.1-3) ... 152s Reading package lists... 153s Building dependency tree... 153s Reading state information... 154s The following packages will be REMOVED: 154s libperl5.38t64* perl-modules-5.38* python3-netifaces* 155s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 155s After this operation, 41.7 MB disk space will be freed. 155s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61507 files and directories currently installed.) 155s Removing libperl5.38t64:armhf (5.38.2-5) ... 155s Removing perl-modules-5.38 (5.38.2-5) ... 155s Removing python3-netifaces:armhf (0.11.0-2build3) ... 155s Processing triggers for man-db (2.12.1-3) ... 155s Processing triggers for libc-bin (2.40-1ubuntu3) ... 158s autopkgtest [07:15:33]: rebooting testbed after setup commands that affected boot 227s autopkgtest [07:16:42]: testbed running kernel: Linux 6.8.0-47-generic #47~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Oct 2 16:39:14 UTC 2 255s autopkgtest [07:17:10]: @@@@@@@@@@@@@@@@@@@@ apt-source uncalled 266s Get:1 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-2 (dsc) [2117 B] 266s Get:2 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-2 (tar) [155 kB] 266s Get:3 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-2 (diff) [5072 B] 266s gpgv: Signature made Wed Aug 21 15:42:41 2024 UTC 266s gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 266s gpgv: Can't check signature: No public key 266s dpkg-source: warning: cannot verify inline signature for ./uncalled_2.3+ds-2.dsc: no acceptable signature found 266s autopkgtest [07:17:21]: testing package uncalled version 2.3+ds-2 268s autopkgtest [07:17:23]: build not needed 270s autopkgtest [07:17:25]: test run-unit-test: preparing testbed 281s Reading package lists... 281s Building dependency tree... 281s Reading state information... 282s Starting pkgProblemResolver with broken count: 0 282s Starting 2 pkgProblemResolver with broken count: 0 282s Done 283s The following additional packages will be installed: 283s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 liblapack3 libsz2 283s python3-numpy uncalled 283s Suggested packages: 283s gcc gfortran python-numpy-doc python3-dev python3-pytest 283s The following NEW packages will be installed: 283s autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64 liblapack3 283s libsz2 python3-numpy uncalled 283s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 283s Need to get 8057 kB/8057 kB of archives. 283s After this operation, 26.5 MB of additional disk space will be used. 283s Get:1 /tmp/autopkgtest.rR7dqh/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [704 B] 283s Get:2 http://ftpmaster.internal/ubuntu plucky/universe armhf libaec0 armhf 1.1.3-1 [20.8 kB] 283s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-3build2 [126 kB] 284s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 284s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf libsz2 armhf 1.1.3-1 [5302 B] 284s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-103-1t64 armhf 1.10.10+repack-4ubuntu3 [1327 kB] 286s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-3build2 [2086 kB] 286s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-11build1 [3570 kB] 286s Get:9 http://ftpmaster.internal/ubuntu plucky/universe armhf uncalled armhf 2.3+ds-2 [611 kB] 286s Fetched 8057 kB in 1s (9096 kB/s) 286s Selecting previously unselected package libaec0:armhf. 286s (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 ... 59567 files and directories currently installed.) 286s Preparing to unpack .../0-libaec0_1.1.3-1_armhf.deb ... 286s Unpacking libaec0:armhf (1.1.3-1) ... 286s Selecting previously unselected package libblas3:armhf. 286s Preparing to unpack .../1-libblas3_3.12.0-3build2_armhf.deb ... 286s Unpacking libblas3:armhf (3.12.0-3build2) ... 286s Selecting previously unselected package libgfortran5:armhf. 