0s autopkgtest [13:53:45]: starting date and time: 2025-12-04 13:53:45+0000 0s autopkgtest [13:53:45]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [13:53:45]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.pagfxnpr/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-4.secgroup --name adt-resolute-arm64-assemblytics-20251204-135345-juju-7f2275-prod-proposed-migration-environment-2-38ac237a-be71-456e-9da0-f7921ce8c60c --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-arm64-assemblytics-20251204-135345-juju-7f2275-prod-proposed-migration-environment-2-38ac237a-be71-456e-9da0-f7921ce8c60c from image adt/ubuntu-resolute-arm64-server-20251204.img (UUID d10d485b-270b-4b77-bdc2-f40c1cd474cf)... 59s autopkgtest [13:54:44]: testbed dpkg architecture: arm64 59s autopkgtest [13:54:44]: testbed apt version: 3.1.12 60s autopkgtest [13:54:45]: @@@@@@@@@@@@@@@@@@@@ test bed setup 60s autopkgtest [13:54:45]: testbed release detected to be: None 61s autopkgtest [13:54:46]: updating testbed package index (apt update) 61s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 62s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 62s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 62s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 62s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [23.1 kB] 62s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [935 kB] 62s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [156 kB] 62s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [219 kB] 62s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [6632 B] 62s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [120 B] 62s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [727 kB] 62s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [20.6 kB] 62s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [8768 B] 62s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [644 B] 65s Fetched 2221 kB in 1s (1684 kB/s) 66s Reading package lists... 67s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 67s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 67s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 67s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 68s Reading package lists... 68s Reading package lists... 68s Building dependency tree... 68s Reading state information... 69s Calculating upgrade... 69s The following packages will be upgraded: 69s libpython3-stdlib python3 python3-gdbm python3-minimal 69s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 69s Need to get 72.9 kB of archives. 69s After this operation, 2048 B of additional disk space will be used. 69s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-minimal arm64 3.13.9-2 [28.1 kB] 69s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3 arm64 3.13.9-2 [23.0 kB] 69s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libpython3-stdlib arm64 3.13.9-2 [10.8 kB] 69s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-gdbm arm64 3.13.9-2 [11.0 kB] 70s dpkg-preconfigure: unable to re-open stdin: No such file or directory 70s Fetched 72.9 kB in 0s (183 kB/s) 70s (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 ... 88300 files and directories currently installed.) 70s Preparing to unpack .../python3-minimal_3.13.9-2_arm64.deb ... 70s Unpacking python3-minimal (3.13.9-2) over (3.13.7-1) ... 70s Setting up python3-minimal (3.13.9-2) ... 71s (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 ... 88300 files and directories currently installed.) 71s Preparing to unpack .../python3_3.13.9-2_arm64.deb ... 71s running python pre-rtupdate hooks for python3.13... 71s Unpacking python3 (3.13.9-2) over (3.13.7-1) ... 71s Preparing to unpack .../libpython3-stdlib_3.13.9-2_arm64.deb ... 71s Unpacking libpython3-stdlib:arm64 (3.13.9-2) over (3.13.7-1) ... 71s Preparing to unpack .../python3-gdbm_3.13.9-2_arm64.deb ... 71s Unpacking python3-gdbm (3.13.9-2) over (3.13.9-1) ... 71s Setting up python3-gdbm (3.13.9-2) ... 71s Setting up libpython3-stdlib:arm64 (3.13.9-2) ... 71s Setting up python3 (3.13.9-2) ... 71s running python rtupdate hooks for python3.13... 71s running python post-rtupdate hooks for python3.13... 71s Processing triggers for man-db (2.13.1-1) ... 72s autopkgtest [13:54:57]: upgrading testbed (apt dist-upgrade and autopurge) 72s Reading package lists... 