0s autopkgtest [01:55:13]: starting date and time: 2025-12-06 01:55:13+0000 0s autopkgtest [01:55:13]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [01:55:13]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ftw_zg68/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade assemblytics --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.13.9-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-ppc64el-1.secgroup --name adt-resolute-ppc64el-assemblytics-20251206-015513-juju-7f2275-prod-proposed-migration-environment-2-f837fbde-7baa-476d-a1ea-54e027ae5f3a --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-ppc64el-assemblytics-20251206-015513-juju-7f2275-prod-proposed-migration-environment-2-f837fbde-7baa-476d-a1ea-54e027ae5f3a from image adt/ubuntu-resolute-ppc64el-server-20251205.img (UUID ec8e7418-51bb-4f88-80fc-4d434bdc97c2)... 53s autopkgtest [01:56:06]: testbed dpkg architecture: ppc64el 53s autopkgtest [01:56:06]: testbed apt version: 3.1.12 54s autopkgtest [01:56:07]: @@@@@@@@@@@@@@@@@@@@ test bed setup 54s autopkgtest [01:56:07]: testbed release detected to be: None 55s autopkgtest [01:56:08]: updating testbed package index (apt update) 55s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 55s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 55s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 55s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 55s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [842 kB] 55s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [140 kB] 55s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [23.4 kB] 55s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [226 kB] 55s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [689 kB] 56s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [6928 B] 56s Fetched 2052 kB in 1s (2180 kB/s) 56s Reading package lists... 57s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 57s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 57s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 57s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 58s Reading package lists... 58s Reading package lists... 58s Building dependency tree... 58s Reading state information... 58s Calculating upgrade... 59s The following packages will be upgraded: 59s libnftnl11 libpython3-stdlib lxd-installer python3 python3-attr python3-gdbm 59s python3-minimal 59s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 59s Need to get 212 kB of archives. 59s After this operation, 16.4 kB of additional disk space will be used. 59s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3-minimal ppc64el 3.13.9-2 [28.1 kB] 59s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3 ppc64el 3.13.9-2 [23.0 kB] 59s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libpython3-stdlib ppc64el 3.13.9-2 [10.8 kB] 59s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libnftnl11 ppc64el 1.3.1-1 [80.0 kB] 59s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3-gdbm ppc64el 3.13.9-2 [11.0 kB] 59s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el lxd-installer all 14ubuntu0 [5428 B] 59s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-attr all 25.4.0-1 [53.6 kB] 66s dpkg-preconfigure: unable to re-open stdin: No such file or directory 66s Fetched 212 kB in 0s (15.6 MB/s) 66s autopkgtest [01:56:19]: upgrading testbed (apt dist-upgrade and autopurge) 66s (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 ... 81185 files and directories currently installed.) 66s Preparing to unpack .../python3-minimal_3.13.9-2_ppc64el.deb ... 66s Unpacking python3-minimal (3.13.9-2) over (3.13.7-1) ... 66s Setting up python3-minimal (3.13.9-2) ... 66s (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 ... 81185 files and directories currently installed.) 66s Preparing to unpack .../0-python3_3.13.9-2_ppc64el.deb ... 66s running python pre-rtupdate hooks for python3.13... 66s Unpacking python3 (3.13.9-2) over (3.13.7-1) ... 66s Preparing to unpack .../1-libpython3-stdlib_3.13.9-2_ppc64el.deb ... 66s Unpacking libpython3-stdlib:ppc64el (3.13.9-2) over (3.13.7-1) ... 66s Preparing to unpack .../2-libnftnl11_1.3.1-1_ppc64el.deb ... 