0s autopkgtest [23:06:14]: starting date and time: 2026-02-09 23:06:14+0000 0s autopkgtest [23:06:14]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [23:06:14]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.anfqctxa/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,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:r-cran-ggplot2 --apt-upgrade assemblytics --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-cran-ggplot2/4.0.2+dfsg-1 -- lxd -r lxd-armhf-10.145.243.240 lxd-armhf-10.145.243.240:autopkgtest/ubuntu/resolute/armhf 26s autopkgtest [23:06:40]: testbed dpkg architecture: armhf 28s autopkgtest [23:06:42]: testbed apt version: 3.1.15 32s autopkgtest [23:06:46]: @@@@@@@@@@@@@@@@@@@@ test bed setup 34s autopkgtest [23:06:48]: testbed release detected to be: None 41s autopkgtest [23:06:55]: updating testbed package index (apt update) 43s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 44s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [124 kB] 44s Get:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease [124 kB] 44s Get:4 http://ftpmaster.internal/ubuntu resolute-security InRelease [124 kB] 45s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1645 kB] 47s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [176 kB] 47s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB] 47s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [246 kB] 48s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [1405 kB] 50s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [7452 B] 50s Get:11 http://ftpmaster.internal/ubuntu resolute/restricted Sources [15.1 kB] 50s Get:12 http://ftpmaster.internal/ubuntu resolute/main Sources [1398 kB] 52s Get:13 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.4 MB] 84s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1374 kB] 86s Get:15 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [15.3 MB] 111s Fetched 43.5 MB in 1min 8s (644 kB/s) 113s Reading package lists... 119s autopkgtest [23:08:13]: upgrading testbed (apt dist-upgrade and autopurge) 120s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s Calculating upgrade... 122s The following packages will be upgraded: 122s cryptsetup-bin dracut-install iproute2 iptables libcryptsetup12 libip4tc2 122s libip6tc2 libxtables12 wget 122s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 122s Need to get 2407 kB of archives. 122s After this operation, 152 kB of additional disk space will be used. 122s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf iptables armhf 1.8.11-2ubuntu3 [345 kB] 122s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libip4tc2 armhf 1.8.11-2ubuntu3 [22.0 kB] 122s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libip6tc2 armhf 1.8.11-2ubuntu3 [22.3 kB] 122s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf libxtables12 armhf 1.8.11-2ubuntu3 [33.5 kB] 122s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf iproute2 armhf 6.18.0-1ubuntu1 [1123 kB] 124s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libcryptsetup12 armhf 2:2.8.0-1ubuntu3 [254 kB] 124s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf wget armhf 1.25.0-2ubuntu4 [327 kB] 125s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf cryptsetup-bin armhf 2:2.8.0-1ubuntu3 [232 kB] 125s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf dracut-install armhf 109-11ubuntu1 [47.9 kB] 126s Preconfiguring packages ... 126s Fetched 2407 kB in 3s (705 kB/s) 126s (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 ... 68683 files and directories currently installed.) 126s Preparing to unpack .../0-iptables_1.8.11-2ubuntu3_armhf.deb ... 126s Unpacking iptables (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 126s Preparing to unpack .../1-libip4tc2_1.8.11-2ubuntu3_armhf.deb ... 126s Unpacking libip4tc2:armhf (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 126s Preparing to unpack .../2-libip6tc2_1.8.11-2ubuntu3_armhf.deb ... 