73s Building dependency tree... 73s Reading state information... 73s Calculating upgrade... 73s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 73s Reading package lists... 74s Building dependency tree... 74s Reading state information... 74s Solving dependencies... 74s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 78s autopkgtest [13:55:03]: testbed running kernel: Linux 6.17.0-6-generic #6-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 7 14:22:06 UTC 2025 78s autopkgtest [13:55:03]: @@@@@@@@@@@@@@@@@@@@ apt-source assemblytics 82s Get:1 http://ftpmaster.internal/ubuntu resolute/universe assemblytics 1.2.1+dfsg-2 (dsc) [2072 B] 82s Get:2 http://ftpmaster.internal/ubuntu resolute/universe assemblytics 1.2.1+dfsg-2 (tar) [15.5 kB] 82s Get:3 http://ftpmaster.internal/ubuntu resolute/universe assemblytics 1.2.1+dfsg-2 (diff) [4640 B] 82s gpgv: Signature made Wed Dec 6 13:41:32 2023 UTC 82s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 82s gpgv: issuer "tillea@rki.de" 82s gpgv: Can't check signature: No public key 82s dpkg-source: warning: cannot verify inline signature for ./assemblytics_1.2.1+dfsg-2.dsc: no acceptable signature found 82s autopkgtest [13:55:07]: testing package assemblytics version 1.2.1+dfsg-2 82s autopkgtest [13:55:07]: build not needed 83s autopkgtest [13:55:08]: test run-unit-test: preparing testbed 83s Reading package lists... 83s Building dependency tree... 83s Reading state information... 83s Solving dependencies... 84s The following NEW packages will be installed: 84s assemblytics fontconfig fontconfig-config fonts-dejavu-core 84s fonts-dejavu-mono libblas3 libcairo2 libdatrie1 libdeflate0 libfontconfig1 84s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 84s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 84s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 84s libpython3.14-minimal libpython3.14-stdlib libsharpyuv0 libsm6 libtcl8.6 84s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 84s libxft2 libxrender1 libxss1 libxt6t64 python-is-python3 python3-all 84s python3-numpy python3-numpy-dev python3.14 python3.14-minimal r-base-core 84s r-cran-cli r-cran-colorspace r-cran-fansi r-cran-farver r-cran-ggplot2 84s r-cran-glue r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lattice 84s r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix 84s r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig 84s r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp 84s r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8 r-cran-vctrs 84s r-cran-viridislite r-cran-withr unzip x11-common xdg-utils zip 84s 0 upgraded, 85 newly installed, 0 to remove and 0 not upgraded. 84s Need to get 82.1 MB of archives. 84s After this operation, 182 MB of additional disk space will be used. 84s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1ubuntu1 [146 kB] 84s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7 [181 kB] 84s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-9ubuntu1 [450 kB] 85s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7 [2300 kB] 85s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.2.4+ds-1ubuntu1 [3986 kB] 85s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-minimal arm64 3.14.0-4 [903 kB] 85s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14-minimal arm64 3.14.0-4 [2543 kB] 85s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 zip arm64 3.0-15ubuntu2 [175 kB] 85s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 unzip arm64 6.0-28ubuntu7 [176 kB] 85s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 85s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 85s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 85s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 85s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 85s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.15.0-2.3ubuntu1 [38.1 kB] 85s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.15.0-2.3ubuntu1 [144 kB] 85s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 libpixman-1-0 arm64 0.46.4-1 [204 kB] 85s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-render0 arm64 1.17.0-2build1 [18.1 kB] 85s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-shm0 arm64 1.17.0-2build1 [6234 B] 