66s Unpacking libnftnl11:ppc64el (1.3.1-1) over (1.3.0-1) ... 66s Preparing to unpack .../3-python3-gdbm_3.13.9-2_ppc64el.deb ... 66s Unpacking python3-gdbm (3.13.9-2) over (3.13.9-1) ... 66s Preparing to unpack .../4-lxd-installer_14ubuntu0_all.deb ... 66s Unpacking lxd-installer (14ubuntu0) over (13ubuntu0) ... 66s Preparing to unpack .../5-python3-attr_25.4.0-1_all.deb ... 66s Unpacking python3-attr (25.4.0-1) over (25.3.0-1) ... 66s Setting up python3-gdbm (3.13.9-2) ... 66s Setting up libnftnl11:ppc64el (1.3.1-1) ... 66s Setting up lxd-installer (14ubuntu0) ... 66s Setting up libpython3-stdlib:ppc64el (3.13.9-2) ... 66s Setting up python3 (3.13.9-2) ... 66s running python rtupdate hooks for python3.13... 66s running python post-rtupdate hooks for python3.13... 66s Setting up python3-attr (25.4.0-1) ... 66s Processing triggers for man-db (2.13.1-1) ... 66s Processing triggers for libc-bin (2.42-2ubuntu2) ... 67s Reading package lists... 67s Building dependency tree... 67s Reading state information... 67s Calculating upgrade... 67s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 67s Reading package lists... 67s Building dependency tree... 67s Reading state information... 67s Solving dependencies... 67s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 68s autopkgtest [01:56:21]: rebooting testbed after setup commands that affected boot 106s autopkgtest [01:56:59]: testbed running kernel: Linux 6.17.0-6-generic #6-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 7 13:47:32 UTC 2025 108s autopkgtest [01:57:01]: @@@@@@@@@@@@@@@@@@@@ apt-source assemblytics 110s Get:1 http://ftpmaster.internal/ubuntu resolute/universe assemblytics 1.2.1+dfsg-2 (dsc) [2072 B] 110s Get:2 http://ftpmaster.internal/ubuntu resolute/universe assemblytics 1.2.1+dfsg-2 (tar) [15.5 kB] 110s Get:3 http://ftpmaster.internal/ubuntu resolute/universe assemblytics 1.2.1+dfsg-2 (diff) [4640 B] 111s gpgv: Signature made Wed Dec 6 13:41:32 2023 UTC 111s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 111s gpgv: issuer "tillea@rki.de" 111s gpgv: Can't check signature: No public key 111s dpkg-source: warning: cannot verify inline signature for ./assemblytics_1.2.1+dfsg-2.dsc: no acceptable signature found 111s autopkgtest [01:57:04]: testing package assemblytics version 1.2.1+dfsg-2 111s autopkgtest [01:57:04]: build not needed 112s autopkgtest [01:57:05]: test run-unit-test: preparing testbed 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s Solving dependencies... 112s The following NEW packages will be installed: 112s assemblytics fontconfig fontconfig-config fonts-dejavu-core 112s fonts-dejavu-mono libblas3 libcairo2 libdatrie1 libdeflate0 libfontconfig1 112s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 112s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 112s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 112s libpython3.14-minimal libpython3.14-stdlib libsharpyuv0 libsm6 libtcl8.6 112s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 112s libxft2 libxrender1 libxss1 libxt6t64 python-is-python3 python3-all 112s python3-numpy python3-numpy-dev python3.14 python3.14-minimal r-base-core 112s r-cran-cli r-cran-colorspace r-cran-fansi r-cran-farver r-cran-ggplot2 112s r-cran-glue r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lattice 112s r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix 112s r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig 112s r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp 112s r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8 r-cran-vctrs 112s r-cran-viridislite r-cran-withr unzip x11-common xdg-utils zip 112s 0 upgraded, 85 newly installed, 0 to remove and 0 not upgraded. 112s Need to get 87.2 MB of archives. 