126s Unpacking libip6tc2:armhf (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 126s Preparing to unpack .../3-libxtables12_1.8.11-2ubuntu3_armhf.deb ... 126s Unpacking libxtables12:armhf (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 126s Preparing to unpack .../4-iproute2_6.18.0-1ubuntu1_armhf.deb ... 126s Unpacking iproute2 (6.18.0-1ubuntu1) over (6.16.0-1ubuntu3) ... 127s Preparing to unpack .../5-libcryptsetup12_2%3a2.8.0-1ubuntu3_armhf.deb ... 127s Unpacking libcryptsetup12:armhf (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 127s Preparing to unpack .../6-wget_1.25.0-2ubuntu4_armhf.deb ... 127s Unpacking wget (1.25.0-2ubuntu4) over (1.25.0-2ubuntu3) ... 127s Preparing to unpack .../7-cryptsetup-bin_2%3a2.8.0-1ubuntu3_armhf.deb ... 127s Unpacking cryptsetup-bin (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 127s Preparing to unpack .../8-dracut-install_109-11ubuntu1_armhf.deb ... 127s Unpacking dracut-install (109-11ubuntu1) over (109-9ubuntu1) ... 127s Setting up libip4tc2:armhf (1.8.11-2ubuntu3) ... 127s Setting up wget (1.25.0-2ubuntu4) ... 127s Setting up libip6tc2:armhf (1.8.11-2ubuntu3) ... 127s Setting up libxtables12:armhf (1.8.11-2ubuntu3) ... 127s Setting up dracut-install (109-11ubuntu1) ... 127s Setting up libcryptsetup12:armhf (2:2.8.0-1ubuntu3) ... 127s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 127s Setting up iptables (1.8.11-2ubuntu3) ... 127s Setting up iproute2 (6.18.0-1ubuntu1) ... 127s Processing triggers for man-db (2.13.1-1build1) ... 128s Processing triggers for install-info (7.2-5) ... 128s Processing triggers for libc-bin (2.42-2ubuntu4) ... 131s Reading package lists... 131s Building dependency tree... 131s Reading state information... 131s Solving dependencies... 131s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 133s autopkgtest [23:08:27]: rebooting testbed after setup commands that affected boot 174s autopkgtest [23:09:08]: testbed running kernel: Linux 6.8.0-87-generic #88~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 14 14:00:09 UTC 2 198s autopkgtest [23:09:32]: @@@@@@@@@@@@@@@@@@@@ apt-source assemblytics 208s Get:1 http://ftpmaster.internal/ubuntu resolute/universe assemblytics 1.2.1+dfsg-2build1 (dsc) [2075 B] 208s Get:2 http://ftpmaster.internal/ubuntu resolute/universe assemblytics 1.2.1+dfsg-2build1 (tar) [15.5 kB] 208s Get:3 http://ftpmaster.internal/ubuntu resolute/universe assemblytics 1.2.1+dfsg-2build1 (diff) [4728 B] 208s gpgv: Signature made Tue Dec 9 22:06:16 2025 UTC 208s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 208s gpgv: Can't check signature: No public key 208s dpkg-source: warning: cannot verify inline signature for ./assemblytics_1.2.1+dfsg-2build1.dsc: no acceptable signature found 209s autopkgtest [23:09:43]: testing package assemblytics version 1.2.1+dfsg-2build1 211s autopkgtest [23:09:45]: build not needed 212s autopkgtest [23:09:46]: test run-unit-test: preparing testbed 214s Reading package lists... 214s Building dependency tree... 214s Reading state information... 215s Solving dependencies... 215s The following NEW packages will be installed: 215s assemblytics fontconfig fontconfig-config fonts-dejavu-core 215s fonts-dejavu-mono libblas3 libcairo2 libdatrie1 libdeflate0 libfontconfig1 215s libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6 215s libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 215s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 215s libpython3.14-minimal libpython3.14-stdlib libsharpyuv0 libsm6 libtcl8.6 215s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 215s libxft2 libxrender1 libxss1 libxt6t64 python-is-python3 python3-all 215s python3-numpy python3-numpy-dev python3.14 python3.14-minimal r-base-core 215s r-cran-cli r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gtable 215s r-cran-isoband r-cran-labeling r-cran-lifecycle r-cran-littler 215s r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp 215s r-cran-rlang r-cran-s7 r-cran-scales r-cran-vctrs r-cran-viridislite 215s r-cran-withr unzip x11-common xdg-utils zip 215s 0 upgraded, 74 newly installed, 0 to remove and 0 not upgraded. 