85s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 85s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo2 arm64 1.18.4-1build1 [592 kB] 85s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 85s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-9ubuntu1 [147 kB] 85s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu2 [165 kB] 85s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 85s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig arm64 2.15.0-2.3ubuntu1 [191 kB] 85s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 85s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.1.0-1 [523 kB] 85s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai-data all 0.1.29-2build2 [153 kB] 85s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 libdatrie1 arm64 0.2.14-1 [19.6 kB] 85s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai0 arm64 0.1.29-2build2 [18.4 kB] 85s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 libpango-1.0-0 arm64 1.56.3-2 [237 kB] 85s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangoft2-1.0-0 arm64 1.56.3-2 [50.2 kB] 85s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangocairo-1.0-0 arm64 1.56.3-2 [27.7 kB] 85s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libtcl8.6 arm64 8.6.17+dfsg-1 [1024 kB] 85s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 85s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 85s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 85s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 85s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB] 85s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 85s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 85s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 86s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 libtk8.6 arm64 8.6.17-1 [811 kB] 86s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 86s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 libsm6 arm64 2:1.2.6-1 [16.6 kB] 86s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 libxt6t64 arm64 1:1.2.1-1.3 [168 kB] 86s Get:48 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-base-core arm64 4.5.2-1 [28.6 MB] 87s Get:49 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cli arm64 3.6.4-1 [1374 kB] 87s Get:50 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-glue arm64 1.8.0-1 [163 kB] 87s Get:51 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rlang arm64 1.1.5-3 [1706 kB] 87s Get:52 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 87s Get:53 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 87s Get:54 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-isoband arm64 0.2.7-1 [1481 kB] 87s Get:55 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-mass arm64 7.3-65-1 [1109 kB] 87s Get:56 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lattice arm64 0.22-7-1 [1365 kB] 88s Get:57 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-nlme arm64 3.1.168-1 [2310 kB] 88s Get:58 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-matrix arm64 1.7-4-1 [4146 kB] 88s Get:59 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-mgcv arm64 1.9-3-1 [3324 kB] 88s Get:60 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-farver arm64 2.1.2-1 [1344 kB] 88s Get:61 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-labeling all 0.4.3-1 [62.1 kB] 88s Get:62 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-colorspace arm64 2.1-1+dfsg-1 [1563 kB] 88s Get:63 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-munsell all 0.5.1-1 [213 kB] 88s Get:64 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-r6 all 2.6.1-1 [101 kB] 88s Get:65 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 88s Get:66 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-viridislite all 0.4.2-2 [1088 kB] 88s Get:67 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-scales all 1.3.0-1 [603 kB] 88s Get:68 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-fansi arm64 1.0.6-2 [627 kB] 88s Get:69 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 88s Get:70 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-utf8 arm64 1.2.4-1 [140 kB] 88s Get:71 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB] 88s Get:72 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pillar all 