0s autopkgtest [23:13:38]: starting date and time: 2026-02-09 23:13:38+0000 0s autopkgtest [23:13:38]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [23:13:38]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.m7df4ueo/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:r-cran-ggplot2 --apt-upgrade qcumber --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-cran-ggplot2/4.0.2+dfsg-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-arm64-17.secgroup --name adt-resolute-arm64-qcumber-20260209-231338-juju-7f2275-prod-proposed-migration-environment-2-0bbb7b20-f658-49d8-9a0c-84bf98b12dc5 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-arm64-qcumber-20260209-231338-juju-7f2275-prod-proposed-migration-environment-2-0bbb7b20-f658-49d8-9a0c-84bf98b12dc5 from image adt/ubuntu-resolute-arm64-server-20260209.img (UUID 793037ca-75af-461b-82de-f8081300b2e3)... 99s autopkgtest [23:15:17]: testbed dpkg architecture: arm64 99s autopkgtest [23:15:17]: testbed apt version: 3.1.15 100s autopkgtest [23:15:18]: @@@@@@@@@@@@@@@@@@@@ test bed setup 100s autopkgtest [23:15:18]: testbed release detected to be: None 101s autopkgtest [23:15:19]: updating testbed package index (apt update) 101s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 101s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 101s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 101s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 101s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1645 kB] 103s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB] 103s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [176 kB] 103s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [246 kB] 103s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [6216 B] 103s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [304 B] 103s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [1580 kB] 106s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [32.0 kB] 106s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [21.7 kB] 106s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [688 B] 107s Fetched 3862 kB in 5s (761 kB/s) 108s Reading package lists... 109s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 109s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 109s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 109s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 110s Reading package lists... 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s Calculating upgrade... 111s The following packages will be upgraded: 111s cryptsetup-bin dracut-install iproute2 iptables libcryptsetup12 libip4tc2 111s libip6tc2 libxtables12 wget 111s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Need to get 2534 kB of archives. 111s After this operation, 18.4 kB of additional disk space will be used. 111s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 iptables arm64 1.8.11-2ubuntu3 [386 kB] 111s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libip4tc2 arm64 1.8.11-2ubuntu3 [24.3 kB] 111s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libip6tc2 arm64 1.8.11-2ubuntu3 [24.7 kB] 111s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libxtables12 arm64 1.8.11-2ubuntu3 [36.7 kB] 111s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 iproute2 arm64 6.18.0-1ubuntu1 [1171 kB] 113s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libcryptsetup12 arm64 2:2.8.0-1ubuntu3 [274 kB] 113s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 wget arm64 1.25.0-2ubuntu4 [344 kB] 113s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 cryptsetup-bin arm64 2:2.8.0-1ubuntu3 [227 kB] 113s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 dracut-install arm64 109-11ubuntu1 [45.3 kB] 113s dpkg-preconfigure: unable to re-open stdin: No such file or directory 113s Fetched 2534 kB in 2s (1149 kB/s) 113s (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 ... 136597 files and directories currently installed.) 113s Preparing to unpack .../0-iptables_1.8.11-2ubuntu3_arm64.deb ... 113s Unpacking iptables (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 114s Preparing to unpack .../1-libip4tc2_1.8.11-2ubuntu3_arm64.deb ... 