215s Need to get 67.2 MB of archives. 215s After this operation, 154 MB of additional disk space will be used. 215s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy-dev armhf 1:2.3.5+ds-3 [141 kB] 216s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libblas3 armhf 3.12.1-7ubuntu1 [133 kB] 216s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran5 armhf 15.2.0-12ubuntu1 [334 kB] 216s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack3 armhf 3.12.1-7ubuntu1 [2090 kB] 219s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy armhf 1:2.3.5+ds-3 [4729 kB] 226s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.14-minimal armhf 3.14.2-1 [905 kB] 227s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf python3.14-minimal armhf 3.14.2-1 [2155 kB] 230s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf zip armhf 3.0-15ubuntu3 [164 kB] 230s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf unzip armhf 6.0-29ubuntu1 [167 kB] 230s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf libpaper2 armhf 2.2.5-0.3build1 [16.3 kB] 230s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf libpaper-utils armhf 2.2.5-0.3build1 [14.2 kB] 230s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 231s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf libfreetype6 armhf 2.14.1+dfsg-2 [345 kB] 231s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-dejavu-mono all 2.37-8build1 [502 kB] 232s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-dejavu-core all 2.37-8build1 [834 kB] 233s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf fontconfig-config armhf 2.17.1-3ubuntu1 [38.5 kB] 233s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf libfontconfig1 armhf 2.17.1-3ubuntu1 [117 kB] 233s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf libpixman-1-0 armhf 0.46.4-1 [196 kB] 233s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf libxcb-render0 armhf 1.17.0-2ubuntu1 [15.5 kB] 233s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf libxcb-shm0 armhf 1.17.0-2ubuntu1 [5956 B] 233s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf libxrender1 armhf 1:0.9.12-1 [16.6 kB] 233s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf libcairo2 armhf 1.18.4-3 [489 kB] 234s Get:23 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate0 armhf 1.23-2build1 [38.8 kB] 234s Get:24 http://ftpmaster.internal/ubuntu resolute/main armhf libgomp1 armhf 15.2.0-12ubuntu1 [129 kB] 234s Get:25 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-turbo8 armhf 2.1.5-4ubuntu3 [129 kB] 234s Get:26 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 234s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf fontconfig armhf 2.17.1-3ubuntu1 [180 kB] 235s Get:28 http://ftpmaster.internal/ubuntu resolute/main armhf libgraphite2-3 armhf 1.3.14-11ubuntu1 [65.2 kB] 235s Get:29 http://ftpmaster.internal/ubuntu resolute/main armhf libharfbuzz0b armhf 12.3.2-1 [501 kB] 236s Get:30 http://ftpmaster.internal/ubuntu resolute/main armhf libthai-data all 0.1.30-1 [155 kB] 236s Get:31 http://ftpmaster.internal/ubuntu resolute/main armhf libdatrie1 armhf 0.2.14-1 [16.4 kB] 236s Get:32 http://ftpmaster.internal/ubuntu resolute/main armhf libthai0 armhf 0.1.30-1 [15.4 kB] 236s Get:33 http://ftpmaster.internal/ubuntu resolute/main armhf libpango-1.0-0 armhf 1.57.0-1 [218 kB] 236s Get:34 http://ftpmaster.internal/ubuntu resolute/main armhf libpangoft2-1.0-0 armhf 1.57.0-1 [45.2 kB] 236s Get:35 http://ftpmaster.internal/ubuntu resolute/main armhf libpangocairo-1.0-0 armhf 1.57.0-1 [25.3 kB] 236s Get:36 http://ftpmaster.internal/ubuntu resolute/main armhf libtcl8.6 armhf 8.6.17+dfsg-1build1 [918 kB] 238s Get:37 http://ftpmaster.internal/ubuntu resolute/main armhf libjbig0 armhf 2.1-6.1ubuntu3 [25.3 kB] 238s Get:38 http://ftpmaster.internal/ubuntu resolute/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu2 [162 kB] 238s Get:39 http://ftpmaster.internal/ubuntu resolute/main armhf libsharpyuv0 armhf 1.5.0-0.1build1 [16.3 kB] 238s Get:40 http://ftpmaster.internal/ubuntu resolute/main armhf libwebp7 armhf 1.5.0-0.1build1 [189 kB] 238s Get:41 http://ftpmaster.internal/ubuntu resolute/main armhf libtiff6 armhf 4.7.0-3ubuntu3 [188 kB] 239s Get:42 http://ftpmaster.internal/ubuntu resolute/main armhf libxft2 armhf 2.3.6-1build2 [37.2 kB] 239s Get:43 http://ftpmaster.internal/ubuntu resolute/main armhf x11-common all 1:7.7+24ubuntu1 [22.4 kB] 239s Get:44 http://ftpmaster.internal/ubuntu resolute/main armhf libxss1 armhf 1:1.2.3-1build4 [6328 B] 239s Get:45 http://ftpmaster.internal/ubuntu resolute/main armhf libtk8.6 armhf 8.6.17-1 [694 kB] 240s Get:46 http://ftpmaster.internal/ubuntu resolute/main armhf libice6 armhf 2:1.1.1-1build1 [37.5 kB] 240s Get:47 http://ftpmaster.internal/ubuntu resolute/main armhf libsm6 armhf 2:1.2.6-1build1 [15.3 kB] 240s Get:48 http://ftpmaster.internal/ubuntu resolute/main armhf libxt6t64 armhf 1:1.2.1-1.3 [145 kB] 240s Get:49 http://ftpmaster.internal/ubuntu resolute/universe armhf r-base-core armhf 4.5.2-1ubuntu2 [28.5 MB] 282s Get:50 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-cli armhf 3.6.4-1 [1377 kB] 284s Get:51 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-glue armhf 1.8.0-1 [162 kB] 284s Get:52 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rlang armhf 1.1.5-3 [1700 kB] 286s Get:53 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 286s Get:54 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 286s Get:55 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-isoband armhf 0.2.7-1 [1477 kB] 289s Get:56 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-s7 armhf 0.2.0-1 [328 kB] 290s Get:57 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-farver armhf 2.1.2-1 [1355 kB] 292s Get:58 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-labeling all 0.4.3-1 [62.1 kB] 292s Get:59 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-r6 all 2.6.1-1 [101 kB] 292s Get:60 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB] 292s Get:61 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-viridislite all 0.4.3-1 [1088 kB] 294s Get:62 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-scales all 1.4.0-1 [725 kB] 295s Get:63 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-vctrs armhf 0.6.5-1 [1310 kB] 297s Get:64 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-withr all 3.0.2+dfsg-1 [214 kB] 297s Get:65 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf r-cran-ggplot2 all 4.0.2+dfsg-1 [4941 kB] 304s Get:66 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-littler armhf 0.3.22-1 [81.0 kB] 304s Get:67 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 304s Get:68 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rcpp armhf 1.1.0-1 [2009 kB] 306s Get:69 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-plyr armhf 1.8.9-1 [832 kB] 307s Get:70 http://ftpmaster.internal/ubuntu resolute/universe armhf assemblytics all 1.2.1+dfsg-2build1 [19.2 kB] 307s Get:71 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.14-stdlib armhf 3.14.2-1 [2270 kB] 310s Get:72 http://ftpmaster.internal/ubuntu resolute/main armhf python-is-python3 all 3.13.3-1+build1 [2832 B] 310s Get:73 http://ftpmaster.internal/ubuntu resolute/main armhf python3.14 armhf 3.14.2-1 [816 kB] 311s Get:74 http://ftpmaster.internal/ubuntu resolute/main armhf python3-all armhf 3.13.9-3 [890 B] 311s Preconfiguring packages ... 312s Fetched 67.2 MB in 1min 36s (700 kB/s) 312s Selecting previously unselected package python3-numpy-dev:armhf. 312s (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 ... 68686 files and directories currently installed.) 312s Preparing to unpack .../00-python3-numpy-dev_1%3a2.3.5+ds-3_armhf.deb ... 312s Unpacking python3-numpy-dev:armhf (1:2.3.5+ds-3) ... 312s Selecting previously unselected package libblas3:armhf. 