1.10.1+dfsg-1 [453 kB] 88s Get:73 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 88s Get:74 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tibble arm64 3.2.1+dfsg-3 [420 kB] 88s Get:75 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 88s Get:76 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB] 89s Get:77 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-littler arm64 0.3.21-2 [83.6 kB] 89s Get:78 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 89s Get:79 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcpp arm64 1.1.0-1 [2011 kB] 89s Get:80 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-plyr arm64 1.8.9-1 [831 kB] 89s Get:81 http://ftpmaster.internal/ubuntu resolute/universe arm64 assemblytics all 1.2.1+dfsg-2 [19.1 kB] 89s Get:82 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-stdlib arm64 3.14.0-4 [2349 kB] 89s Get:83 http://ftpmaster.internal/ubuntu resolute/main arm64 python-is-python3 all 3.13.3-1 [2768 B] 89s Get:84 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14 arm64 3.14.0-4 [805 kB] 89s Get:85 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-all arm64 3.13.9-2 [892 B] 89s Preconfiguring packages ... 89s Fetched 82.1 MB in 5s (15.8 MB/s) 89s Selecting previously unselected package python3-numpy-dev:arm64. 90s (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 ... 88300 files and directories currently installed.) 90s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 90s Unpacking python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 90s Selecting previously unselected package libblas3:arm64. 90s Preparing to unpack .../01-libblas3_3.12.1-7_arm64.deb ... 90s Unpacking libblas3:arm64 (3.12.1-7) ... 90s Selecting previously unselected package libgfortran5:arm64. 90s Preparing to unpack .../02-libgfortran5_15.2.0-9ubuntu1_arm64.deb ... 90s Unpacking libgfortran5:arm64 (15.2.0-9ubuntu1) ... 90s Selecting previously unselected package liblapack3:arm64. 90s Preparing to unpack .../03-liblapack3_3.12.1-7_arm64.deb ... 90s Unpacking liblapack3:arm64 (3.12.1-7) ... 90s Selecting previously unselected package python3-numpy. 90s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 90s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 90s Selecting previously unselected package libpython3.14-minimal:arm64. 90s Preparing to unpack .../05-libpython3.14-minimal_3.14.0-4_arm64.deb ... 90s Unpacking libpython3.14-minimal:arm64 (3.14.0-4) ... 90s Selecting previously unselected package python3.14-minimal. 90s Preparing to unpack .../06-python3.14-minimal_3.14.0-4_arm64.deb ... 90s Unpacking python3.14-minimal (3.14.0-4) ... 90s Selecting previously unselected package zip. 90s Preparing to unpack .../07-zip_3.0-15ubuntu2_arm64.deb ... 90s Unpacking zip (3.0-15ubuntu2) ... 90s Selecting previously unselected package unzip. 90s Preparing to unpack .../08-unzip_6.0-28ubuntu7_arm64.deb ... 90s Unpacking unzip (6.0-28ubuntu7) ... 90s Selecting previously unselected package libpaper2:arm64. 90s Preparing to unpack .../09-libpaper2_2.2.5-0.3_arm64.deb ... 90s Unpacking libpaper2:arm64 (2.2.5-0.3) ... 90s Selecting previously unselected package libpaper-utils. 90s Preparing to unpack .../10-libpaper-utils_2.2.5-0.3_arm64.deb ... 90s Unpacking libpaper-utils (2.2.5-0.3) ... 90s Selecting previously unselected package xdg-utils. 90s Preparing to unpack .../11-xdg-utils_1.2.1-2ubuntu1_all.deb ... 90s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 90s Selecting previously unselected package fonts-dejavu-mono. 90s Preparing to unpack .../12-fonts-dejavu-mono_2.37-8_all.deb ... 90s Unpacking fonts-dejavu-mono (2.37-8) ... 90s Selecting previously unselected package fonts-dejavu-core. 90s Preparing to unpack .../13-fonts-dejavu-core_2.37-8_all.deb ... 90s Unpacking fonts-dejavu-core (2.37-8) ... 90s Selecting previously unselected package fontconfig-config. 90s Preparing to unpack .../14-fontconfig-config_2.15.0-2.3ubuntu1_arm64.deb ... 91s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 91s Selecting previously unselected package libfontconfig1:arm64. 91s Preparing to unpack .../15-libfontconfig1_2.15.0-2.3ubuntu1_arm64.deb ... 91s Unpacking libfontconfig1:arm64 (2.15.0-2.3ubuntu1) ... 91s Selecting previously unselected package libpixman-1-0:arm64. 