114s Unpacking libip4tc2:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 114s Preparing to unpack .../2-libip6tc2_1.8.11-2ubuntu3_arm64.deb ... 114s Unpacking libip6tc2:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 114s Preparing to unpack .../3-libxtables12_1.8.11-2ubuntu3_arm64.deb ... 114s Unpacking libxtables12:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 114s Preparing to unpack .../4-iproute2_6.18.0-1ubuntu1_arm64.deb ... 114s Unpacking iproute2 (6.18.0-1ubuntu1) over (6.16.0-1ubuntu3) ... 114s Preparing to unpack .../5-libcryptsetup12_2%3a2.8.0-1ubuntu3_arm64.deb ... 114s Unpacking libcryptsetup12:arm64 (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 114s Preparing to unpack .../6-wget_1.25.0-2ubuntu4_arm64.deb ... 114s Unpacking wget (1.25.0-2ubuntu4) over (1.25.0-2ubuntu3) ... 114s Preparing to unpack .../7-cryptsetup-bin_2%3a2.8.0-1ubuntu3_arm64.deb ... 114s Unpacking cryptsetup-bin (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 114s Preparing to unpack .../8-dracut-install_109-11ubuntu1_arm64.deb ... 114s Unpacking dracut-install (109-11ubuntu1) over (109-9ubuntu1) ... 114s Setting up libip4tc2:arm64 (1.8.11-2ubuntu3) ... 114s Setting up wget (1.25.0-2ubuntu4) ... 114s Setting up libip6tc2:arm64 (1.8.11-2ubuntu3) ... 114s Setting up libxtables12:arm64 (1.8.11-2ubuntu3) ... 114s Setting up dracut-install (109-11ubuntu1) ... 114s Setting up libcryptsetup12:arm64 (2:2.8.0-1ubuntu3) ... 114s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 114s Setting up iptables (1.8.11-2ubuntu3) ... 114s Setting up iproute2 (6.18.0-1ubuntu1) ... 115s Processing triggers for man-db (2.13.1-1build1) ... 116s Processing triggers for install-info (7.2-5) ... 116s Processing triggers for libc-bin (2.42-2ubuntu4) ... 116s autopkgtest [23:15:34]: upgrading testbed (apt dist-upgrade and autopurge) 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 116s Calculating upgrade... 117s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 117s Reading package lists... 117s Building dependency tree... 117s Reading state information... 117s Solving dependencies... 118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 120s autopkgtest [23:15:38]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 19:46:27 UTC 2026 120s autopkgtest [23:15:38]: @@@@@@@@@@@@@@@@@@@@ apt-source qcumber 122s Get:1 http://ftpmaster.internal/ubuntu resolute/universe qcumber 2.3.0-3 (dsc) [1784 B] 122s Get:2 http://ftpmaster.internal/ubuntu resolute/universe qcumber 2.3.0-3 (tar) [262 kB] 122s Get:3 http://ftpmaster.internal/ubuntu resolute/universe qcumber 2.3.0-3 (diff) [130 kB] 123s gpgv: Signature made Thu Nov 20 17:33:23 2025 UTC 123s gpgv: using RSA key D54C3BFAFFB042DE382DA5D741CE7F0B9F1B8B32 123s gpgv: Can't check signature: No public key 123s dpkg-source: warning: cannot verify inline signature for ./qcumber_2.3.0-3.dsc: no acceptable signature found 123s autopkgtest [23:15:41]: testing package qcumber version 2.3.0-3 123s autopkgtest [23:15:41]: build not needed 124s autopkgtest [23:15:42]: test run-unit-test: preparing testbed 124s Reading package lists... 125s Building dependency tree... 125s Reading state information... 125s Solving dependencies... 125s The following NEW packages will be installed: 125s coinor-cbc coinor-libcbc3.1 coinor-libcgl1 coinor-libclp1 125s coinor-libcoinutils3v5 coinor-libosi1v5 docutils-common dwgsim 125s fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono 125s fonts-glyphicons-halflings fonts-urw-base35 git git-man libblas3 libcairo2 125s libdatrie1 libdeflate0 liberror-perl libfontconfig1 libfontenc1 libgfortran5 125s libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 125s libjpeg8 libjs-bootstrap libjs-jquery liblapack3 liblcms2-2 liblerc4 125s libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 125s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 125s python3-biopython python3-cairo python3-charset-normalizer 125s python3-configargparse python3-connection-pool python3-datrie 125s python3-decorator python3-docutils python3-dpath python3-fastjsonschema 125s python3-freetype python3-git python3-gitdb python3-humanfriendly 125s python3-jupyter-core python3-nbformat python3-numpy python3-numpy-dev 125s python3-pandas python3-pandas-lib python3-pil python3-plac 125s python3-platformdirs python3-psutil python3-pulp python3-pytz 125s python3-reportlab python3-retry python3-rlpycairo python3-roman-numerals 125s python3-smart-open python3-smmap python3-stopit python3-tabulate 125s python3-throttler python3-toposort python3-traitlets python3-wrapt 125s python3-yte sgml-base snakemake w3c-sgml-lib x11-common xfonts-encodings 125s xfonts-utils xml-core 125s 0 upgraded, 93 newly installed, 0 to remove and 0 not upgraded. 