312s Preparing to unpack .../01-libblas3_3.12.1-7ubuntu1_armhf.deb ... 312s Unpacking libblas3:armhf (3.12.1-7ubuntu1) ... 312s Selecting previously unselected package libgfortran5:armhf. 312s Preparing to unpack .../02-libgfortran5_15.2.0-12ubuntu1_armhf.deb ... 312s Unpacking libgfortran5:armhf (15.2.0-12ubuntu1) ... 312s Selecting previously unselected package liblapack3:armhf. 312s Preparing to unpack .../03-liblapack3_3.12.1-7ubuntu1_armhf.deb ... 312s Unpacking liblapack3:armhf (3.12.1-7ubuntu1) ... 312s Selecting previously unselected package python3-numpy. 312s Preparing to unpack .../04-python3-numpy_1%3a2.3.5+ds-3_armhf.deb ... 312s Unpacking python3-numpy (1:2.3.5+ds-3) ... 312s Selecting previously unselected package libpython3.14-minimal:armhf. 312s Preparing to unpack .../05-libpython3.14-minimal_3.14.2-1_armhf.deb ... 312s Unpacking libpython3.14-minimal:armhf (3.14.2-1) ... 312s Selecting previously unselected package python3.14-minimal. 312s Preparing to unpack .../06-python3.14-minimal_3.14.2-1_armhf.deb ... 312s Unpacking python3.14-minimal (3.14.2-1) ... 312s Selecting previously unselected package zip. 312s Preparing to unpack .../07-zip_3.0-15ubuntu3_armhf.deb ... 312s Unpacking zip (3.0-15ubuntu3) ... 312s Selecting previously unselected package unzip. 312s Preparing to unpack .../08-unzip_6.0-29ubuntu1_armhf.deb ... 312s Unpacking unzip (6.0-29ubuntu1) ... 312s Selecting previously unselected package libpaper2:armhf. 312s Preparing to unpack .../09-libpaper2_2.2.5-0.3build1_armhf.deb ... 312s Unpacking libpaper2:armhf (2.2.5-0.3build1) ... 312s Selecting previously unselected package libpaper-utils. 312s Preparing to unpack .../10-libpaper-utils_2.2.5-0.3build1_armhf.deb ... 312s Unpacking libpaper-utils (2.2.5-0.3build1) ... 313s Selecting previously unselected package xdg-utils. 313s Preparing to unpack .../11-xdg-utils_1.2.1-2ubuntu2_all.deb ... 313s Unpacking xdg-utils (1.2.1-2ubuntu2) ... 313s Selecting previously unselected package libfreetype6:armhf. 313s Preparing to unpack .../12-libfreetype6_2.14.1+dfsg-2_armhf.deb ... 313s Unpacking libfreetype6:armhf (2.14.1+dfsg-2) ... 313s Selecting previously unselected package fonts-dejavu-mono. 313s Preparing to unpack .../13-fonts-dejavu-mono_2.37-8build1_all.deb ... 313s Unpacking fonts-dejavu-mono (2.37-8build1) ... 313s Selecting previously unselected package fonts-dejavu-core. 313s Preparing to unpack .../14-fonts-dejavu-core_2.37-8build1_all.deb ... 313s Unpacking fonts-dejavu-core (2.37-8build1) ... 313s Selecting previously unselected package fontconfig-config. 313s Preparing to unpack .../15-fontconfig-config_2.17.1-3ubuntu1_armhf.deb ... 313s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 313s Selecting previously unselected package libfontconfig1:armhf. 313s Preparing to unpack .../16-libfontconfig1_2.17.1-3ubuntu1_armhf.deb ... 313s Unpacking libfontconfig1:armhf (2.17.1-3ubuntu1) ... 313s Selecting previously unselected package libpixman-1-0:armhf. 313s Preparing to unpack .../17-libpixman-1-0_0.46.4-1_armhf.deb ... 313s Unpacking libpixman-1-0:armhf (0.46.4-1) ... 313s Selecting previously unselected package libxcb-render0:armhf. 313s 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313s Unpacking libgomp1:armhf (15.2.0-12ubuntu1) ... 313s Selecting previously unselected package libjpeg-turbo8:armhf. 313s Preparing to unpack .../24-libjpeg-turbo8_2.1.5-4ubuntu3_armhf.deb ... 313s Unpacking libjpeg-turbo8:armhf (2.1.5-4ubuntu3) ... 313s Selecting previously unselected package libjpeg8:armhf. 313s Preparing to unpack .../25-libjpeg8_8c-2ubuntu11_armhf.deb ... 313s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 313s Selecting previously unselected package fontconfig. 313s Preparing to unpack .../26-fontconfig_2.17.1-3ubuntu1_armhf.deb ... 313s Unpacking fontconfig (2.17.1-3ubuntu1) ... 313s Selecting previously unselected package libgraphite2-3:armhf. 313s Preparing to unpack .../27-libgraphite2-3_1.3.14-11ubuntu1_armhf.deb ... 