112s After this operation, 202 MB of additional disk space will be used. 112s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-numpy-dev ppc64el 1:2.2.4+ds-1ubuntu1 [153 kB] 112s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas3 ppc64el 3.12.1-7 [291 kB] 112s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran5 ppc64el 15.2.0-9ubuntu1 [620 kB] 113s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblapack3 ppc64el 3.12.1-7 [2960 kB] 113s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-numpy ppc64el 1:2.2.4+ds-1ubuntu1 [4887 kB] 113s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpython3.14-minimal ppc64el 3.14.0-4 [908 kB] 113s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3.14-minimal ppc64el 3.14.0-4 [2705 kB] 113s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el zip ppc64el 3.0-15ubuntu2 [198 kB] 113s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el unzip ppc64el 6.0-28ubuntu7 [201 kB] 113s Get:10 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpaper2 ppc64el 2.2.5-0.3 [18.0 kB] 113s Get:11 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpaper-utils ppc64el 2.2.5-0.3 [15.6 kB] 113s Get:12 http://ftpmaster.internal/ubuntu resolute/main ppc64el xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 113s Get:13 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 113s Get:14 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 113s Get:15 http://ftpmaster.internal/ubuntu resolute/main ppc64el fontconfig-config ppc64el 2.15.0-2.3ubuntu1 [38.1 kB] 113s Get:16 http://ftpmaster.internal/ubuntu resolute/main ppc64el libfontconfig1 ppc64el 2.15.0-2.3ubuntu1 [188 kB] 113s Get:17 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpixman-1-0 ppc64el 0.46.4-1 [347 kB] 113s Get:18 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxcb-render0 ppc64el 1.17.0-2build1 [17.2 kB] 113s Get:19 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxcb-shm0 ppc64el 1.17.0-2build1 [6078 B] 113s Get:20 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxrender1 ppc64el 1:0.9.12-1 [23.0 kB] 113s Get:21 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcairo2 ppc64el 1.18.4-1build1 [759 kB] 113s Get:22 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdeflate0 ppc64el 1.23-2 [63.3 kB] 113s Get:23 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgomp1 ppc64el 15.2.0-9ubuntu1 [169 kB] 113s Get:24 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-4ubuntu2 [215 kB] 113s Get:25 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 113s Get:26 http://ftpmaster.internal/ubuntu resolute/main ppc64el fontconfig ppc64el 2.15.0-2.3ubuntu1 [192 kB] 113s Get:27 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgraphite2-3 ppc64el 1.3.14-2ubuntu1 [84.6 kB] 113s Get:28 http://ftpmaster.internal/ubuntu resolute/main ppc64el libharfbuzz0b ppc64el 12.1.0-1 [679 kB] 113s Get:29 http://ftpmaster.internal/ubuntu resolute/main ppc64el libthai-data all 0.1.29-2build2 [153 kB] 113s Get:30 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdatrie1 ppc64el 0.2.14-1 [22.7 kB] 113s Get:31 http://ftpmaster.internal/ubuntu resolute/main ppc64el libthai0 ppc64el 0.1.29-2build2 [22.6 kB] 113s Get:32 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpango-1.0-0 ppc64el 1.56.3-2 [281 kB] 113s Get:33 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpangoft2-1.0-0 ppc64el 1.56.3-2 [59.1 kB] 113s Get:34 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpangocairo-1.0-0 ppc64el 1.56.3-2 [31.0 kB] 113s Get:35 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtcl8.6 ppc64el 8.6.17+dfsg-1 [1239 kB] 113s Get:36 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu2 [35.9 kB] 113s Get:37 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblerc4 ppc64el 4.0.0+ds-5ubuntu1 [298 kB] 113s Get:38 http://ftpmaster.internal/ubuntu resolute/main ppc64el libsharpyuv0 ppc64el 1.5.0-0.1 [22.3 kB] 113s Get:39 http://ftpmaster.internal/ubuntu resolute/main ppc64el libwebp7 ppc64el 1.5.0-0.1 [315 kB] 113s Get:40 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtiff6 ppc64el 4.7.0-3ubuntu3 [307 kB] 113s Get:41 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxft2 ppc64el 2.3.6-1build2 [61.6 kB] 113s Get:42 http://ftpmaster.internal/ubuntu resolute/main ppc64el x11-common all 1:7.7+24ubuntu1 [22.4 kB] 113s Get:43 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxss1 ppc64el 1:1.2.3-1build4 [7470 B] 113s Get:44 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtk8.6 ppc64el 8.6.17-1 [968 kB] 113s Get:45 http://ftpmaster.internal/ubuntu resolute/main ppc64el libice6 ppc64el 2:1.1.1-1 [49.9 kB] 113s Get:46 