0s autopkgtest [18:33:57]: starting date and time: 2025-12-03 18:33:57+0000 0s autopkgtest [18:33:57]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [18:33:57]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.h2_tyjcb/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-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-3.secgroup --name adt-resolute-amd64-assemblytics-20251203-183356-juju-7f2275-prod-proposed-migration-environment-15-e2a8430e-d5b6-49b3-a97d-c3e88d343338 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-amd64-assemblytics-20251203-183356-juju-7f2275-prod-proposed-migration-environment-15-e2a8430e-d5b6-49b3-a97d-c3e88d343338 from image adt/ubuntu-resolute-amd64-server-20251203.img (UUID c6e78f39-c16c-48bb-9815-0096f6be052e)... 48s autopkgtest [18:34:45]: testbed dpkg architecture: amd64 48s autopkgtest [18:34:45]: testbed apt version: 3.1.12 48s autopkgtest [18:34:45]: @@@@@@@@@@@@@@@@@@@@ test bed setup 48s autopkgtest [18:34:45]: testbed release detected to be: None 49s autopkgtest [18:34:46]: updating testbed package index (apt update) 49s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 49s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 49s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 49s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 49s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [157 kB] 49s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [23.1 kB] 49s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [954 kB] 50s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [220 kB] 50s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [161 kB] 50s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [6252 B] 50s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [120 B] 50s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [349 kB] 50s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [764 kB] 50s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [23.0 kB] 50s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4040 B] 50s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [9636 B] 50s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [764 B] 50s Fetched 2796 kB in 1s (3051 kB/s) 51s Reading package lists... 51s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 51s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 51s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 52s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 52s Reading package lists... 52s Reading package lists... 52s Building dependency tree... 52s Reading state information... 52s Calculating upgrade... 52s The following packages will be upgraded: 52s libpython3-stdlib python3 python3-gdbm python3-minimal 52s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 52s Need to get 72.9 kB of archives. 52s After this operation, 2048 B of additional disk space will be used. 52s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.13.9-2 [28.1 kB] 52s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.13.9-2 [23.0 kB] 52s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.13.9-2 [10.8 kB] 52s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-gdbm amd64 3.13.9-2 [11.0 kB] 53s dpkg-preconfigure: unable to re-open stdin: No such file or directory 53s Fetched 72.9 kB in 0s (721 kB/s) 53s (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 ... 83538 files and directories currently installed.) 53s Preparing to unpack .../python3-minimal_3.13.9-2_amd64.deb ... 53s Unpacking python3-minimal (3.13.9-2) over (3.13.7-1) ... 53s Setting up python3-minimal (3.13.9-2) ... 53s (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 ... 83538 files and directories currently installed.) 53s Preparing to unpack .../python3_3.13.9-2_amd64.deb ... 53s running python pre-rtupdate hooks for python3.13... 53s Unpacking python3 (3.13.9-2) over (3.13.7-1) ... 53s Preparing to unpack .../libpython3-stdlib_3.13.9-2_amd64.deb ... 53s Unpacking libpython3-stdlib:amd64 (3.13.9-2) over (3.13.7-1) ... 53s Preparing to unpack .../python3-gdbm_3.13.9-2_amd64.deb ... 53s Unpacking python3-gdbm (3.13.9-2) over (3.13.9-1) ... 53s Setting up python3-gdbm (3.13.9-2) ... 53s Setting up libpython3-stdlib:amd64 (3.13.9-2) ... 53s Setting up python3 (3.13.9-2) ... 53s running python rtupdate hooks for python3.13... 53s running python post-rtupdate hooks for python3.13... 53s Processing triggers for man-db (2.13.1-1) ... 