313s Unpacking libgraphite2-3:armhf (1.3.14-11ubuntu1) ... 313s Selecting previously unselected package libharfbuzz0b:armhf. 313s Preparing to unpack .../28-libharfbuzz0b_12.3.2-1_armhf.deb ... 313s Unpacking libharfbuzz0b:armhf (12.3.2-1) ... 313s Selecting previously unselected package libthai-data. 313s Preparing to unpack .../29-libthai-data_0.1.30-1_all.deb ... 313s Unpacking libthai-data (0.1.30-1) ... 313s Selecting previously unselected package libdatrie1:armhf. 314s Preparing to unpack .../30-libdatrie1_0.2.14-1_armhf.deb ... 314s Unpacking libdatrie1:armhf (0.2.14-1) ... 314s Selecting previously unselected package libthai0:armhf. 314s Preparing to unpack .../31-libthai0_0.1.30-1_armhf.deb ... 314s Unpacking libthai0:armhf (0.1.30-1) ... 314s Selecting previously unselected package libpango-1.0-0:armhf. 314s Preparing to unpack .../32-libpango-1.0-0_1.57.0-1_armhf.deb ... 314s Unpacking libpango-1.0-0:armhf (1.57.0-1) ... 314s Selecting previously unselected package libpangoft2-1.0-0:armhf. 314s Preparing to unpack .../33-libpangoft2-1.0-0_1.57.0-1_armhf.deb ... 314s Unpacking libpangoft2-1.0-0:armhf (1.57.0-1) ... 314s Selecting previously unselected package libpangocairo-1.0-0:armhf. 314s Preparing to unpack .../34-libpangocairo-1.0-0_1.57.0-1_armhf.deb ... 314s Unpacking libpangocairo-1.0-0:armhf (1.57.0-1) ... 314s Selecting previously unselected package libtcl8.6:armhf. 314s Preparing to unpack .../35-libtcl8.6_8.6.17+dfsg-1build1_armhf.deb ... 314s Unpacking libtcl8.6:armhf (8.6.17+dfsg-1build1) ... 314s Selecting previously unselected package libjbig0:armhf. 314s Preparing to unpack .../36-libjbig0_2.1-6.1ubuntu3_armhf.deb ... 314s Unpacking libjbig0:armhf (2.1-6.1ubuntu3) ... 314s Selecting previously unselected package liblerc4:armhf. 314s Preparing to unpack .../37-liblerc4_4.0.0+ds-5ubuntu2_armhf.deb ... 314s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu2) ... 314s Selecting previously unselected package libsharpyuv0:armhf. 314s Preparing to unpack .../38-libsharpyuv0_1.5.0-0.1build1_armhf.deb ... 314s Unpacking libsharpyuv0:armhf (1.5.0-0.1build1) ... 314s Selecting previously unselected package libwebp7:armhf. 314s Preparing to unpack .../39-libwebp7_1.5.0-0.1build1_armhf.deb ... 314s Unpacking libwebp7:armhf (1.5.0-0.1build1) ... 314s Selecting previously unselected package libtiff6:armhf. 314s Preparing to unpack .../40-libtiff6_4.7.0-3ubuntu3_armhf.deb ... 314s Unpacking libtiff6:armhf (4.7.0-3ubuntu3) ... 314s Selecting previously unselected package libxft2:armhf. 314s Preparing to unpack .../41-libxft2_2.3.6-1build2_armhf.deb ... 314s Unpacking libxft2:armhf (2.3.6-1build2) ... 314s Selecting previously unselected package x11-common. 314s Preparing to unpack .../42-x11-common_1%3a7.7+24ubuntu1_all.deb ... 314s Unpacking x11-common (1:7.7+24ubuntu1) ... 314s Selecting previously unselected package libxss1:armhf. 314s Preparing to unpack .../43-libxss1_1%3a1.2.3-1build4_armhf.deb ... 314s Unpacking libxss1:armhf (1:1.2.3-1build4) ... 314s Selecting previously unselected package libtk8.6:armhf. 314s Preparing to unpack .../44-libtk8.6_8.6.17-1_armhf.deb ... 314s Unpacking libtk8.6:armhf (8.6.17-1) ... 314s Selecting previously unselected package libice6:armhf. 314s Preparing to unpack .../45-libice6_2%3a1.1.1-1build1_armhf.deb ... 314s Unpacking libice6:armhf (2:1.1.1-1build1) ... 314s Selecting previously unselected package libsm6:armhf. 314s Preparing to unpack .../46-libsm6_2%3a1.2.6-1build1_armhf.deb ... 314s Unpacking libsm6:armhf (2:1.2.6-1build1) ... 314s Selecting previously unselected package libxt6t64:armhf. 314s Preparing to unpack .../47-libxt6t64_1%3a1.2.1-1.3_armhf.deb ... 314s Unpacking libxt6t64:armhf (1:1.2.1-1.3) ... 314s Selecting previously unselected package r-base-core. 314s Preparing to unpack .../48-r-base-core_4.5.2-1ubuntu2_armhf.deb ... 314s Unpacking r-base-core (4.5.2-1ubuntu2) ... 315s Selecting previously unselected package r-cran-cli. 315s Preparing to unpack .../49-r-cran-cli_3.6.4-1_armhf.deb ... 