91s Preparing to unpack .../16-libpixman-1-0_0.46.4-1_arm64.deb ... 91s Unpacking libpixman-1-0:arm64 (0.46.4-1) ... 91s Selecting previously unselected package libxcb-render0:arm64. 91s Preparing to unpack .../17-libxcb-render0_1.17.0-2build1_arm64.deb ... 91s Unpacking libxcb-render0:arm64 (1.17.0-2build1) ... 91s Selecting previously unselected package libxcb-shm0:arm64. 91s Preparing to unpack .../18-libxcb-shm0_1.17.0-2build1_arm64.deb ... 91s Unpacking libxcb-shm0:arm64 (1.17.0-2build1) ... 91s Selecting previously unselected package libxrender1:arm64. 91s Preparing to unpack .../19-libxrender1_1%3a0.9.12-1_arm64.deb ... 91s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 91s Selecting previously unselected package libcairo2:arm64. 91s Preparing to unpack .../20-libcairo2_1.18.4-1build1_arm64.deb ... 91s Unpacking libcairo2:arm64 (1.18.4-1build1) ... 91s Selecting previously unselected package libdeflate0:arm64. 91s Preparing to unpack .../21-libdeflate0_1.23-2_arm64.deb ... 91s Unpacking libdeflate0:arm64 (1.23-2) ... 91s Selecting previously unselected package libgomp1:arm64. 91s Preparing to unpack .../22-libgomp1_15.2.0-9ubuntu1_arm64.deb ... 91s Unpacking libgomp1:arm64 (15.2.0-9ubuntu1) ... 91s Selecting previously unselected package libjpeg-turbo8:arm64. 91s Preparing to unpack .../23-libjpeg-turbo8_2.1.5-4ubuntu2_arm64.deb ... 91s Unpacking libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 91s Selecting previously unselected package libjpeg8:arm64. 91s Preparing to unpack .../24-libjpeg8_8c-2ubuntu11_arm64.deb ... 91s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 91s Selecting previously unselected package fontconfig. 91s Preparing to unpack .../25-fontconfig_2.15.0-2.3ubuntu1_arm64.deb ... 91s Unpacking fontconfig (2.15.0-2.3ubuntu1) ... 91s Selecting previously unselected package libgraphite2-3:arm64. 91s Preparing to unpack .../26-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 91s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 91s Selecting previously unselected package libharfbuzz0b:arm64. 91s Preparing to unpack .../27-libharfbuzz0b_12.1.0-1_arm64.deb ... 91s Unpacking libharfbuzz0b:arm64 (12.1.0-1) ... 91s Selecting previously unselected package libthai-data. 91s Preparing to unpack .../28-libthai-data_0.1.29-2build2_all.deb ... 91s Unpacking libthai-data (0.1.29-2build2) ... 91s Selecting previously unselected package libdatrie1:arm64. 91s Preparing to unpack .../29-libdatrie1_0.2.14-1_arm64.deb ... 91s Unpacking libdatrie1:arm64 (0.2.14-1) ... 91s Selecting previously unselected package libthai0:arm64. 91s Preparing to unpack .../30-libthai0_0.1.29-2build2_arm64.deb ... 91s Unpacking libthai0:arm64 (0.1.29-2build2) ... 91s Selecting previously unselected package libpango-1.0-0:arm64. 91s Preparing to unpack .../31-libpango-1.0-0_1.56.3-2_arm64.deb ... 91s Unpacking libpango-1.0-0:arm64 (1.56.3-2) ... 91s Selecting previously unselected package libpangoft2-1.0-0:arm64. 91s Preparing to unpack .../32-libpangoft2-1.0-0_1.56.3-2_arm64.deb ... 91s Unpacking libpangoft2-1.0-0:arm64 (1.56.3-2) ... 91s Selecting previously unselected package libpangocairo-1.0-0:arm64. 91s Preparing to unpack .../33-libpangocairo-1.0-0_1.56.3-2_arm64.deb ... 91s Unpacking libpangocairo-1.0-0:arm64 (1.56.3-2) ... 91s Selecting previously unselected package libtcl8.6:arm64. 92s Preparing to unpack .../34-libtcl8.6_8.6.17+dfsg-1_arm64.deb ... 92s Unpacking libtcl8.6:arm64 (8.6.17+dfsg-1) ... 92s Selecting previously unselected package libjbig0:arm64. 92s Preparing to unpack .../35-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 92s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 92s Selecting previously unselected package liblerc4:arm64. 92s Preparing to unpack .../36-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 92s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 92s Selecting previously unselected package libsharpyuv0:arm64. 92s Preparing to unpack .../37-libsharpyuv0_1.5.0-0.1_arm64.deb ... 92s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 92s Selecting previously unselected package libwebp7:arm64. 92s Preparing to unpack .../38-libwebp7_1.5.0-0.1_arm64.deb ... 92s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 92s Selecting previously unselected package libtiff6:arm64. 