0s autopkgtest [06:52:03]: starting date and time: 2025-12-04 06:52:03+0000 0s autopkgtest [06:52:03]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [06:52:03]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.vw28j2k7/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade mapdamage --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-2@sto01-9.secgroup --name adt-resolute-amd64-mapdamage-20251204-065202-juju-7f2275-prod-proposed-migration-environment-2-094d6249-aced-4fc3-8dcd-0a591a0de282 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-amd64-mapdamage-20251204-065202-juju-7f2275-prod-proposed-migration-environment-2-094d6249-aced-4fc3-8dcd-0a591a0de282 from image adt/ubuntu-resolute-amd64-server-20251204.img (UUID 51c52a3c-b973-44be-bcc8-3a3ff6355fda)... 52s autopkgtest [06:52:55]: testbed dpkg architecture: amd64 53s autopkgtest [06:52:56]: testbed apt version: 3.1.12 53s autopkgtest [06:52:56]: @@@@@@@@@@@@@@@@@@@@ test bed setup 53s autopkgtest [06:52:56]: testbed release detected to be: None 54s autopkgtest [06:52:57]: updating testbed package index (apt update) 54s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 54s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 54s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 54s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 54s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [152 kB] 54s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [23.1 kB] 54s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [928 kB] 54s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [218 kB] 54s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [162 kB] 54s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [6652 B] 54s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [120 B] 54s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [752 kB] 54s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [344 kB] 55s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [24.1 kB] 55s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4040 B] 55s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [9636 B] 55s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [748 B] 55s Fetched 2749 kB in 1s (3308 kB/s) 56s Reading package lists... 56s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 56s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 56s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 56s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 57s Reading package lists... 57s Reading package lists... 57s Building dependency tree... 57s Reading state information... 57s Calculating upgrade... 57s The following packages will be upgraded: 57s libpython3-stdlib python3 python3-gdbm python3-minimal 57s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 57s Need to get 72.9 kB of archives. 57s After this operation, 2048 B of additional disk space will be used. 57s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.13.9-2 [28.1 kB] 57s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.13.9-2 [23.0 kB] 57s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.13.9-2 [10.8 kB] 57s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-gdbm amd64 3.13.9-2 [11.0 kB] 58s dpkg-preconfigure: unable to re-open stdin: No such file or directory 58s Fetched 72.9 kB in 0s (0 B/s) 58s (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 ... 83537 files and directories currently installed.) 58s Preparing to unpack .../python3-minimal_3.13.9-2_amd64.deb ... 58s Unpacking python3-minimal (3.13.9-2) over (3.13.7-1) ... 58s Setting up python3-minimal (3.13.9-2) ... 58s (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 ... 83537 files and directories currently installed.) 58s Preparing to unpack .../python3_3.13.9-2_amd64.deb ... 58s running python pre-rtupdate hooks for python3.13... 58s Unpacking python3 (3.13.9-2) over (3.13.7-1) ... 58s Preparing to unpack .../libpython3-stdlib_3.13.9-2_amd64.deb ... 58s Unpacking libpython3-stdlib:amd64 (3.13.9-2) over (3.13.7-1) ... 58s Preparing to unpack .../python3-gdbm_3.13.9-2_amd64.deb ... 58s Unpacking python3-gdbm (3.13.9-2) over (3.13.9-1) ... 58s Setting up python3-gdbm (3.13.9-2) ... 58s Setting up libpython3-stdlib:amd64 (3.13.9-2) ... 58s Setting up python3 (3.13.9-2) ... 58s running python rtupdate hooks for python3.13... 58s running python post-rtupdate hooks for python3.13... 58s Processing triggers for man-db (2.13.1-1) ... 58s autopkgtest [06:53:01]: upgrading testbed (apt dist-upgrade and autopurge) 59s Reading package lists... 