315s Unpacking r-cran-cli (3.6.4-1) ... 315s Selecting previously unselected package r-cran-glue. 315s Preparing to unpack .../50-r-cran-glue_1.8.0-1_armhf.deb ... 315s Unpacking r-cran-glue (1.8.0-1) 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unselected package r-cran-plyr. 316s Preparing to unpack .../68-r-cran-plyr_1.8.9-1_armhf.deb ... 316s Unpacking r-cran-plyr (1.8.9-1) ... 316s Selecting previously unselected package assemblytics. 316s Preparing to unpack .../69-assemblytics_1.2.1+dfsg-2build1_all.deb ... 316s Unpacking assemblytics (1.2.1+dfsg-2build1) ... 316s Selecting previously unselected package libpython3.14-stdlib:armhf. 316s Preparing to unpack .../70-libpython3.14-stdlib_3.14.2-1_armhf.deb ... 316s Unpacking libpython3.14-stdlib:armhf (3.14.2-1) ... 316s Selecting previously unselected package python-is-python3. 316s Preparing to unpack .../71-python-is-python3_3.13.3-1+build1_all.deb ... 316s Unpacking python-is-python3 (3.13.3-1+build1) ... 316s Selecting previously unselected package python3.14. 316s Preparing to unpack .../72-python3.14_3.14.2-1_armhf.deb ... 316s Unpacking python3.14 (3.14.2-1) ... 316s Selecting previously unselected package python3-all. 316s Preparing to unpack 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/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 316s Setting up libfreetype6:armhf (2.14.1+dfsg-2) ... 316s Setting up fonts-dejavu-mono (2.37-8build1) ... 316s Setting up python3-numpy-dev:armhf (1:2.3.5+ds-3) ... 316s Setting up libtcl8.6:armhf (8.6.17+dfsg-1build1) ... 316s Setting up fonts-dejavu-core (2.37-8build1) ... 316s Setting up libjpeg-turbo8:armhf (2.1.5-4ubuntu3) ... 316s Setting up libgfortran5:armhf (15.2.0-12ubuntu1) ... 316s Setting up libwebp7:armhf (1.5.0-0.1build1) ... 316s Setting up libharfbuzz0b:armhf (12.3.2-1) ... 316s Setting up libthai-data (0.1.30-1) ... 316s Setting up libxss1:armhf (1:1.2.3-1build4) ... 316s Setting up libpaper2:armhf (2.2.5-0.3build1) ... 316s Setting up python-is-python3 (3.13.3-1+build1) ... 316s Setting up xdg-utils (1.2.1-2ubuntu2) ... 316s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 316s Setting up python3.14-minimal (3.14.2-1) ... 318s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 318s Setting up libice6:armhf (2:1.1.1-1build1) ... 318s Setting up liblapack3:armhf (3.12.1-7ubuntu1) ... 318s 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 318s Setting up libpython3.14-stdlib:armhf (3.14.2-1) ... 318s Setting up fontconfig-config (2.17.1-3ubuntu1) ... 318s Setting up libpaper-utils (2.2.5-0.3build1) ... 318s Setting up libthai0:armhf (0.1.30-1) ... 318s Setting up python3-numpy (1:2.3.5+ds-3) ... 322s Setting up libtiff6:armhf (4.7.0-3ubuntu3) ... 322s Setting up libfontconfig1:armhf (2.17.1-3ubuntu1) ... 322s Setting up python3.14 (3.14.2-1) ... 323s Setting up libsm6:armhf (2:1.2.6-1build1) ... 323s Setting up fontconfig (2.17.1-3ubuntu1) ... 325s Regenerating fonts cache... done. 325s Setting up libxft2:armhf (2.3.6-1build2) ... 325s Setting up libtk8.6:armhf (8.6.17-1) ... 325s Setting up libpango-1.0-0:armhf (1.57.0-1) ... 325s Setting up python3-all (3.13.9-3) ... 325s Setting up libcairo2:armhf (1.18.4-3) ... 325s Setting up libxt6t64:armhf (1:1.2.1-1.3) ... 325s Setting up libpangoft2-1.0-0:armhf (1.57.0-1) ... 325s Setting up libpangocairo-1.0-0:armhf (1.57.0-1) ... 325s Setting up r-base-core (4.5.2-1ubuntu2) ... 325s Creating config file /etc/R/Renviron with new version 325s Setting up r-cran-labeling (0.4.3-1) ... 325s Setting up r-cran-farver (2.1.2-1) ... 325s Setting up r-cran-viridislite (0.4.3-1) ... 325s Setting up r-cran-r6 (2.6.1-1) ... 325s Setting up r-cran-pkgkitten (0.2.4-1) ... 325s Setting up r-cran-littler (0.3.22-1) ... 325s Setting up r-cran-rcpp (1.1.0-1) ... 325s Setting up r-cran-rlang (1.1.5-3) ... 325s Setting up r-cran-withr (3.0.2+dfsg-1) ... 325s Setting up r-cran-glue (1.8.0-1) ... 