125s Need to get 50.1 MB of archives. 125s After this operation, 212 MB of additional disk space will be used. 125s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.3.5+ds-3 [366 kB] 125s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7ubuntu1 [181 kB] 125s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-12ubuntu1 [451 kB] 125s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7ubuntu1 [2299 kB] 129s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.3.5+ds-3 [4569 kB] 134s Get:6 http://ftpmaster.internal/ubuntu resolute/universe arm64 coinor-libcoinutils3v5 arm64 2.11.12+ds-1 [450 kB] 135s Get:7 http://ftpmaster.internal/ubuntu resolute/universe arm64 coinor-libosi1v5 arm64 0.108.11+ds-1 [258 kB] 135s Get:8 http://ftpmaster.internal/ubuntu resolute/universe arm64 coinor-libclp1 arm64 1.17.10+ds-1build1 [851 kB] 137s Get:9 http://ftpmaster.internal/ubuntu resolute/universe arm64 coinor-libcgl1 arm64 0.60.9+ds-1build1 [394 kB] 137s Get:10 http://ftpmaster.internal/ubuntu resolute/universe arm64 coinor-libcbc3.1 arm64 2.10.12+ds-1build1 [720 kB] 138s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 sgml-base all 1.31+nmu1build1 [11.2 kB] 138s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 xml-core all 0.19build1 [20.3 kB] 138s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 docutils-common all 0.22.4+dfsg-1 [130 kB] 138s Get:14 http://ftpmaster.internal/ubuntu resolute/universe arm64 dwgsim arm64 0.1.14-4build1 [50.2 kB] 138s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 138s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-core all 2.37-8build1 [834 kB] 139s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontenc1 arm64 1:1.1.8-1build2 [13.9 kB] 139s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 139s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu3 [576 kB] 140s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 xfonts-utils arm64 1:7.7+7build1 [94.8 kB] 140s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-urw-base35 all 20200910-8build1 [10.9 MB] 155s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.17.1-3ubuntu1 [38.5 kB] 155s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-extra all 2.37-8build1 [1944 kB] 158s Get:24 http://ftpmaster.internal/ubuntu resolute/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB] 158s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 liberror-perl all 0.17030-1 [23.5 kB] 158s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 git-man all 1:2.51.0-1ubuntu1 [1179 kB] 160s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 git arm64 1:2.51.0-1ubuntu1 [4431 kB] 167s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.17.1-3ubuntu1 [144 kB] 167s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 libpixman-1-0 arm64 0.46.4-1 [204 kB] 167s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-render0 arm64 1.17.0-2ubuntu1 [16.4 kB] 167s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-shm0 arm64 1.17.0-2ubuntu1 [5938 B] 167s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 167s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo2 arm64 1.18.4-3 [556 kB] 168s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 libdatrie1 arm64 0.2.14-1 [19.6 kB] 168s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2build1 [46.8 kB] 168s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-12ubuntu1 [147 kB] 168s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-11ubuntu1 [72.1 kB] 168s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.3.2-1 [510 kB] 168s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 168s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu3 [161 kB] 168s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 