54s autopkgtest [18:34:51]: upgrading testbed (apt dist-upgrade and autopurge) 54s Reading package lists... 54s Building dependency tree... 54s Reading state information... 54s Calculating upgrade... 54s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 54s Reading package lists... 54s Building dependency tree... 54s Reading state information... 54s Solving dependencies... 54s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 56s autopkgtest [18:34:53]: testbed running kernel: Linux 6.17.0-6-generic #6-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 7 13:34:17 UTC 2025 57s autopkgtest [18:34:54]: @@@@@@@@@@@@@@@@@@@@ apt-source assemblytics 58s Get:1 http://ftpmaster.internal/ubuntu resolute/universe assemblytics 1.2.1+dfsg-2 (dsc) [2072 B] 58s Get:2 http://ftpmaster.internal/ubuntu resolute/universe assemblytics 1.2.1+dfsg-2 (tar) [15.5 kB] 58s Get:3 http://ftpmaster.internal/ubuntu resolute/universe assemblytics 1.2.1+dfsg-2 (diff) [4640 B] 58s gpgv: Signature made Wed Dec 6 13:41:32 2023 UTC 58s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 58s gpgv: issuer "tillea@rki.de" 58s gpgv: Can't check signature: No public key 58s dpkg-source: warning: cannot verify inline signature for ./assemblytics_1.2.1+dfsg-2.dsc: no acceptable signature found 58s autopkgtest [18:34:55]: testing package assemblytics version 1.2.1+dfsg-2 58s autopkgtest [18:34:55]: build not needed 58s autopkgtest [18:34:55]: test run-unit-test: preparing testbed 58s Reading package lists... 58s Building dependency tree... 58s Reading state information... 58s Solving dependencies... 58s The following NEW packages will be installed: 58s assemblytics fontconfig fontconfig-config fonts-dejavu-core 58s fonts-dejavu-mono libblas3 libcairo2 libdatrie1 libdeflate0 libfontconfig1 58s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 58s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 58s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 58s libpython3.14-minimal libpython3.14-stdlib libsharpyuv0 libsm6 libtcl8.6 58s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 58s libxft2 libxrender1 libxss1 libxt6t64 python-is-python3 python3-all 58s python3-numpy python3-numpy-dev python3.14 python3.14-minimal r-base-core 58s r-cran-cli r-cran-colorspace r-cran-fansi r-cran-farver r-cran-ggplot2 58s r-cran-glue r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lattice 58s r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix 58s r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig 58s r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp 58s r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8 r-cran-vctrs 58s r-cran-viridislite r-cran-withr unzip x11-common xdg-utils zip 58s 0 upgraded, 85 newly installed, 0 to remove and 0 not upgraded. 58s Need to get 85.4 MB of archives. 58s After this operation, 191 MB of additional disk space will be used. 58s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1ubuntu1 [147 kB] 58s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7 [259 kB] 59s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-9ubuntu1 [939 kB] 59s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7 [2739 kB] 60s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.2.4+ds-1ubuntu1 [5377 kB] 60s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.0-4 [906 kB] 60s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-minimal amd64 3.14.0-4 [2559 kB] 60s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 zip amd64 3.0-15ubuntu2 [178 kB] 60s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 unzip amd64 6.0-28ubuntu7 [180 kB] 60s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB] 60s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB] 60s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 60s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 60s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 60s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.15.0-2.3ubuntu1 [38.0 kB] 60s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.15.0-2.3ubuntu1 [141 kB] 60s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB] 60s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2build1 [17.4 kB] 60s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2build1 [6120 B] 60s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 60s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-1build1 [611 kB] 60s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 