92s Preparing to unpack .../39-libtiff6_4.7.0-3ubuntu3_arm64.deb ... 92s Unpacking libtiff6:arm64 (4.7.0-3ubuntu3) ... 92s Selecting previously unselected package libxft2:arm64. 92s Preparing to unpack .../40-libxft2_2.3.6-1build1_arm64.deb ... 92s Unpacking libxft2:arm64 (2.3.6-1build1) ... 92s Selecting previously unselected package x11-common. 92s Preparing to unpack .../41-x11-common_1%3a7.7+24ubuntu1_all.deb ... 92s Unpacking x11-common (1:7.7+24ubuntu1) ... 92s Selecting previously unselected package libxss1:arm64. 92s Preparing to unpack .../42-libxss1_1%3a1.2.3-1build3_arm64.deb ... 92s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 92s Selecting previously unselected package libtk8.6:arm64. 92s Preparing to unpack .../43-libtk8.6_8.6.17-1_arm64.deb ... 92s Unpacking libtk8.6:arm64 (8.6.17-1) ... 92s Selecting previously unselected package libice6:arm64. 92s Preparing to unpack .../44-libice6_2%3a1.1.1-1_arm64.deb ... 92s Unpacking libice6:arm64 (2:1.1.1-1) ... 92s Selecting previously unselected package libsm6:arm64. 92s Preparing to unpack .../45-libsm6_2%3a1.2.6-1_arm64.deb ... 92s Unpacking libsm6:arm64 (2:1.2.6-1) ... 92s Selecting previously unselected package libxt6t64:arm64. 92s Preparing to unpack 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to unpack .../52-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 93s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 93s Selecting previously unselected package r-cran-isoband. 93s Preparing to unpack .../53-r-cran-isoband_0.2.7-1_arm64.deb ... 93s Unpacking r-cran-isoband (0.2.7-1) ... 93s Selecting previously unselected package r-cran-mass. 93s Preparing to unpack .../54-r-cran-mass_7.3-65-1_arm64.deb ... 93s Unpacking r-cran-mass (7.3-65-1) ... 93s Selecting previously unselected package r-cran-lattice. 93s Preparing to unpack .../55-r-cran-lattice_0.22-7-1_arm64.deb ... 93s Unpacking r-cran-lattice (0.22-7-1) ... 93s Selecting previously unselected package r-cran-nlme. 93s Preparing to unpack .../56-r-cran-nlme_3.1.168-1_arm64.deb ... 93s Unpacking r-cran-nlme (3.1.168-1) ... 93s Selecting previously unselected package r-cran-matrix. 93s Preparing to unpack .../57-r-cran-matrix_1.7-4-1_arm64.deb ... 93s Unpacking r-cran-matrix (1.7-4-1) ... 93s Selecting previously unselected package r-cran-mgcv. 93s Preparing to unpack .../58-r-cran-mgcv_1.9-3-1_arm64.deb ... 93s Unpacking r-cran-mgcv (1.9-3-1) ... 93s Selecting previously unselected package r-cran-farver. 93s Preparing to unpack .../59-r-cran-farver_2.1.2-1_arm64.deb ... 93s Unpacking r-cran-farver (2.1.2-1) ... 93s Selecting previously unselected package r-cran-labeling. 93s Preparing to unpack .../60-r-cran-labeling_0.4.3-1_all.deb ... 93s Unpacking r-cran-labeling (0.4.3-1) ... 93s Selecting previously unselected package r-cran-colorspace. 93s Preparing to unpack .../61-r-cran-colorspace_2.1-1+dfsg-1_arm64.deb ... 93s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ... 93s Selecting previously unselected package r-cran-munsell. 93s Preparing to unpack .../62-r-cran-munsell_0.5.1-1_all.deb ... 93s Unpacking r-cran-munsell (0.5.1-1) ... 93s Selecting previously unselected package r-cran-r6. 93s Preparing to unpack .../63-r-cran-r6_2.6.1-1_all.deb ... 93s Unpacking r-cran-r6 (2.6.1-1) ... 93s Selecting previously unselected package r-cran-rcolorbrewer. 93s Preparing to unpack .../64-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ... 93s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ... 93s Selecting previously unselected package r-cran-viridislite. 93s Preparing to unpack .../65-r-cran-viridislite_0.4.2-2_all.deb ... 93s Unpacking r-cran-viridislite (0.4.2-2) ... 93s Selecting previously unselected package r-cran-scales. 93s Preparing to unpack .../66-r-cran-scales_1.3.0-1_all.deb ... 93s Unpacking r-cran-scales (1.3.0-1) ... 93s Selecting previously unselected package r-cran-fansi. 93s Preparing to unpack .../67-r-cran-fansi_1.0.6-2_arm64.deb ... 93s Unpacking r-cran-fansi (1.0.6-2) ... 93s Selecting previously unselected package r-cran-magrittr. 93s Preparing to unpack .../68-r-cran-magrittr_2.0.3-1_arm64.deb ... 93s Unpacking r-cran-magrittr (2.0.3-1) ... 93s Selecting previously unselected package r-cran-utf8. 