325s Setting up r-cran-cli (3.6.4-1) ... 325s Setting up r-cran-lifecycle (1.0.5+dfsg-1) ... 325s Setting up r-cran-s7 (0.2.0-1) ... 325s Setting up r-cran-plyr (1.8.9-1) ... 325s Setting up r-cran-rcolorbrewer (1.1-3-1build2) ... 325s Setting up r-cran-isoband (0.2.7-1) ... 325s Setting up r-cran-scales (1.4.0-1) ... 325s Setting up r-cran-gtable (0.3.6+dfsg-1) ... 325s Setting up r-cran-vctrs (0.6.5-1) ... 325s Setting up r-cran-ggplot2 (4.0.2+dfsg-1) ... 325s Setting up assemblytics (1.2.1+dfsg-2build1) ... 325s Processing triggers for systemd (259-1ubuntu3) ... 325s Processing triggers for man-db (2.13.1-1build1) ... 326s Processing triggers for install-info (7.2-5) ... 326s Processing triggers for libc-bin (2.42-2ubuntu4) ... 334s autopkgtest [23:11:48]: test run-unit-test: [----------------------- 336s Input delta file: sample.delta 336s Output prefix: myfirstorganism 336s Unique anchor length: 10000 336s Minimum variant size to call: 10000 336s Maximum variant size to call: 50 336s Logging progress updates in myfirstorganism/progress.log 336s script path: /usr/share/assemblytics/bin 336s 1. Filter delta file 336s Keeping fully unique alignments even if they are below the unique anchor length of 10000 bp 336s Use --unique-length X to set the unique anchor length requirement. Default is 10000, such that each alignment must have at least 10000 bp from the query that are not included in any other alignments. 336s Detected uncompressed delta file. Reading... 336s 336s 336s Header (2 lines): 336s /seq/schatz/mnattest/Assemblytics/Ecoli/GCF_000005845.2_ASM584v2_genomic.fna /seq/schatz/mnattest/Assemblytics/Ecoli/GCF_000801205.1_ASM80120v1_genomic.fna 336s NUCMER 336s 336s 336s First read through the file: 0 seconds for 0 query-reference combinations 336s Filtering alignments of 1 queries 336s Progress: 100% 336s Progress: 100% 336s Deciding which alignments to keep: 0 seconds for 1 queries 336s Detected uncompressed delta file. Reading... 336s Reading file and recording all the entries we decided to keep: 0 seconds for 54 total lines in file 336s 2. Finding variants between alignments 336s Loaded 6 alignments 336s 3. Finding variants within alignments 336s Detected gzipped delta file. Reading... 336s 336s 336s Header (2 lines): 336s /seq/schatz/mnattest/Assemblytics/Ecoli/GCF_000005845.2_ASM584v2_genomic.fna /seq/schatz/mnattest/Assemblytics/Ecoli/GCF_000801205.1_ASM80120v1_genomic.fna 336s NUCMER 336s 336s 336s 4. Combine variants between and within alignments 337s Error in revalue(bed$type, c(Repeat_expansion = "Repeat expansion", Repeat_contraction = "Repeat contraction", : 337s x is not a factor or a character vector. 337s Execution halted 339s Warning messages: 339s 1: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. 339s ℹ Please use `linewidth` instead. 339s 2: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0. 339s ℹ Please use the `linewidth` argument instead. 339s null device 339s 1 341s Warning message: 341s Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. 341s ℹ Please use `linewidth` instead. 341s adding: myfirstorganism.Assemblytics.Dotplot_filtered.png (deflated 11%) 341s adding: myfirstorganism.Assemblytics.Nchart.pdf (deflated 11%) 341s adding: myfirstorganism.Assemblytics.Nchart.png (deflated 6%) 341s adding: myfirstorganism.Assemblytics.unique_length_filtered_l10000.delta.gz (stored 0%) 341s adding: myfirstorganism.Assemblytics_assembly_stats.txt (deflated 58%) 341s adding: myfirstorganism.Assemblytics_structural_variants.bed (deflated 26%) 342s adding: myfirstorganism.Assemblytics_structural_variants.summary (deflated 49%) 342s adding: myfirstorganism.Assemblytics_structural_variants.summary.csv (deflated 35%) 342s PASS 342s autopkgtest [23:11:56]: test run-unit-test: -----------------------] 346s run-unit-test PASS 346s autopkgtest [23:12:00]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 349s autopkgtest [23:12:03]: @@@@@@@@@@@@@@@@@@@@ summary 349s run-unit-test PASS