60s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-9ubuntu1 [151 kB] 60s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB] 60s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 60s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig amd64 2.15.0-2.3ubuntu1 [180 kB] 60s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 61s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.1.0-1 [535 kB] 61s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai-data all 0.1.29-2build2 [153 kB] 61s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libdatrie1 amd64 0.2.14-1 [19.8 kB] 61s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai0 amd64 0.1.29-2build2 [19.2 kB] 61s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libpango-1.0-0 amd64 1.56.3-2 [239 kB] 61s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoft2-1.0-0 amd64 1.56.3-2 [52.5 kB] 61s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangocairo-1.0-0 amd64 1.56.3-2 [29.0 kB] 61s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1036 kB] 61s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 61s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 61s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 61s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 61s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 61s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 61s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 61s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 61s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB] 61s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 61s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libsm6 amd64 2:1.2.6-1 [16.4 kB] 61s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libxt6t64 amd64 1:1.2.1-1.3 [173 kB] 61s Get:48 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-core amd64 4.5.2-1 [28.8 MB] 62s Get:49 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB] 62s Get:50 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB] 62s Get:51 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rlang amd64 1.1.5-3 [1721 kB] 62s Get:52 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 62s Get:53 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 62s Get:54 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-isoband amd64 0.2.7-1 [1481 kB] 62s Get:55 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mass amd64 7.3-65-1 [1116 kB] 62s Get:56 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lattice amd64 0.22-7-1 [1367 kB] 62s Get:57 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-nlme amd64 3.1.168-1 [2320 kB] 63s Get:58 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrix amd64 1.7-4-1 [4220 kB] 63s Get:59 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mgcv amd64 1.9-3-1 [3414 kB] 64s Get:60 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-farver amd64 2.1.2-1 [1355 kB] 64s Get:61 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-labeling all 0.4.3-1 [62.1 kB] 64s Get:62 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1563 kB] 64s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-munsell all 0.5.1-1 [213 kB] 64s Get:64 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r6 all 2.6.1-1 [101 kB] 64s Get:65 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 64s Get:66 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-viridislite all 0.4.2-2 [1088 kB] 64s Get:67 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-scales all 1.3.0-1 [603 kB] 64s Get:68 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fansi amd64 1.0.6-2 [626 kB] 64s Get:69 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB] 64s Get:70 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-utf8 amd64 1.2.4-1 [140 kB] 64s Get:71 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB] 64s Get:72 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pillar all 1.10.1+dfsg-1 [453 kB] 64s Get:73 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 64s Get:74 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [419 kB] 64s Get:75 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 64s Get:76 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB] 64s Get:77 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-littler amd64 0.3.21-2 [84.4 kB] 64s Get:78 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 64s Get:79 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcpp amd64 1.1.0-1 [2021 kB] 64s Get:80 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-plyr amd64 1.8.9-1 [832 kB] 64s Get:81 http://ftpmaster.internal/ubuntu resolute/universe amd64 assemblytics all 1.2.1+dfsg-2 [19.1 kB] 64s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.0-4 [2397 kB] 64s Get:83 http://ftpmaster.internal/ubuntu resolute/main amd64 python-is-python3 all 3.13.3-1 [2768 B] 64s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14 amd64 3.14.0-4 [805 kB] 65s Get:85 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-all amd64 3.13.9-2 [892 B] 65s Preconfiguring packages ... 