93s Preparing to unpack .../69-r-cran-utf8_1.2.4-1_arm64.deb ... 93s Unpacking 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libpython3.14-stdlib:arm64. 94s Preparing to unpack .../81-libpython3.14-stdlib_3.14.0-4_arm64.deb ... 94s Unpacking libpython3.14-stdlib:arm64 (3.14.0-4) ... 94s Selecting previously unselected package python-is-python3. 94s Preparing to unpack .../82-python-is-python3_3.13.3-1_all.deb ... 94s Unpacking python-is-python3 (3.13.3-1) ... 94s Selecting previously unselected package python3.14. 94s Preparing to unpack .../83-python3.14_3.14.0-4_arm64.deb ... 94s Unpacking python3.14 (3.14.0-4) ... 94s Selecting previously unselected package python3-all. 94s Preparing to unpack .../84-python3-all_3.13.9-2_arm64.deb ... 94s Unpacking python3-all (3.13.9-2) ... 94s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 94s Setting up libpixman-1-0:arm64 (0.46.4-1) ... 94s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 94s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 94s Setting up libxrender1:arm64 (1:0.9.12-1) ... 94s Setting up libdatrie1:arm64 (0.2.14-1) ... 94s Setting up libxcb-render0:arm64 (1.17.0-2build1) ... 94s Setting up unzip (6.0-28ubuntu7) ... 94s Setting up libpython3.14-minimal:arm64 (3.14.0-4) ... 94s Setting up x11-common (1:7.7+24ubuntu1) ... 95s Setting up libdeflate0:arm64 (1.23-2) ... 95s Setting up libxcb-shm0:arm64 (1.17.0-2build1) ... 95s Setting up libgomp1:arm64 (15.2.0-9ubuntu1) ... 95s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 95s Setting up zip (3.0-15ubuntu2) ... 95s Setting up libblas3:arm64 (3.12.1-7) ... 95s 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 95s Setting up fonts-dejavu-mono (2.37-8) ... 95s Setting up python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 95s Setting up libtcl8.6:arm64 (8.6.17+dfsg-1) ... 95s Setting up fonts-dejavu-core (2.37-8) ... 95s Setting up libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 95s Setting up libgfortran5:arm64 (15.2.0-9ubuntu1) ... 95s Setting up libwebp7:arm64 (1.5.0-0.1) ... 95s Setting up libharfbuzz0b:arm64 (12.1.0-1) ... 95s Setting up libthai-data (0.1.29-2build2) ... 95s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 95s Setting up libpaper2:arm64 (2.2.5-0.3) ... 95s Setting up python-is-python3 (3.13.3-1) ... 95s Setting up xdg-utils (1.2.1-2ubuntu1) ... 95s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 95s Setting up python3.14-minimal (3.14.0-4) ... 96s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 96s Setting up libice6:arm64 (2:1.1.1-1) ... 96s Setting up liblapack3:arm64 (3.12.1-7) ... 96s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 96s Setting up libpython3.14-stdlib:arm64 (3.14.0-4) ... 96s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 96s Setting up libpaper-utils (2.2.5-0.3) ... 96s Setting up libthai0:arm64 (0.1.29-2build2) ... 96s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 100s Setting up libtiff6:arm64 (4.7.0-3ubuntu3) ... 100s Setting up libfontconfig1:arm64 (2.15.0-2.3ubuntu1) ... 100s Setting up python3.14 (3.14.0-4) ... 101s Setting up libsm6:arm64 (2:1.2.6-1) ... 101s Setting up fontconfig (2.15.0-2.3ubuntu1) ... 103s Regenerating fonts cache... done. 103s Setting up libxft2:arm64 (2.3.6-1build1) ... 103s Setting up libtk8.6:arm64 (8.6.17-1) ... 103s Setting up libpango-1.0-0:arm64 (1.56.3-2) ... 103s Setting up python3-all (3.13.9-2) ... 103s Setting up libcairo2:arm64 (1.18.4-1build1) ... 103s Setting up libxt6t64:arm64 (1:1.2.1-1.3) ... 103s Setting up libpangoft2-1.0-0:arm64 (1.56.3-2) ... 103s Setting up libpangocairo-1.0-0:arm64 (1.56.3-2) ... 103s Setting up r-base-core (4.5.2-1) ... 103s Creating config file /etc/R/Renviron with new version 104s Setting up r-cran-labeling (0.4.3-1) ... 104s Setting up r-cran-lattice (0.22-7-1) ... 104s Setting up r-cran-nlme (3.1.168-1) ... 104s Setting up r-cran-farver (2.1.2-1) ... 104s Setting up r-cran-viridislite (0.4.2-2) ... 104s Setting up r-cran-r6 (2.6.1-1) ... 104s Setting up r-cran-pkgkitten (0.2.4-1) ... 104s Setting up r-cran-magrittr (2.0.3-1) ... 104s Setting up r-cran-littler (0.3.21-2) ... 104s Setting up r-cran-rcpp (1.1.0-1) ... 104s Setting up r-cran-rlang (1.1.5-3) ... 104s Setting up r-cran-withr (3.0.2+dfsg-1) ... 104s Setting up r-cran-fansi (1.0.6-2) ... 