http://ftpmaster.internal/ubuntu resolute/main ppc64el libsm6 ppc64el 2:1.2.6-1 [18.6 kB] 113s Get:47 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxt6t64 ppc64el 1:1.2.1-1.3 [203 kB] 113s Get:48 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-base-core ppc64el 4.5.2-1 [29.3 MB] 114s Get:49 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-cli ppc64el 3.6.4-1 [1411 kB] 114s Get:50 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-glue ppc64el 1.8.0-1 [165 kB] 114s Get:51 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rlang ppc64el 1.1.5-3 [1738 kB] 114s Get:52 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 114s Get:53 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 114s Get:54 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-isoband ppc64el 0.2.7-1 [1486 kB] 114s Get:55 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-mass ppc64el 7.3-65-1 [1116 kB] 114s Get:56 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lattice ppc64el 0.22-7-1 [1366 kB] 114s Get:57 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-nlme ppc64el 3.1.168-1 [2327 kB] 114s Get:58 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-matrix ppc64el 1.7-4-1 [4584 kB] 114s Get:59 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-mgcv ppc64el 1.9-3-1 [3453 kB] 114s Get:60 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-farver ppc64el 2.1.2-1 [1389 kB] 114s Get:61 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-labeling all 0.4.3-1 [62.1 kB] 114s Get:62 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-colorspace ppc64el 2.1-1+dfsg-1 [1570 kB] 114s Get:63 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-munsell all 0.5.1-1 [213 kB] 114s Get:64 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-r6 all 2.6.1-1 [101 kB] 114s Get:65 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 114s Get:66 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-viridislite all 0.4.2-2 [1088 kB] 114s Get:67 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-scales all 1.3.0-1 [603 kB] 114s Get:68 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-fansi ppc64el 1.0.6-2 [637 kB] 114s Get:69 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-magrittr ppc64el 2.0.3-1 [154 kB] 114s Get:70 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-utf8 ppc64el 1.2.4-1 [148 kB] 114s Get:71 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-vctrs ppc64el 0.6.5-1 [1399 kB] 114s Get:72 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pillar all 1.10.1+dfsg-1 [453 kB] 114s Get:73 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 114s Get:74 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-tibble ppc64el 3.2.1+dfsg-3 [420 kB] 115s Get:75 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-withr all 3.0.2+dfsg-1 [214 kB] 115s Get:76 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB] 115s Get:77 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-littler ppc64el 0.3.21-2 [84.2 kB] 115s Get:78 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 115s Get:79 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rcpp ppc64el 1.1.0-1 [2037 kB] 115s Get:80 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-plyr ppc64el 1.8.9-1 [834 kB] 115s Get:81 http://ftpmaster.internal/ubuntu resolute/universe ppc64el assemblytics all 1.2.1+dfsg-2 [19.1 kB] 115s Get:82 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpython3.14-stdlib ppc64el 3.14.0-4 [2446 kB] 115s Get:83 http://ftpmaster.internal/ubuntu resolute/main ppc64el python-is-python3 all 3.13.3-1 [2768 B] 115s Get:84 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3.14 ppc64el 3.14.0-4 [805 kB] 115s Get:85 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3-all ppc64el 3.13.9-2 [890 B] 115s Preconfiguring packages ... 115s Fetched 87.2 MB in 3s (33.3 MB/s) 115s Selecting previously unselected package python3-numpy-dev:ppc64el. 116s (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 ... 81185 files and directories currently installed.) 116s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_ppc64el.deb ... 116s Unpacking python3-numpy-dev:ppc64el (1:2.2.4+ds-1ubuntu1) ... 