65s Fetched 85.4 MB in 6s (14.1 MB/s) 65s Selecting previously unselected package python3-numpy-dev:amd64. 65s (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 ... 83538 files and directories currently installed.) 65s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 65s Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 65s Selecting previously unselected package libblas3:amd64. 65s Preparing to unpack .../01-libblas3_3.12.1-7_amd64.deb ... 65s Unpacking libblas3:amd64 (3.12.1-7) ... 65s Selecting previously unselected package libgfortran5:amd64. 65s Preparing to unpack .../02-libgfortran5_15.2.0-9ubuntu1_amd64.deb ... 65s Unpacking libgfortran5:amd64 (15.2.0-9ubuntu1) ... 65s Selecting previously unselected package liblapack3:amd64. 65s Preparing to unpack .../03-liblapack3_3.12.1-7_amd64.deb ... 65s Unpacking liblapack3:amd64 (3.12.1-7) ... 65s Selecting previously unselected package python3-numpy. 65s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 65s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 65s Selecting previously unselected package libpython3.14-minimal:amd64. 65s Preparing to unpack .../05-libpython3.14-minimal_3.14.0-4_amd64.deb ... 65s Unpacking libpython3.14-minimal:amd64 (3.14.0-4) ... 65s Selecting previously unselected package python3.14-minimal. 65s Preparing to unpack .../06-python3.14-minimal_3.14.0-4_amd64.deb ... 65s Unpacking python3.14-minimal (3.14.0-4) ... 65s Selecting previously unselected package zip. 65s Preparing to unpack .../07-zip_3.0-15ubuntu2_amd64.deb ... 65s Unpacking zip 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unselected package libjbig0:amd64. 65s Preparing to unpack .../35-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 65s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 65s Selecting previously unselected package liblerc4:amd64. 65s Preparing to unpack .../36-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 65s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 65s Selecting previously unselected package libsharpyuv0:amd64. 65s Preparing to unpack .../37-libsharpyuv0_1.5.0-0.1_amd64.deb ... 65s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 65s Selecting previously unselected package libwebp7:amd64. 65s Preparing to unpack .../38-libwebp7_1.5.0-0.1_amd64.deb ... 65s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 65s Selecting previously unselected package libtiff6:amd64. 65s Preparing to unpack .../39-libtiff6_4.7.0-3ubuntu3_amd64.deb ... 65s Unpacking libtiff6:amd64 (4.7.0-3ubuntu3) ... 65s Selecting previously unselected package libxft2:amd64. 65s Preparing to unpack .../40-libxft2_2.3.6-1build1_amd64.deb ... 65s 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python3-numpy (1:2.2.4+ds-1ubuntu1) ... 69s Setting up libtiff6:amd64 (4.7.0-3ubuntu3) ... 69s Setting up libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 69s Setting up python3.14 (3.14.0-4) ... 70s Setting up libsm6:amd64 (2:1.2.6-1) ... 70s Setting up fontconfig (2.15.0-2.3ubuntu1) ... 72s Regenerating fonts cache... done. 72s Setting up libxft2:amd64 (2.3.6-1build1) ... 72s Setting up libtk8.6:amd64 (8.6.17-1) ... 72s Setting up libpango-1.0-0:amd64 (1.56.3-2) ... 72s Setting up python3-all (3.13.9-2) ... 72s Setting up libcairo2:amd64 (1.18.4-1build1) ... 72s Setting up libxt6t64:amd64 (1:1.2.1-1.3) ... 72s Setting up libpangoft2-1.0-0:amd64 (1.56.3-2) ... 72s Setting up libpangocairo-1.0-0:amd64 (1.56.3-2) ... 72s Setting up r-base-core (4.5.2-1) ... 72s Creating config file /etc/R/Renviron with new version 72s Setting up r-cran-labeling (0.4.3-1) ... 72s Setting up r-cran-lattice (0.22-7-1) ... 72s Setting up r-cran-nlme (3.1.168-1) ... 72s Setting up r-cran-farver (2.1.2-1) ... 72s Setting up r-cran-viridislite (0.4.2-2) ... 72s Setting up r-cran-r6 (2.6.1-1) ... 72s Setting up r-cran-pkgkitten (0.2.4-1) ... 