104s Setting up r-cran-mass (7.3-65-1) ... 104s Setting up r-cran-glue (1.8.0-1) ... 104s Setting up r-cran-cli (3.6.4-1) ... 104s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... 104s Setting up r-cran-pkgconfig (2.0.3-2build2) ... 104s Setting up r-cran-utf8 (1.2.4-1) ... 104s Setting up r-cran-colorspace (2.1-1+dfsg-1) ... 104s Setting up r-cran-plyr (1.8.9-1) ... 104s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ... 104s Setting up r-cran-isoband (0.2.7-1) ... 104s Setting up r-cran-gtable (0.3.6+dfsg-1) ... 104s Setting up r-cran-matrix (1.7-4-1) ... 104s Setting up r-cran-mgcv (1.9-3-1) ... 104s Setting up r-cran-vctrs (0.6.5-1) ... 104s Setting up r-cran-pillar (1.10.1+dfsg-1) ... 104s Setting up r-cran-munsell (0.5.1-1) ... 104s Setting up r-cran-tibble (3.2.1+dfsg-3) ... 104s Setting up r-cran-scales (1.3.0-1) ... 104s Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... 104s Setting up assemblytics (1.2.1+dfsg-2) ... 104s Processing triggers for systemd (257.9-0ubuntu2) ... 104s Processing triggers for man-db (2.13.1-1) ... 105s Processing triggers for install-info (7.2-5) ... 105s Processing triggers for libc-bin (2.42-2ubuntu2) ... 106s autopkgtest [13:55:31]: test run-unit-test: [----------------------- 106s Input delta file: sample.delta 106s Output prefix: myfirstorganism 106s Unique anchor length: 10000 106s Minimum variant size to call: 10000 106s Maximum variant size to call: 50 106s script path: /usr/share/assemblytics/bin 106s Logging progress updates in myfirstorganism/progress.log 106s 1. Filter delta file 106s Keeping fully unique alignments even if they are below the unique anchor length of 10000 bp 106s 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. 106s Detected uncompressed delta file. Reading... 106s 106s 106s Header (2 lines): 106s /seq/schatz/mnattest/Assemblytics/Ecoli/GCF_000005845.2_ASM584v2_genomic.fna /seq/schatz/mnattest/Assemblytics/Ecoli/GCF_000801205.1_ASM80120v1_genomic.fna 106s NUCMER 106s 106s 106s First read through the file: 0 seconds for 0 query-reference combinations 106s Filtering alignments of 1 queries 106s Progress: 100% 106s Progress: 100% 106s Deciding which alignments to keep: 0 seconds for 1 queries 106s Detected uncompressed delta file. Reading... 106s Reading file and recording all the entries we decided to keep: 0 seconds for 54 total lines in file 106s 2. Finding variants between alignments 106s Loaded 6 alignments 106s 3. Finding variants within alignments 106s Detected gzipped delta file. Reading... 106s 106s 106s Header (2 lines): 106s /seq/schatz/mnattest/Assemblytics/Ecoli/GCF_000005845.2_ASM584v2_genomic.fna /seq/schatz/mnattest/Assemblytics/Ecoli/GCF_000801205.1_ASM80120v1_genomic.fna 106s NUCMER 106s 106s 106s 4. Combine variants between and within alignments 107s Error in revalue(bed$type, c(Repeat_expansion = "Repeat expansion", Repeat_contraction = "Repeat contraction", : 107s x is not a factor or a character vector. 107s Execution halted 108s Warning messages: 108s 1: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. 108s ℹ Please use `linewidth` instead. 108s 2: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0. 108s ℹ Please use the `linewidth` argument instead. 108s null device 108s 1 110s Warning message: 110s Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. 110s ℹ Please use `linewidth` instead. 110s adding: myfirstorganism.Assemblytics.Dotplot_filtered.png (deflated 11%) 110s adding: myfirstorganism.Assemblytics.Nchart.pdf (deflated 11%) 110s adding: myfirstorganism.Assemblytics.Nchart.png (deflated 6%) 110s adding: myfirstorganism.Assemblytics.unique_length_filtered_l10000.delta.gz (stored 0%) 110s adding: myfirstorganism.Assemblytics_assembly_stats.txt (deflated 58%) 110s adding: myfirstorganism.Assemblytics_structural_variants.bed (deflated 26%) 110s adding: myfirstorganism.Assemblytics_structural_variants.summary (deflated 49%) 110s adding: myfirstorganism.Assemblytics_structural_variants.summary.csv (deflated 35%) 110s PASS 110s autopkgtest [13:55:35]: test run-unit-test: -----------------------] 111s run-unit-test PASS 111s autopkgtest [13:55:36]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 112s autopkgtest [13:55:37]: @@@@@@@@@@@@@@@@@@@@ summary 112s run-unit-test PASS