0s autopkgtest [23:12:02]: starting date and time: 2026-02-09 23:12:02+0000 0s autopkgtest [23:12:02]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [23:12:02]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.6dhu1h6z/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 assemblytics --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-arm64-10.secgroup --name adt-resolute-arm64-assemblytics-20260209-231202-juju-7f2275-prod-proposed-migration-environment-2-50941c01-8354-48f4-8bf1-9b88c939ff52 --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-assemblytics-20260209-231202-juju-7f2275-prod-proposed-migration-environment-2-50941c01-8354-48f4-8bf1-9b88c939ff52 from image adt/ubuntu-resolute-arm64-server-20260209.img (UUID 793037ca-75af-461b-82de-f8081300b2e3)... 85s autopkgtest [23:13:27]: testbed dpkg architecture: arm64 86s autopkgtest [23:13:28]: testbed apt version: 3.1.15 86s autopkgtest [23:13:28]: @@@@@@@@@@@@@@@@@@@@ test bed setup 86s autopkgtest [23:13:28]: testbed release detected to be: None 87s autopkgtest [23:13:29]: updating testbed package index (apt update) 87s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 87s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 87s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 87s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 87s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB] 87s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1645 kB] 90s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [176 kB] 90s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [246 kB] 90s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [6216 B] 90s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [304 B] 90s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [1580 kB] 92s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [32.0 kB] 92s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [21.7 kB] 92s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [688 B] 94s Fetched 3862 kB in 5s (759 kB/s) 94s Reading package lists... 95s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 95s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 95s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 95s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 96s Reading package lists... 96s Reading package lists... 96s Building dependency tree... 96s Reading state information... 97s Calculating upgrade... 97s The following packages will be upgraded: 97s cryptsetup-bin dracut-install iproute2 iptables libcryptsetup12 libip4tc2 97s libip6tc2 libxtables12 wget 97s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 97s Need to get 2534 kB of archives. 97s After this operation, 18.4 kB of additional disk space will be used. 97s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 iptables arm64 1.8.11-2ubuntu3 [386 kB] 97s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libip4tc2 arm64 1.8.11-2ubuntu3 [24.3 kB] 97s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libip6tc2 arm64 1.8.11-2ubuntu3 [24.7 kB] 97s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libxtables12 arm64 1.8.11-2ubuntu3 [36.7 kB] 97s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 iproute2 arm64 6.18.0-1ubuntu1 [1171 kB] 99s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libcryptsetup12 arm64 2:2.8.0-1ubuntu3 [274 kB] 99s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 wget arm64 1.25.0-2ubuntu4 [344 kB] 99s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 cryptsetup-bin arm64 2:2.8.0-1ubuntu3 [227 kB] 99s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 dracut-install arm64 109-11ubuntu1 [45.3 kB] 99s dpkg-preconfigure: unable to re-open stdin: No such file or directory 100s Fetched 2534 kB in 2s (1235 kB/s) 100s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 136597 files and directories currently installed.) 100s Preparing to unpack .../0-iptables_1.8.11-2ubuntu3_arm64.deb ... 100s Unpacking iptables (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 100s Preparing to unpack .../1-libip4tc2_1.8.11-2ubuntu3_arm64.deb ... 