72s Setting up r-cran-magrittr (2.0.3-1) ... 72s Setting up r-cran-littler (0.3.21-2) ... 72s Setting up r-cran-rcpp (1.1.0-1) ... 72s Setting up r-cran-rlang (1.1.5-3) ... 72s Setting up r-cran-withr (3.0.2+dfsg-1) ... 72s Setting up r-cran-fansi (1.0.6-2) ... 72s Setting up r-cran-mass (7.3-65-1) ... 72s Setting up r-cran-glue (1.8.0-1) ... 72s Setting up r-cran-cli (3.6.4-1) ... 72s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... 72s Setting up r-cran-pkgconfig (2.0.3-2build2) ... 72s Setting up r-cran-utf8 (1.2.4-1) ... 72s Setting up r-cran-colorspace (2.1-1+dfsg-1) ... 72s Setting up r-cran-plyr (1.8.9-1) ... 72s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ... 72s Setting up r-cran-isoband (0.2.7-1) ... 72s Setting up r-cran-gtable (0.3.6+dfsg-1) ... 72s Setting up r-cran-matrix (1.7-4-1) ... 72s Setting up r-cran-mgcv (1.9-3-1) ... 72s Setting up r-cran-vctrs (0.6.5-1) ... 72s Setting up r-cran-pillar (1.10.1+dfsg-1) ... 72s Setting up r-cran-munsell (0.5.1-1) ... 72s Setting up r-cran-tibble (3.2.1+dfsg-3) ... 72s Setting up r-cran-scales (1.3.0-1) ... 72s Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... 72s Setting up assemblytics (1.2.1+dfsg-2) ... 72s Processing triggers for systemd (257.9-0ubuntu2) ... 72s Processing triggers for man-db (2.13.1-1) ... 73s Processing triggers for install-info (7.2-5) ... 73s Processing triggers for libc-bin (2.42-2ubuntu2) ... 73s autopkgtest [18:35:10]: test run-unit-test: [----------------------- 74s Input delta file: sample.delta 74s Output prefix: myfirstorganism 74s Unique anchor length: 10000 74s Minimum variant size to call: 10000 74s Maximum variant size to call: 50 74s script path: /usr/share/assemblytics/bin 74s Logging progress updates in myfirstorganism/progress.log 74s 1. Filter delta file 74s Keeping fully unique alignments even if they are below the unique anchor length of 10000 bp 74s 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. 74s Detected uncompressed delta file. Reading... 74s 74s 74s Header (2 lines): 74s /seq/schatz/mnattest/Assemblytics/Ecoli/GCF_000005845.2_ASM584v2_genomic.fna /seq/schatz/mnattest/Assemblytics/Ecoli/GCF_000801205.1_ASM80120v1_genomic.fna 74s NUCMER 74s 74s 74s First read through the file: 0 seconds for 0 query-reference combinations 74s Filtering alignments of 1 queries 74s Progress: 100% 74s Progress: 100% 74s Deciding which alignments to keep: 0 seconds for 1 queries 74s Detected uncompressed delta file. Reading... 74s Reading file and recording all the entries we decided to keep: 0 seconds for 54 total lines in file 74s 2. Finding variants between alignments 74s Loaded 6 alignments 74s 3. Finding variants within alignments 74s Detected gzipped delta file. Reading... 74s 74s 74s Header (2 lines): 74s /seq/schatz/mnattest/Assemblytics/Ecoli/GCF_000005845.2_ASM584v2_genomic.fna /seq/schatz/mnattest/Assemblytics/Ecoli/GCF_000801205.1_ASM80120v1_genomic.fna 74s NUCMER 74s 74s 74s 4. Combine variants between and within alignments 74s Error in revalue(bed$type, c(Repeat_expansion = "Repeat expansion", Repeat_contraction = "Repeat contraction", : 74s x is not a factor or a character vector. 74s Execution halted 75s Warning messages: 75s 1: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. 75s ℹ Please use `linewidth` instead. 75s 2: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0. 75s ℹ Please use the `linewidth` argument instead. 75s null device 75s 1 76s Warning message: 76s Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. 76s ℹ Please use `linewidth` instead. 76s adding: myfirstorganism.Assemblytics.Dotplot_filtered.png (deflated 11%) 76s adding: myfirstorganism.Assemblytics.Nchart.pdf (deflated 11%) 76s adding: myfirstorganism.Assemblytics.Nchart.png (deflated 6%) 76s adding: myfirstorganism.Assemblytics.unique_length_filtered_l10000.delta.gz (stored 0%) 76s adding: myfirstorganism.Assemblytics_assembly_stats.txt (deflated 58%) 76s adding: myfirstorganism.Assemblytics_structural_variants.bed (deflated 26%) 76s adding: myfirstorganism.Assemblytics_structural_variants.summary (deflated 49%) 76s adding: myfirstorganism.Assemblytics_structural_variants.summary.csv (deflated 35%) 76s PASS 76s autopkgtest [18:35:13]: test run-unit-test: -----------------------] 76s run-unit-test PASS 76s autopkgtest [18:35:13]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 77s autopkgtest [18:35:14]: @@@@@@@@@@@@@@@@@@@@ summary 77s run-unit-test PASS