168s Get:42 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-bootstrap all 3.4.1+dfsg-6 [129 kB] 168s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 168s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 liblcms2-2 arm64 2.17-1 [170 kB] 168s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu2 [174 kB] 168s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 libraqm0 arm64 0.10.4-1 [15.1 kB] 168s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1build1 [16.7 kB] 168s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu3 [29.2 kB] 168s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1build1 [205 kB] 168s Get:50 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB] 168s Get:51 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebpdemux2 arm64 1.5.0-0.1build1 [12.5 kB] 168s Get:52 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebpmux3 arm64 1.5.0-0.1build1 [25.2 kB] 168s Get:53 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-charset-normalizer arm64 3.4.4-2 [169 kB] 168s Get:54 http://ftpmaster.internal/ubuntu resolute/main arm64 libopenjp2-7 arm64 2.5.4-1 [180 kB] 168s Get:55 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-pil arm64 12.0.0-1ubuntu1 [486 kB] 168s Get:56 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-cairo arm64 1.27.0-2build1 [141 kB] 168s Get:57 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-freetype all 2.5.1-2 [92.2 kB] 168s Get:58 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-rlpycairo all 0.3.0-4 [9332 B] 168s Get:59 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-reportlab all 4.4.9-1 [1149 kB] 170s Get:60 http://ftpmaster.internal/ubuntu resolute/universe arm64 w3c-sgml-lib all 1.3-3build1 [278 kB] 170s Get:61 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-biopython arm64 1.86+dfsg-1 [1675 kB] 172s Get:62 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-configargparse all 1.7-2 [31.7 kB] 172s Get:63 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-connection-pool all 0.0.3-2build1 [5792 B] 172s Get:64 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-datrie arm64 0.8.3-2 [184 kB] 172s Get:65 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-decorator all 5.2.1-2 [28.1 kB] 172s Get:66 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-roman-numerals all 4.1.0-1 [8660 B] 172s Get:67 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-docutils all 0.22.4+dfsg-1 [439 kB] 172s Get:68 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-dpath all 2.2.0-2 [20.3 kB] 172s Get:69 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-fastjsonschema all 2.21.1-1 [20.4 kB] 172s Get:70 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-smmap all 6.0.0-1build1 [20.7 kB] 172s Get:71 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-gitdb all 4.0.12-1 [46.4 kB] 172s Get:72 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-git all 3.1.46-1 [149 kB] 173s Get:73 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-humanfriendly all 10.0-6build1 [70.9 kB] 173s Get:74 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-platformdirs all 4.5.1-1 [17.1 kB] 173s Get:75 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-traitlets all 5.14.3+really5.14.3-2 [71.7 kB] 173s Get:76 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-jupyter-core all 5.9.1-1 [28.9 kB] 173s Get:77 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-nbformat all 5.10.4-1 [39.2 kB] 173s Get:78 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytz all 2025.2-5 [32.4 kB] 173s Get:79 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas-lib arm64 2.3.3+dfsg-3 [6290 kB] 184s Get:80 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas all 2.3.3+dfsg-3 [2948 kB] 189s Get:81 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-plac all 1.4.3-2 [63.2 kB] 189s Get:82 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-psutil arm64 7.1.0-1ubuntu1 [191 kB] 189s Get:83 http://ftpmaster.internal/ubuntu resolute/universe arm64 coinor-cbc arm64 2.10.12+ds-1build1 [14.3 kB] 189s Get:84 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pulp all 2.7.0+dfsg-4 [71.4 kB] 190s Get:85 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-retry