100s Unpacking libip4tc2:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 100s Preparing to unpack .../2-libip6tc2_1.8.11-2ubuntu3_arm64.deb ... 100s Unpacking libip6tc2:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 100s Preparing to unpack .../3-libxtables12_1.8.11-2ubuntu3_arm64.deb ... 100s Unpacking libxtables12:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 100s Preparing to unpack .../4-iproute2_6.18.0-1ubuntu1_arm64.deb ... 100s Unpacking iproute2 (6.18.0-1ubuntu1) over (6.16.0-1ubuntu3) ... 100s Preparing to unpack .../5-libcryptsetup12_2%3a2.8.0-1ubuntu3_arm64.deb ... 100s Unpacking libcryptsetup12:arm64 (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 101s Preparing to unpack .../6-wget_1.25.0-2ubuntu4_arm64.deb ... 101s Unpacking wget (1.25.0-2ubuntu4) over (1.25.0-2ubuntu3) ... 101s Preparing to unpack .../7-cryptsetup-bin_2%3a2.8.0-1ubuntu3_arm64.deb ... 101s Unpacking cryptsetup-bin (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 101s Preparing to unpack .../8-dracut-install_109-11ubuntu1_arm64.deb ... 101s Unpacking dracut-install (109-11ubuntu1) over (109-9ubuntu1) ... 101s Setting up libip4tc2:arm64 (1.8.11-2ubuntu3) ... 101s Setting up wget (1.25.0-2ubuntu4) ... 101s Setting up libip6tc2:arm64 (1.8.11-2ubuntu3) ... 101s Setting up libxtables12:arm64 (1.8.11-2ubuntu3) ... 101s Setting up dracut-install (109-11ubuntu1) ... 101s Setting up libcryptsetup12:arm64 (2:2.8.0-1ubuntu3) ... 101s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 101s Setting up iptables (1.8.11-2ubuntu3) ... 101s Setting up iproute2 (6.18.0-1ubuntu1) ... 101s Processing triggers for man-db (2.13.1-1build1) ... 102s Processing triggers for install-info (7.2-5) ... 102s Processing triggers for libc-bin (2.42-2ubuntu4) ... 102s autopkgtest [23:13:44]: upgrading testbed (apt dist-upgrade and autopurge) 103s Reading package lists... 103s Building dependency tree... 103s Reading state information... 103s Calculating upgrade... 103s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 104s Reading package lists... 104s Building dependency tree... 104s Reading state information... 104s Solving dependencies... 104s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s autopkgtest [23:13:49]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 19:46:27 UTC 2026 107s autopkgtest [23:13:49]: @@@@@@@@@@@@@@@@@@@@ apt-source assemblytics 108s Get:1 http://ftpmaster.internal/ubuntu resolute/universe assemblytics 1.2.1+dfsg-2build1 (dsc) [2075 B] 108s Get:2 http://ftpmaster.internal/ubuntu resolute/universe assemblytics 1.2.1+dfsg-2build1 (tar) [15.5 kB] 108s Get:3 http://ftpmaster.internal/ubuntu resolute/universe assemblytics 1.2.1+dfsg-2build1 (diff) [4728 B] 108s gpgv: Signature made Tue Dec 9 22:06:16 2025 UTC 108s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 108s gpgv: Can't check signature: No public key 108s dpkg-source: warning: cannot verify inline signature for ./assemblytics_1.2.1+dfsg-2build1.dsc: no acceptable signature found 108s autopkgtest [23:13:50]: testing package assemblytics version 1.2.1+dfsg-2build1 108s autopkgtest [23:13:50]: build not needed 109s autopkgtest [23:13:51]: test run-unit-test: preparing testbed 109s Reading package lists... 109s Building dependency tree... 109s Reading state information... 109s Solving dependencies... 110s The following NEW packages will be installed: 110s assemblytics fontconfig fontconfig-config fonts-dejavu-core 110s fonts-dejavu-mono libblas3 libcairo2 libdatrie1 libdeflate0 libfontconfig1 110s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 110s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 110s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 110s libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 110s libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 110s python-is-python3 python3-all python3-numpy python3-numpy-dev python3.14 110s python3.14-minimal r-base-core r-cran-cli r-cran-farver r-cran-ggplot2 110s r-cran-glue r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lifecycle 110s r-cran-littler r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer 110s r-cran-rcpp r-cran-rlang r-cran-s7 r-cran-scales r-cran-vctrs 110s r-cran-viridislite r-cran-withr unzip x11-common xdg-utils zip 111s 0 upgraded, 71 newly installed, 0 to remove and 0 not upgraded. 