116s Selecting previously unselected package libblas3:ppc64el. 116s Preparing to unpack .../01-libblas3_3.12.1-7_ppc64el.deb ... 116s Unpacking libblas3:ppc64el (3.12.1-7) ... 116s Selecting previously unselected package libgfortran5:ppc64el. 116s 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fonts-dejavu-core. 117s Preparing to unpack .../13-fonts-dejavu-core_2.37-8_all.deb ... 117s Unpacking fonts-dejavu-core (2.37-8) ... 117s Selecting previously unselected package fontconfig-config. 117s Preparing to unpack .../14-fontconfig-config_2.15.0-2.3ubuntu1_ppc64el.deb ... 117s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 117s Selecting previously unselected package libfontconfig1:ppc64el. 117s Preparing to unpack .../15-libfontconfig1_2.15.0-2.3ubuntu1_ppc64el.deb ... 117s Unpacking libfontconfig1:ppc64el (2.15.0-2.3ubuntu1) ... 117s Selecting previously unselected package libpixman-1-0:ppc64el. 117s Preparing to unpack .../16-libpixman-1-0_0.46.4-1_ppc64el.deb ... 117s Unpacking libpixman-1-0:ppc64el (0.46.4-1) ... 117s Selecting previously unselected package libxcb-render0:ppc64el. 117s Preparing to unpack .../17-libxcb-render0_1.17.0-2build1_ppc64el.deb ... 117s Unpacking libxcb-render0:ppc64el (1.17.0-2build1) ... 117s Selecting previously unselected package libxcb-shm0:ppc64el. 117s Preparing to unpack .../18-libxcb-shm0_1.17.0-2build1_ppc64el.deb ... 117s Unpacking libxcb-shm0:ppc64el (1.17.0-2build1) ... 117s Selecting previously unselected package libxrender1:ppc64el. 117s Preparing to unpack .../19-libxrender1_1%3a0.9.12-1_ppc64el.deb ... 117s Unpacking libxrender1:ppc64el (1:0.9.12-1) ... 117s Selecting previously unselected package libcairo2:ppc64el. 117s Preparing to unpack .../20-libcairo2_1.18.4-1build1_ppc64el.deb ... 117s Unpacking libcairo2:ppc64el (1.18.4-1build1) ... 117s Selecting previously unselected package libdeflate0:ppc64el. 117s Preparing to unpack .../21-libdeflate0_1.23-2_ppc64el.deb ... 117s Unpacking libdeflate0:ppc64el (1.23-2) ... 117s Selecting previously unselected package libgomp1:ppc64el. 117s Preparing to unpack .../22-libgomp1_15.2.0-9ubuntu1_ppc64el.deb ... 117s Unpacking libgomp1:ppc64el (15.2.0-9ubuntu1) ... 117s Selecting previously unselected package libjpeg-turbo8:ppc64el. 117s Preparing to unpack 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package libice6:ppc64el. 118s Preparing to unpack .../44-libice6_2%3a1.1.1-1_ppc64el.deb ... 118s Unpacking libice6:ppc64el (2:1.1.1-1) ... 118s Selecting previously unselected package libsm6:ppc64el. 118s Preparing to unpack .../45-libsm6_2%3a1.2.6-1_ppc64el.deb ... 118s Unpacking libsm6:ppc64el (2:1.2.6-1) ... 118s Selecting previously unselected package libxt6t64:ppc64el. 118s Preparing to unpack .../46-libxt6t64_1%3a1.2.1-1.3_ppc64el.deb ... 118s Unpacking libxt6t64:ppc64el (1:1.2.1-1.3) ... 118s Selecting previously unselected package r-base-core. 118s Preparing to unpack .../47-r-base-core_4.5.2-1_ppc64el.deb ... 118s Unpacking r-base-core (4.5.2-1) ... 118s Selecting previously unselected package r-cran-cli. 118s Preparing to unpack .../48-r-cran-cli_3.6.4-1_ppc64el.deb ... 118s Unpacking r-cran-cli (3.6.4-1) ... 118s Selecting previously unselected package r-cran-glue. 118s Preparing to unpack .../49-r-cran-glue_1.8.0-1_ppc64el.deb ... 118s Unpacking r-cran-glue (1.8.0-1) ... 118s Selecting previously unselected package r-cran-rlang. 118s Preparing to unpack .../50-r-cran-rlang_1.1.5-3_ppc64el.deb ... 118s Unpacking r-cran-rlang (1.1.5-3) ... 118s Selecting previously unselected package r-cran-lifecycle. 118s Preparing to unpack .../51-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 118s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 118s Selecting previously unselected package r-cran-gtable. 118s Preparing to unpack .../52-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 118s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 118s Selecting previously unselected package r-cran-isoband. 118s Preparing to unpack .../53-r-cran-isoband_0.2.7-1_ppc64el.deb ... 118s Unpacking r-cran-isoband (0.2.7-1) ... 118s Selecting previously unselected package r-cran-mass. 118s Preparing to unpack .../54-r-cran-mass_7.3-65-1_ppc64el.deb ... 