all 0.9.2-5 [6160 B] 190s Get:86 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-wrapt arm64 1.17.3-3 [40.1 kB] 190s Get:87 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-smart-open all 7.5.0-1 [56.9 kB] 190s Get:88 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-stopit all 1.1.2-4 [12.9 kB] 190s Get:89 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-tabulate all 0.9.0-1build1 [45.4 kB] 190s Get:90 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-throttler all 1.2.2-4ubuntu1 [7758 B] 190s Get:91 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-toposort all 1.10-2build1 [6454 B] 190s Get:92 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-yte all 1.5.4-1build1 [12.2 kB] 190s Get:93 http://ftpmaster.internal/ubuntu resolute/universe arm64 snakemake all 7.32.4-8.1 [275 kB] 190s Fetched 50.1 MB in 1min 5s (774 kB/s) 190s Selecting previously unselected package python3-numpy-dev:arm64. 191s (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 ... 136600 files and directories currently installed.) 191s Preparing to unpack .../00-python3-numpy-dev_1%3a2.3.5+ds-3_arm64.deb ... 191s Unpacking python3-numpy-dev:arm64 (1:2.3.5+ds-3) ... 191s Selecting previously unselected package libblas3:arm64. 191s Preparing to unpack .../01-libblas3_3.12.1-7ubuntu1_arm64.deb ... 191s Unpacking libblas3:arm64 (3.12.1-7ubuntu1) ... 191s Selecting previously unselected package libgfortran5:arm64. 191s Preparing to 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snakemake. 196s Preparing to unpack .../92-snakemake_7.32.4-8.1_all.deb ... 196s Unpacking snakemake (7.32.4-8.1) ... 196s Setting up python3-toposort (1.10-2build1) ... 196s Setting up libgraphite2-3:arm64 (1.3.14-11ubuntu1) ... 196s Setting up python3-configargparse (1.7-2) ... 196s Setting up liblcms2-2:arm64 (2.17-1) ... 196s Setting up libpixman-1-0:arm64 (0.46.4-1) ... 196s Setting up libsharpyuv0:arm64 (1.5.0-0.1build1) ... 196s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu2) ... 196s Setting up libxrender1:arm64 (1:0.9.12-1) ... 196s Setting up libdatrie1:arm64 (0.2.14-1) ... 196s Setting up libxcb-render0:arm64 (1.17.0-2ubuntu1) ... 196s Setting up python3-charset-normalizer (3.4.4-2) ... 196s Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 196s Setting up x11-common (1:7.7+24ubuntu1) ... 196s Setting up libdeflate0:arm64 (1.23-2build1) ... 196s Setting up python3-tabulate (0.9.0-1build1) ... 196s Setting up python3-pytz (2025.2-5) ... 197s Setting up libxcb-shm0:arm64 (1.17.0-2ubuntu1) ... 197s Setting up libgomp1:arm64 (15.2.0-12ubuntu1) ... 197s Setting up python3-freetype (2.5.1-2) ... 197s Setting up libjbig0:arm64 (2.1-6.1ubuntu3) ... 197s Setting up python3-plac (1.4.3-2) ... 197s Setting up python3-platformdirs (4.5.1-1) ... 197s Setting up python3-psutil (7.1.0-1ubuntu1) ... 197s Setting up liberror-perl (0.17030-1) ... 197s Setting up python3-decorator (5.2.1-2) ... 197s Setting up libfontenc1:arm64 (1:1.1.8-1build2) ... 197s Setting up libblas3:arm64 (3.12.1-7ubuntu1) ... 197s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 197s Setting up python3-humanfriendly (10.0-6build1) ... 198s Setting up xfonts-encodings (1:1.0.5-0ubuntu3) ... 198s Setting up python3-dpath (2.2.0-2) ... 198s Setting up python3-connection-pool (0.0.3-2build1) ... 198s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 198s Setting up fonts-dejavu-mono (2.37-8build1) ... 198s Setting up python3-numpy-dev:arm64 (1:2.3.5+ds-3) ... 198s Setting up python3-wrapt (1.17.3-3) ... 198s Setting up python3-throttler (1.2.2-4ubuntu1) ... 198s Setting up dwgsim (0.1.14-4build1) ... 198s Setting up fonts-dejavu-core (2.37-8build1) ... 198s Setting up python3-retry (0.9.2-5) ... 198s Setting up libjpeg-turbo8:arm64 (2.1.5-4ubuntu3) ... 198s Setting up libgfortran5:arm64 (15.2.0-12ubuntu1) ... 198s Setting up libwebp7:arm64 (1.5.0-0.1build1) ... 198s Setting up python3-fastjsonschema (2.21.1-1) ... 198s Setting up fonts-dejavu-extra (2.37-8build1) ... 198s Setting up python3-stopit (1.1.2-4) ... 198s Setting up python3-traitlets (5.14.3+really5.14.3-2) ... 199s Setting up python3-roman-numerals (4.1.0-1) ... 199s Setting up libopenjp2-7:arm64 (2.5.4-1) ... 