111s Need to get 65.2 MB of archives. 111s After this operation, 152 MB of additional disk space will be used. 111s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.3.5+ds-3 [366 kB] 111s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7ubuntu1 [181 kB] 111s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-12ubuntu1 [451 kB] 111s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7ubuntu1 [2299 kB] 114s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.3.5+ds-3 [4569 kB] 119s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14-minimal arm64 3.14.2-1 [2548 kB] 123s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 zip arm64 3.0-15ubuntu3 [170 kB] 123s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 unzip arm64 6.0-29ubuntu1 [176 kB] 123s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper2 arm64 2.2.5-0.3build1 [17.3 kB] 123s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper-utils arm64 2.2.5-0.3build1 [15.4 kB] 123s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 123s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 123s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-core all 2.37-8build1 [834 kB] 124s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.17.1-3ubuntu1 [38.5 kB] 124s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.17.1-3ubuntu1 [144 kB] 124s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 libpixman-1-0 arm64 0.46.4-1 [204 kB] 124s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-render0 arm64 1.17.0-2ubuntu1 [16.4 kB] 124s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-shm0 arm64 1.17.0-2ubuntu1 [5938 B] 124s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 124s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo2 arm64 1.18.4-3 [556 kB] 125s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2build1 [46.8 kB] 125s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-12ubuntu1 [147 kB] 125s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu3 [161 kB] 125s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 125s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig arm64 2.17.1-3ubuntu1 [181 kB] 125s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-11ubuntu1 [72.1 kB] 125s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.3.2-1 [510 kB] 125s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai-data all 0.1.30-1 [155 kB] 125s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 libdatrie1 arm64 0.2.14-1 [19.6 kB] 125s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai0 arm64 0.1.30-1 [18.3 kB] 125s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 libpango-1.0-0 arm64 1.57.0-1 [238 kB] 125s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangoft2-1.0-0 arm64 1.57.0-1 [51.5 kB] 125s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangocairo-1.0-0 arm64 1.57.0-1 [27.9 kB] 125s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 libtcl8.6 arm64 8.6.17+dfsg-1build1 [983 kB] 126s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu3 [29.2 kB] 126s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu2 [174 kB] 126s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1build1 [16.7 kB] 126s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1build1 [205 kB] 126s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB] 126s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 libxft2 arm64 2.3.6-1build2 [43.2 kB] 126s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 126s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 libxss1 arm64 1:1.2.3-1build4 [7102 B] 126s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 libtk8.6 arm64 8.6.17-1 [811 kB] 