118s Unpacking r-cran-mass (7.3-65-1) ... 118s Selecting previously unselected package r-cran-lattice. 118s Preparing to unpack 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119s Selecting previously unselected package r-cran-rcpp. 119s Preparing to unpack .../78-r-cran-rcpp_1.1.0-1_ppc64el.deb ... 119s Unpacking r-cran-rcpp (1.1.0-1) ... 119s Selecting previously unselected package r-cran-plyr. 119s Preparing to unpack .../79-r-cran-plyr_1.8.9-1_ppc64el.deb ... 119s Unpacking r-cran-plyr (1.8.9-1) ... 119s Selecting previously unselected package assemblytics. 119s Preparing to unpack .../80-assemblytics_1.2.1+dfsg-2_all.deb ... 119s Unpacking assemblytics (1.2.1+dfsg-2) ... 119s Selecting previously unselected package libpython3.14-stdlib:ppc64el. 119s Preparing to unpack .../81-libpython3.14-stdlib_3.14.0-4_ppc64el.deb ... 119s Unpacking libpython3.14-stdlib:ppc64el (3.14.0-4) ... 119s Selecting previously unselected package python-is-python3. 119s Preparing to unpack .../82-python-is-python3_3.13.3-1_all.deb ... 119s Unpacking python-is-python3 (3.13.3-1) ... 119s Selecting previously unselected package python3.14. 119s Preparing to unpack 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(2.1-6.1ubuntu2) ... 120s Setting up zip (3.0-15ubuntu2) ... 120s Setting up libblas3:ppc64el (3.12.1-7) ... 120s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 120s Setting up fonts-dejavu-mono (2.37-8) ... 120s Setting up python3-numpy-dev:ppc64el (1:2.2.4+ds-1ubuntu1) ... 120s Setting up libtcl8.6:ppc64el (8.6.17+dfsg-1) ... 120s Setting up fonts-dejavu-core (2.37-8) ... 120s Setting up libjpeg-turbo8:ppc64el (2.1.5-4ubuntu2) ... 120s Setting up libgfortran5:ppc64el (15.2.0-9ubuntu1) ... 120s Setting up libwebp7:ppc64el (1.5.0-0.1) ... 120s Setting up libharfbuzz0b:ppc64el (12.1.0-1) ... 120s Setting up libthai-data (0.1.29-2build2) ... 120s Setting up libxss1:ppc64el (1:1.2.3-1build4) ... 120s Setting up libpaper2:ppc64el (2.2.5-0.3) ... 120s Setting up python-is-python3 (3.13.3-1) ... 120s Setting up xdg-utils (1.2.1-2ubuntu1) ... 120s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 120s Setting up python3.14-minimal (3.14.0-4) ... 121s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 121s Setting up libice6:ppc64el (2:1.1.1-1) ... 121s Setting up liblapack3:ppc64el (3.12.1-7) ... 121s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 121s Setting up libpython3.14-stdlib:ppc64el (3.14.0-4) ... 121s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 121s Setting up libpaper-utils (2.2.5-0.3) ... 121s Setting up libthai0:ppc64el (0.1.29-2build2) ... 121s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 125s Setting up libtiff6:ppc64el (4.7.0-3ubuntu3) ... 125s Setting up libfontconfig1:ppc64el (2.15.0-2.3ubuntu1) ... 125s Setting up python3.14 (3.14.0-4) ... 126s Setting up libsm6:ppc64el (2:1.2.6-1) ... 126s Setting up fontconfig (2.15.0-2.3ubuntu1) ... 128s Regenerating fonts cache... done. 128s Setting up libxft2:ppc64el (2.3.6-1build2) ... 128s Setting up libtk8.6:ppc64el (8.6.17-1) ... 128s Setting up libpango-1.0-0:ppc64el (1.56.3-2) ... 128s Setting up python3-all (3.13.9-2) ... 128s Setting up libcairo2:ppc64el (1.18.4-1build1) ... 128s Setting up libxt6t64:ppc64el (1:1.2.1-1.3) ... 128s Setting up libpangoft2-1.0-0:ppc64el (1.56.3-2) ... 128s Setting up libpangocairo-1.0-0:ppc64el (1.56.3-2) ... 128s Setting up r-base-core (4.5.2-1) ... 128s Creating config file /etc/R/Renviron with new version 128s Setting up r-cran-labeling (0.4.3-1) ... 128s Setting up r-cran-lattice (0.22-7-1) ... 128s Setting up r-cran-nlme (3.1.168-1) ... 128s Setting up r-cran-farver (2.1.2-1) ... 128s Setting up r-cran-viridislite (0.4.2-2) ... 128s Setting up r-cran-r6 (2.6.1-1) ... 128s Setting up r-cran-pkgkitten (0.2.4-1) ... 128s Setting up r-cran-magrittr (2.0.3-1) ... 128s Setting up r-cran-littler (0.3.21-2) ... 128s Setting up r-cran-rcpp (1.1.0-1) ... 128s Setting up r-cran-rlang (1.1.5-3) ... 128s Setting up r-cran-withr (3.0.2+dfsg-1) ... 128s Setting up r-cran-fansi (1.0.6-2) ... 128s Setting up r-cran-mass (7.3-65-1) ... 128s Setting up r-cran-glue (1.8.0-1) ... 