199s Setting up git-man (1:2.51.0-1ubuntu1) ... 199s Setting up libharfbuzz0b:arm64 (12.3.2-1) ... 199s Setting up sgml-base (1.31+nmu1build1) ... 199s Setting up python3-datrie (0.8.3-2) ... 199s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 199s Setting up libwebpmux3:arm64 (1.5.0-0.1build1) ... 199s Setting up python3-smmap (6.0.0-1build1) ... 199s Setting up python3-jupyter-core (5.9.1-1) ... 199s Setting up libjs-bootstrap (3.4.1+dfsg-6) ... 199s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 199s Setting up liblapack3:arm64 (3.12.1-7ubuntu1) ... 199s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 199s Setting up python3-smart-open (7.5.0-1) ... 199s Setting up fontconfig-config (2.17.1-3ubuntu1) ... 199s Setting up libwebpdemux2:arm64 (1.5.0-0.1build1) ... 199s Setting up python3-nbformat (5.10.4-1) ... 199s Setting up python3-gitdb (4.0.12-1) ... 200s Setting up xfonts-utils (1:7.7+7build1) ... 200s Setting up python3-yte (1.5.4-1build1) ... 200s Setting up coinor-libcoinutils3v5:arm64 (2.11.12+ds-1) ... 200s Setting up libraqm0:arm64 (0.10.4-1) ... 200s Setting up git (1:2.51.0-1ubuntu1) ... 200s Setting up python3-numpy (1:2.3.5+ds-3) ... 201s Setting up coinor-libosi1v5:arm64 (0.108.11+ds-1) ... 201s Setting up libtiff6:arm64 (4.7.0-3ubuntu3) ... 201s Setting up xml-core (0.19build1) ... 201s Setting up libfontconfig1:arm64 (2.17.1-3ubuntu1) ... 201s Setting up python3-pandas-lib:arm64 (2.3.3+dfsg-3) ... 201s Setting up fonts-urw-base35 (20200910-8build1) ... 202s Setting up libcairo2:arm64 (1.18.4-3) ... 202s Setting up python3-pil:arm64 (12.0.0-1ubuntu1) ... 202s Setting up python3-pandas (2.3.3+dfsg-3) ... 206s Setting up coinor-libclp1:arm64 (1.17.10+ds-1build1) ... 206s Setting up python3-git (3.1.46-1) ... 206s Setting up coinor-libcgl1:arm64 (0.60.9+ds-1build1) ... 206s Setting up python3-cairo (1.27.0-2build1) ... 206s Setting up python3-rlpycairo (0.3.0-4) ... 206s Setting up coinor-libcbc3.1:arm64 (2.10.12+ds-1build1) ... 206s Setting up python3-reportlab (4.4.9-1) ... 207s Setting up coinor-cbc (2.10.12+ds-1build1) ... 207s Setting up python3-pulp (2.7.0+dfsg-4) ... 207s /usr/lib/python3/dist-packages/pulp/apis/xpress_api.py:325: SyntaxWarning: invalid escape sequence '\ ' 207s otherwise be interpreted by the Tcl shell: \ $ " [ 207s Processing triggers for libc-bin (2.42-2ubuntu4) ... 207s Processing triggers for man-db (2.13.1-1build1) ... 208s Processing triggers for sgml-base (1.31+nmu1build1) ... 208s Setting up w3c-sgml-lib (1.3-3build1) ... 232s Setting up docutils-common (0.22.4+dfsg-1) ... 232s Setting up python3-biopython (1.86+dfsg-1) ... 233s Processing triggers for sgml-base (1.31+nmu1build1) ... 233s Setting up python3-docutils (0.22.4+dfsg-1) ... 233s Setting up snakemake (7.32.4-8.1) ... 234s autopkgtest [23:17:32]: test run-unit-test: [----------------------- 234s Running simulators... 234s Prepended http:// to '' 234s http://: Invalid host name. 234s --2026-02-09 23:17:33-- https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna.gz 240s Resolving egress.ps7.internal (egress.ps7.internal)... 10.151.41.7, 10.151.41.6, 10.151.41.5 240s Connecting to egress.ps7.internal (egress.ps7.internal)|10.151.41.7|:3128... connected. 240s Proxy request sent, awaiting response... 200 OK 240s Length: 1379902 (1.3M) [application/x-gzip] 240s Saving to: ‘data/GCF_000005845.2_ASM584v2_genomic.fna.gz’ 240s 240s 0K .......... .......... .......... .......... .......... 3% 228K 6s 240s 50K .......... .......... .......... .......... .......... 7% 1.11M 3s 240s 100K .......... .......... .......... .......... .......... 11% 456K 3s 241s 150K .......... .......... .......... .......... .......... 14% 750K 3s 241s 200K .......... .......... .......... .......... .......... 18% 169M 2s 241s 250K .......... .......... .......... .......... .......... 22% 1.13M 2s 241s 300K .......... .......... .......... .......... .......... 25% 755K 2s 241s 350K .......... .......... .......... .......... .......... 29% 147M 1s 241s 400K .......... .......... .......... .......... .......... 33% 208M 1s 241s 450K .......... .......... .......... .......... .......... 