127s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 libice6 arm64 2:1.1.1-1build1 [43.0 kB] 127s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 libsm6 arm64 2:1.2.6-1build1 [16.8 kB] 127s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 libxt6t64 arm64 1:1.2.1-1.3 [168 kB] 127s Get:47 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-base-core arm64 4.5.2-1ubuntu2 [28.6 MB] 162s Get:48 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cli arm64 3.6.4-1 [1374 kB] 163s Get:49 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-glue arm64 1.8.0-1 [163 kB] 163s Get:50 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rlang arm64 1.1.5-3 [1706 kB] 165s Get:51 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 165s Get:52 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 165s Get:53 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-isoband arm64 0.2.7-1 [1481 kB] 167s Get:54 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-s7 arm64 0.2.0-1 [329 kB] 167s Get:55 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-farver arm64 2.1.2-1 [1344 kB] 169s Get:56 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-labeling all 0.4.3-1 [62.1 kB] 169s Get:57 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-r6 all 2.6.1-1 [101 kB] 169s Get:58 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB] 169s Get:59 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-viridislite all 0.4.3-1 [1088 kB] 171s Get:60 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-scales all 1.4.0-1 [725 kB] 172s Get:61 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB] 174s Get:62 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 174s Get:63 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 r-cran-ggplot2 all 4.0.2+dfsg-1 [4941 kB] 179s Get:64 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-littler arm64 0.3.22-1 [85.1 kB] 179s Get:65 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 179s Get:66 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcpp arm64 1.1.0-1 [2011 kB] 182s Get:67 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-plyr arm64 1.8.9-1 [831 kB] 183s Get:68 http://ftpmaster.internal/ubuntu resolute/universe arm64 assemblytics all 1.2.1+dfsg-2build1 [19.2 kB] 183s Get:69 http://ftpmaster.internal/ubuntu resolute/main arm64 python-is-python3 all 3.13.3-1+build1 [2832 B] 183s Get:70 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14 arm64 3.14.2-1 [816 kB] 184s Get:71 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-all arm64 3.13.9-3 [890 B] 184s Preconfiguring packages ... 184s Fetched 65.2 MB in 1min 14s (880 kB/s) 184s Selecting previously unselected package python3-numpy-dev:arm64. 184s (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.) 184s Preparing to unpack .../00-python3-numpy-dev_1%3a2.3.5+ds-3_arm64.deb ... 184s Unpacking python3-numpy-dev:arm64 (1:2.3.5+ds-3) ... 184s Selecting previously unselected package libblas3:arm64. 184s Preparing to unpack .../01-libblas3_3.12.1-7ubuntu1_arm64.deb ... 184s Unpacking libblas3:arm64 (3.12.1-7ubuntu1) ... 184s Selecting previously unselected package libgfortran5:arm64. 184s Preparing to unpack .../02-libgfortran5_15.2.0-12ubuntu1_arm64.deb ... 184s Unpacking libgfortran5:arm64 (15.2.0-12ubuntu1) ... 184s Selecting previously unselected package liblapack3:arm64. 184s Preparing to unpack .../03-liblapack3_3.12.1-7ubuntu1_arm64.deb ... 184s Unpacking liblapack3:arm64 (3.12.1-7ubuntu1) ... 184s Selecting previously unselected package python3-numpy. 184s Preparing to unpack .../04-python3-numpy_1%3a2.3.5+ds-3_arm64.deb ... 184s Unpacking python3-numpy (1:2.3.5+ds-3) ... 185s Selecting previously unselected package python3.14-minimal. 185s Preparing to unpack .../05-python3.14-minimal_3.14.2-1_arm64.deb ... 185s Unpacking python3.14-minimal (3.14.2-1) ... 185s Selecting previously unselected package zip. 185s Preparing to unpack .../06-zip_3.0-15ubuntu3_arm64.deb ... 185s Unpacking zip (3.0-15ubuntu3) ... 185s Selecting previously unselected package unzip. 