128s Setting up r-cran-cli (3.6.4-1) ... 128s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... 128s Setting up r-cran-pkgconfig (2.0.3-2build2) ... 128s Setting up r-cran-utf8 (1.2.4-1) ... 128s Setting up r-cran-colorspace (2.1-1+dfsg-1) ... 128s Setting up r-cran-plyr (1.8.9-1) ... 128s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ... 128s Setting up r-cran-isoband (0.2.7-1) ... 128s Setting up r-cran-gtable (0.3.6+dfsg-1) ... 128s Setting up r-cran-matrix (1.7-4-1) ... 128s Setting up r-cran-mgcv (1.9-3-1) ... 128s Setting up r-cran-vctrs (0.6.5-1) ... 128s Setting up r-cran-pillar (1.10.1+dfsg-1) ... 128s Setting up r-cran-munsell (0.5.1-1) ... 128s Setting up r-cran-tibble (3.2.1+dfsg-3) ... 128s Setting up r-cran-scales (1.3.0-1) ... 128s Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... 128s Setting up assemblytics (1.2.1+dfsg-2) ... 128s Processing triggers for systemd (257.9-0ubuntu2) ... 128s Processing triggers for man-db (2.13.1-1) ... 131s Processing triggers for install-info (7.2-5) ... 131s Processing triggers for libc-bin (2.42-2ubuntu2) ... 132s autopkgtest [01:57:25]: test run-unit-test: [----------------------- 132s Input delta file: sample.delta 132s Output prefix: myfirstorganism 132s Unique anchor length: 10000 132s Minimum variant size to call: 10000 132s Maximum variant size to call: 50 132s Logging progress updates in myfirstorganism/progress.log 132s script path: /usr/share/assemblytics/bin 132s 1. Filter delta file 132s Keeping fully unique alignments even if they are below the unique anchor length of 10000 bp 132s 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. 132s Detected uncompressed delta file. Reading... 132s 132s 132s Header (2 lines): 132s /seq/schatz/mnattest/Assemblytics/Ecoli/GCF_000005845.2_ASM584v2_genomic.fna /seq/schatz/mnattest/Assemblytics/Ecoli/GCF_000801205.1_ASM80120v1_genomic.fna 132s NUCMER 132s 132s 132s First read through the file: 0 seconds for 0 query-reference combinations 132s Filtering alignments of 1 queries 132s Progress: 100% 132s Progress: 100% 132s Deciding which alignments to keep: 0 seconds for 1 queries 132s Detected uncompressed delta file. Reading... 132s Reading file and recording all the entries we decided to keep: 0 seconds for 54 total lines in file 132s 2. Finding variants between alignments 132s Loaded 6 alignments 132s 3. Finding variants within alignments 132s Detected gzipped delta file. Reading... 132s 132s 132s Header (2 lines): 132s /seq/schatz/mnattest/Assemblytics/Ecoli/GCF_000005845.2_ASM584v2_genomic.fna /seq/schatz/mnattest/Assemblytics/Ecoli/GCF_000801205.1_ASM80120v1_genomic.fna 132s NUCMER 132s 132s 132s 4. Combine variants between and within alignments 133s Error in revalue(bed$type, c(Repeat_expansion = "Repeat expansion", Repeat_contraction = "Repeat contraction", : 133s x is not a factor or a character vector. 133s Execution halted 134s Warning messages: 134s 1: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. 134s ℹ Please use `linewidth` instead. 134s 2: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0. 134s ℹ Please use the `linewidth` argument instead. 134s null device 134s 1 136s Warning message: 136s Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. 136s ℹ Please use `linewidth` instead. 136s adding: myfirstorganism.Assemblytics.Dotplot_filtered.png (deflated 11%) 136s adding: myfirstorganism.Assemblytics.Nchart.pdf (deflated 11%) 136s adding: myfirstorganism.Assemblytics.Nchart.png (deflated 6%) 136s adding: myfirstorganism.Assemblytics.unique_length_filtered_l10000.delta.gz (stored 0%) 136s adding: myfirstorganism.Assemblytics_assembly_stats.txt (deflated 58%) 136s adding: myfirstorganism.Assemblytics_structural_variants.bed (deflated 26%) 136s adding: myfirstorganism.Assemblytics_structural_variants.summary (deflated 49%) 136s adding: myfirstorganism.Assemblytics_structural_variants.summary.csv (deflated 35%) 136s PASS 136s autopkgtest [01:57:29]: test run-unit-test: -----------------------] 137s autopkgtest [01:57:30]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 137s run-unit-test PASS 137s autopkgtest [01:57:30]: @@@@@@@@@@@@@@@@@@@@ summary 137s run-unit-test PASS