286s Preparing to unpack .../2-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 286s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 286s Selecting previously unselected package libsz2:armhf. 286s Preparing to unpack .../3-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 .../4-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_armhf.deb ... 286s Unpacking libhdf5-103-1t64:armhf (1.10.10+repack-4ubuntu3) ... 286s Selecting previously unselected package liblapack3:armhf. 286s Preparing to unpack .../5-liblapack3_3.12.0-3build2_armhf.deb ... 286s Unpacking liblapack3:armhf (3.12.0-3build2) ... 286s Selecting previously unselected package python3-numpy. 286s Preparing to unpack .../6-python3-numpy_1%3a1.26.4+ds-11build1_armhf.deb ... 286s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 286s Selecting previously unselected package uncalled. 286s Preparing to unpack .../7-uncalled_2.3+ds-2_armhf.deb ... 286s Unpacking uncalled (2.3+ds-2) ... 286s Selecting previously unselected package autopkgtest-satdep. 286s Preparing to unpack .../8-1-autopkgtest-satdep.deb ... 286s Unpacking autopkgtest-satdep (0) ... 286s Setting up libaec0:armhf (1.1.3-1) ... 286s Setting up libblas3:armhf (3.12.0-3build2) ... 286s 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 286s Setting up libgfortran5:armhf (14.2.0-8ubuntu1) ... 286s Setting up libsz2:armhf (1.1.3-1) ... 286s Setting up liblapack3:armhf (3.12.0-3build2) ... 286s 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 286s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 288s Setting up libhdf5-103-1t64:armhf (1.10.10+repack-4ubuntu3) ... 288s Setting up uncalled (2.3+ds-2) ... 288s /usr/lib/python3/dist-packages/uncalled/debug.py:23: SyntaxWarning: invalid escape sequence '\d' 288s CIG_RE = re.compile("(\d+)(["+CIG_OPS_STR+"])") 288s Setting up autopkgtest-satdep (0) ... 288s Processing triggers for man-db (2.12.1-3) ... 289s Processing triggers for libc-bin (2.40-1ubuntu3) ... 301s (Reading database ... 60528 files and directories currently installed.) 301s Removing autopkgtest-satdep (0) ... 308s autopkgtest [07:18:03]: test run-unit-test: [----------------------- 311s /usr/bin/uncalled:307: SyntaxWarning: invalid escape sequence '\-' 311s log_re = re.compile("^([0-9\-]+ [0-9:]+).+ :.+instance_started.+") 311s /usr/bin/uncalled:308: SyntaxWarning: invalid escape sequence '\d' 311s port_re = re.compile("grpc_port = (\d+)") 311s /usr/bin/uncalled:309: SyntaxWarning: invalid escape sequence '\s' 311s device_re = re.compile("(device_id|instance) = ([^\s,]+)") 311s f41a60f7-de4a-4b17-9f54-387e52d60b65 106 73 106 - Escherichia_coli_chromosome:2400000-2410000 10000 6938 6976 38 39 255 ch:i:486 st:i:257117 mt:f:14.089926 311s [bwa_index] Pack FASTA... 0.00 sec 311s [bwa_index] Construct BWT for the packed sequence... 311s [bwa_index] 0.00 seconds elapse. 311s [bwa_index] Update BWT... 0.00 sec 311s [bwa_index] Pack forward-only FASTA... 0.00 sec 311s [bwa_index] Construct SA from BWT and Occ... 0.00 sec 311s Initializing parameter search 311s Computing default parameters 311s Writing default parameters 311s Done 311s /usr/bin/uncalled:307: SyntaxWarning: invalid escape sequence '\-' 311s log_re = re.compile("^([0-9\-]+ [0-9:]+).+ :.+instance_started.+") 311s /usr/bin/uncalled:308: SyntaxWarning: invalid escape sequence '\d' 311s port_re = re.compile("grpc_port = (\d+)") 311s /usr/bin/uncalled:309: SyntaxWarning: invalid escape sequence '\s' 311s device_re = re.compile("(device_id|instance) = ([^\s,]+)") 311s Loading fast5s 311s Mapping 311s Finishing 311s autopkgtest [07:18:06]: test run-unit-test: -----------------------] 315s autopkgtest [07:18:10]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 315s run-unit-test PASS 319s autopkgtest [07:18:14]: @@@@@@@@@@@@@@@@@@@@ summary 319s run-unit-test PASS