185s Preparing to unpack .../07-unzip_6.0-29ubuntu1_arm64.deb ... 185s Unpacking unzip (6.0-29ubuntu1) ... 185s Selecting previously unselected package libpaper2:arm64. 185s Preparing to unpack .../08-libpaper2_2.2.5-0.3build1_arm64.deb ... 185s Unpacking libpaper2:arm64 (2.2.5-0.3build1) ... 185s Selecting previously unselected package libpaper-utils. 185s Preparing to unpack .../09-libpaper-utils_2.2.5-0.3build1_arm64.deb ... 185s Unpacking libpaper-utils (2.2.5-0.3build1) ... 185s Selecting previously unselected package xdg-utils. 185s Preparing to unpack .../10-xdg-utils_1.2.1-2ubuntu2_all.deb ... 185s Unpacking xdg-utils (1.2.1-2ubuntu2) ... 185s Selecting previously unselected package fonts-dejavu-mono. 185s Preparing to unpack .../11-fonts-dejavu-mono_2.37-8build1_all.deb ... 185s Unpacking fonts-dejavu-mono (2.37-8build1) ... 185s Selecting previously unselected package fonts-dejavu-core. 185s Preparing to unpack .../12-fonts-dejavu-core_2.37-8build1_all.deb ... 185s Unpacking fonts-dejavu-core (2.37-8build1) ... 185s Selecting previously unselected package fontconfig-config. 185s Preparing to unpack .../13-fontconfig-config_2.17.1-3ubuntu1_arm64.deb ... 185s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 185s Selecting previously unselected package libfontconfig1:arm64. 185s Preparing to unpack .../14-libfontconfig1_2.17.1-3ubuntu1_arm64.deb ... 185s Unpacking libfontconfig1:arm64 (2.17.1-3ubuntu1) ... 185s Selecting previously unselected package libpixman-1-0:arm64. 185s Preparing to unpack .../15-libpixman-1-0_0.46.4-1_arm64.deb ... 185s Unpacking libpixman-1-0:arm64 (0.46.4-1) ... 185s Selecting previously unselected package libxcb-render0:arm64. 185s Preparing to unpack .../16-libxcb-render0_1.17.0-2ubuntu1_arm64.deb ... 185s Unpacking libxcb-render0:arm64 (1.17.0-2ubuntu1) ... 185s Selecting previously unselected package libxcb-shm0:arm64. 185s Preparing to unpack .../17-libxcb-shm0_1.17.0-2ubuntu1_arm64.deb ... 185s Unpacking libxcb-shm0:arm64 (1.17.0-2ubuntu1) ... 185s Selecting previously unselected package libxrender1:arm64. 185s Preparing to unpack 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libdeflate0:arm64 (1.23-2build1) ... 188s Setting up libxcb-shm0:arm64 (1.17.0-2ubuntu1) ... 188s Setting up libgomp1:arm64 (15.2.0-12ubuntu1) ... 188s Setting up libjbig0:arm64 (2.1-6.1ubuntu3) ... 188s Setting up zip (3.0-15ubuntu3) ... 188s Setting up libblas3:arm64 (3.12.1-7ubuntu1) ... 188s 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 188s Setting up fonts-dejavu-mono (2.37-8build1) ... 188s Setting up python3-numpy-dev:arm64 (1:2.3.5+ds-3) ... 188s Setting up libtcl8.6:arm64 (8.6.17+dfsg-1build1) ... 188s Setting up fonts-dejavu-core (2.37-8build1) ... 188s Setting up libjpeg-turbo8:arm64 (2.1.5-4ubuntu3) ... 188s Setting up libgfortran5:arm64 (15.2.0-12ubuntu1) ... 188s Setting up libwebp7:arm64 (1.5.0-0.1build1) ... 188s Setting up libharfbuzz0b:arm64 (12.3.2-1) ... 188s Setting up libthai-data (0.1.30-1) ... 188s Setting up libxss1:arm64 (1:1.2.3-1build4) 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... 194s Setting up libsm6:arm64 (2:1.2.6-1build1) ... 194s Setting up fontconfig (2.17.1-3ubuntu1) ... 196s Regenerating fonts cache... done. 196s Setting up libxft2:arm64 (2.3.6-1build2) ... 196s Setting up libtk8.6:arm64 (8.6.17-1) ... 196s Setting up libpango-1.0-0:arm64 (1.57.0-1) ... 196s Setting up python3-all (3.13.9-3) ... 196s Setting up libcairo2:arm64 (1.18.4-3) ... 196s Setting up libxt6t64:arm64 (1:1.2.1-1.3) ... 196s Setting up libpangoft2-1.0-0:arm64 (1.57.0-1) ... 196s Setting up libpangocairo-1.0-0:arm64 (1.57.0-1) ... 196s Setting up r-base-core (4.5.2-1ubuntu2) ... 197s Creating config file /etc/R/Renviron with new version 197s Setting up r-cran-labeling (0.4.3-1) ... 197s Setting up r-cran-farver (2.1.2-1) ... 197s Setting up r-cran-viridislite (0.4.3-1) ... 197s Setting up r-cran-r6 (2.6.1-1) ... 197s Setting up r-cran-pkgkitten (0.2.4-1) ... 197s Setting up r-cran-littler (0.3.22-1) ... 