37% 152M 1s 241s 500K .......... .......... .......... .......... .......... 40% 199M 1s 241s 550K .......... .......... .......... .......... .......... 44% 1.14M 1s 241s 600K .......... .......... .......... .......... .......... 48% 756K 1s 241s 650K .......... .......... .......... .......... .......... 51% 125M 1s 241s 700K .......... .......... .......... .......... .......... 55% 174M 1s 241s 750K .......... .......... .......... .......... .......... 59% 209M 0s 241s 800K .......... .......... .......... .......... .......... 63% 189M 0s 241s 850K .......... .......... .......... .......... .......... 66% 190M 0s 241s 900K .......... .......... .......... .......... .......... 70% 216M 0s 241s 950K .......... .......... .......... .......... .......... 74% 180M 0s 241s 1000K .......... .......... .......... .......... .......... 77% 198M 0s 241s 1050K .......... .......... .......... .......... .......... 81% 204M 0s 241s 1100K .......... .......... .......... .......... .......... 85% 1.19M 0s 241s 1150K .......... .......... .......... .......... .......... 89% 98.9M 0s 241s 1200K .......... .......... .......... .......... .......... 92% 1.16M 0s 241s 1250K .......... .......... .......... .......... .......... 96% 2.04M 0s 241s 1300K .......... .......... .......... .......... ....... 100% 174M=0.8s 241s 241s 2026-02-09 23:17:39 (1.71 MB/s) - ‘data/GCF_000005845.2_ASM584v2_genomic.fna.gz’ saved [1379902/1379902] 241s 241s FINISHED --2026-02-09 23:17:39-- 241s Total wall clock time: 6.5s 241s Downloaded: 1 files, 1.3M in 0.8s (1.71 MB/s) 241s [dwgsim_core] NC_000913.3 length: 4641652 241s [dwgsim_core] 1 sequences, total length: 4641652 241s [dwgsim_core] Currently on: 241s 0 [dwgsim_core] 0 [dwgsim_core] 1000 241s [dwgsim_core] Complete! 241s Cleanup simulated data... 242s FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpwfquqxt_/testData42dwgsim-e-coli4cd473993fb5297c262806b154139fd517216272/testData42dwgsim-e-coli4cd473993fb5297c262806b154139fd517216272_S1_L001_R2_001.fastq' 242s Command 'QCumber encountered an error' returned non-zero exit status 1. 242s Running simulators... 242s Cleanup simulated data... 243s FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpwfquqxt_/testData42dwgsim-e-colica1f17628ed45b58a10b74a9fe7d8023079a1856/testData42dwgsim-e-colica1f17628ed45b58a10b74a9fe7d8023079a1856_S1_L001_R2_001.fastq' 243s Command 'QCumber encountered an error' returned non-zero exit status 1. 243s Running simulators... 243s [dwgsim_core] NC_000913.3 length: 4641652 243s [dwgsim_core] 1 sequences, total length: 4641652 243s [dwgsim_core] Currently on: 260s 0 [dwgsim_core] 0 [dwgsim_core] 10000 [dwgsim_core] 20000 [dwgsim_core] 30000 [dwgsim_core] 40000 [dwgsim_core] 50000 [dwgsim_core] 60000 [dwgsim_core] 70000 [dwgsim_core] 80000 [dwgsim_core] 90000 [dwgsim_core] 100000 260s [dwgsim_core] Complete! 260s Cleanup simulated data... 261s UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte 261s Command 'QCumber encountered an error' returned non-zero exit status 1. 261s wget -Pdata https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna.gz 261s 261s Run Qcumber: testData42dwgsim-e-coli4cd473993fb5297c262806b154139fd517216272 261s ../QCumber-2 -i/tmp/tmpwfquqxt_/testData42dwgsim-e-coli4cd473993fb5297c262806b154139fd517216272 -t2 -K -otestData42dwgsim-e-coli4cd473993fb5297c262806b154139fd517216272 261s 261s Run Qcumber: testData42dwgsim-e-colica1f17628ed45b58a10b74a9fe7d8023079a1856 261s ../QCumber-2 -i/tmp/tmpwfquqxt_/testData42dwgsim-e-colica1f17628ed45b58a10b74a9fe7d8023079a1856 -t2 -K --trimBetter mapping -otestData42dwgsim-e-colica1f17628ed45b58a10b74a9fe7d8023079a1856 261s 261s Run Qcumber: testData42dwgsim-e-colidd57828f1167d5db3d40ca2590a921efd93d508c 261s ../QCumber-2 -i/tmp/tmpwfquqxt_/testData42dwgsim-e-colidd57828f1167d5db3d40ca2590a921efd93d508c -t4 -K -S -otestData42dwgsim-e-colidd57828f1167d5db3d40ca2590a921efd93d508c -rdata/GCF_000005845.2_ASM584v2_genomic.fna.gz 261s autopkgtest [23:17:59]: test run-unit-test: -----------------------] 261s run-unit-test PASS 261s autopkgtest [23:17:59]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 262s autopkgtest [23:18:00]: @@@@@@@@@@@@@@@@@@@@ summary 262s run-unit-test PASS