197s Setting up r-cran-rcpp (1.1.0-1) ... 197s Setting up r-cran-rlang (1.1.5-3) ... 197s Setting up r-cran-withr (3.0.2+dfsg-1) ... 197s Setting up r-cran-glue (1.8.0-1) ... 197s Setting up r-cran-cli (3.6.4-1) ... 197s Setting up r-cran-lifecycle (1.0.5+dfsg-1) ... 197s Setting up r-cran-s7 (0.2.0-1) ... 197s Setting up r-cran-plyr (1.8.9-1) ... 197s Setting up r-cran-rcolorbrewer (1.1-3-1build2) ... 197s Setting up r-cran-isoband (0.2.7-1) ... 197s Setting up r-cran-scales (1.4.0-1) ... 197s Setting up r-cran-gtable (0.3.6+dfsg-1) ... 197s Setting up r-cran-vctrs (0.6.5-1) ... 197s Setting up r-cran-ggplot2 (4.0.2+dfsg-1) ... 197s Setting up assemblytics (1.2.1+dfsg-2build1) ... 197s Processing triggers for systemd (259-1ubuntu3) ... 197s Processing triggers for man-db (2.13.1-1build1) ... 197s Processing triggers for install-info (7.2-5) ... 197s Processing triggers for libc-bin (2.42-2ubuntu4) ... 198s autopkgtest [23:15:20]: test run-unit-test: [----------------------- 199s Input delta file: sample.delta 199s Output prefix: myfirstorganism 199s Unique anchor length: 10000 199s Minimum variant size to call: 10000 199s Maximum variant size to call: 50 199s Logging progress updates in myfirstorganism/progress.log 199s script path: /usr/share/assemblytics/bin 199s 1. Filter delta file 199s Keeping fully unique alignments even if they are below the unique anchor length of 10000 bp 199s 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. 199s Detected uncompressed delta file. Reading... 199s 199s 199s Header (2 lines): 199s /seq/schatz/mnattest/Assemblytics/Ecoli/GCF_000005845.2_ASM584v2_genomic.fna /seq/schatz/mnattest/Assemblytics/Ecoli/GCF_000801205.1_ASM80120v1_genomic.fna 199s NUCMER 199s 199s 199s First read through the file: 0 seconds for 0 query-reference combinations 199s Filtering alignments of 1 queries 199s Progress: 100% 199s Progress: 100% 199s Deciding which alignments to keep: 0 seconds for 1 queries 199s Detected uncompressed delta file. Reading... 199s Reading file and recording all the entries we decided to keep: 0 seconds for 54 total lines in file 199s 2. Finding variants between alignments 199s Loaded 6 alignments 199s 3. Finding variants within alignments 199s 4. Combine variants between and within alignments 199s Detected gzipped delta file. Reading... 199s 199s 199s Header (2 lines): 199s /seq/schatz/mnattest/Assemblytics/Ecoli/GCF_000005845.2_ASM584v2_genomic.fna /seq/schatz/mnattest/Assemblytics/Ecoli/GCF_000801205.1_ASM80120v1_genomic.fna 199s NUCMER 199s 199s 200s Error in revalue(bed$type, c(Repeat_expansion = "Repeat expansion", Repeat_contraction = "Repeat contraction", : 200s x is not a factor or a character vector. 200s Execution halted 201s Warning messages: 201s 1: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. 201s ℹ Please use `linewidth` instead. 201s 2: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0. 201s ℹ Please use the `linewidth` argument instead. 201s null device 201s 1 203s Warning message: 203s Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. 203s ℹ Please use `linewidth` instead. 203s adding: myfirstorganism.Assemblytics.Dotplot_filtered.png (deflated 11%) 203s adding: myfirstorganism.Assemblytics.Nchart.pdf (deflated 11%) 203s adding: myfirstorganism.Assemblytics.Nchart.png (deflated 6%) 203s adding: myfirstorganism.Assemblytics.unique_length_filtered_l10000.delta.gz (stored 0%) 203s adding: myfirstorganism.Assemblytics_assembly_stats.txt (deflated 58%) 203s adding: myfirstorganism.Assemblytics_structural_variants.bed (deflated 26%) 203s adding: myfirstorganism.Assemblytics_structural_variants.summary (deflated 49%) 203s adding: myfirstorganism.Assemblytics_structural_variants.summary.csv (deflated 35%) 203s PASS 203s autopkgtest [23:15:25]: test run-unit-test: -----------------------] 204s autopkgtest [23:15:26]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 204s run-unit-test PASS 204s autopkgtest [23:15:26]: @@@@@@@@@@@@@@@@@@@@ summary 204s run-unit-test PASS