59s Building dependency tree... 59s Reading state information... 59s Calculating upgrade... 59s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 59s Reading package lists... 59s Building dependency tree... 59s Reading state information... 59s Solving dependencies... 59s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 62s autopkgtest [06:53:05]: testbed running kernel: Linux 6.17.0-6-generic #6-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 7 13:34:17 UTC 2025 62s autopkgtest [06:53:05]: @@@@@@@@@@@@@@@@@@@@ apt-source mapdamage 63s Get:1 http://ftpmaster.internal/ubuntu resolute/universe mapdamage 2.2.2+dfsg-1 (dsc) [2396 B] 63s Get:2 http://ftpmaster.internal/ubuntu resolute/universe mapdamage 2.2.2+dfsg-1 (tar) [36.2 kB] 63s Get:3 http://ftpmaster.internal/ubuntu resolute/universe mapdamage 2.2.2+dfsg-1 (diff) [7824 B] 63s gpgv: Signature made Sun Aug 25 16:49:00 2024 UTC 63s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 63s gpgv: issuer "emollier@debian.org" 63s gpgv: Can't check signature: No public key 63s dpkg-source: warning: cannot verify inline signature for ./mapdamage_2.2.2+dfsg-1.dsc: no acceptable signature found 63s autopkgtest [06:53:06]: testing package mapdamage version 2.2.2+dfsg-1 63s autopkgtest [06:53:06]: build not needed 63s autopkgtest [06:53:06]: test run-unit-test: preparing testbed 63s Reading package lists... 63s Building dependency tree... 63s Reading state information... 64s Solving dependencies... 64s The following NEW packages will be installed: 64s cpp cpp-15 cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu fontconfig 64s fontconfig-config fonts-dejavu-core fonts-dejavu-mono gcc gcc-15 64s gcc-15-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-15 64s gfortran-15-x86-64-linux-gnu gfortran-x86-64-linux-gnu libasan8 libblas3 64s libcairo2 libcc1-0 libdatrie1 libdeflate0 libfontconfig1 libgcc-15-dev 64s libgfortran-15-dev libgfortran5 libgomp1 libgraphite2-3 libgsl-dev libgsl28 64s libgslcblas0 libharfbuzz0b libhts3t64 libhtscodecs2 libhwasan0 libice6 64s libisl23 libitm1 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 64s liblsan0 libmpc3 libopenblas-dev libopenblas-pthread-dev libopenblas0 64s libopenblas0-pthread libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 64s libpaper-utils libpaper2 libpixman-1-0 libquadmath0 libsharpyuv0 libsm6 64s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libtsan2 libubsan1 64s libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 64s mapdamage python3-pysam r-base-core r-cran-cli r-cran-codetools 64s r-cran-colorspace r-cran-fansi r-cran-farver r-cran-foreach r-cran-gam 64s r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-inline r-cran-isoband 64s r-cran-iterators r-cran-labeling r-cran-lattice r-cran-lifecycle 64s r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv 64s r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten 64s r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rcppgsl r-cran-rlang 64s r-cran-runit r-cran-scales r-cran-tibble r-cran-utf8 r-cran-vctrs 64s r-cran-viridislite r-cran-withr seqtk unzip x11-common xdg-utils zip 64s 0 upgraded, 118 newly installed, 0 to remove and 0 not upgraded. 64s Need to get 160 MB of archives. 64s After this operation, 524 MB of additional disk space will be used. 64s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 libisl23 amd64 0.27-1 [685 kB] 64s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libmpc3 amd64 1.3.1-2 [54.8 kB] 64s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-9ubuntu1 [12.9 MB] 64s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15 amd64 15.2.0-9ubuntu1 [1030 B] 64s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [5746 B] 64s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp amd64 4:15.2.0-4ubuntu1 [22.4 kB] 64s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 64s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 64s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.15.0-2.3ubuntu1 [38.0 kB] 64s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.15.0-2.3ubuntu1 [141 kB] 64s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig amd64 2.15.0-2.3ubuntu1 [180 kB] 64s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libcc1-0 amd64 15.2.0-9ubuntu1 [47.4 kB] 64s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-9ubuntu1 [151 kB] 64s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libitm1 amd64 15.2.0-9ubuntu1 [29.6 kB] 64s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libasan8 amd64 15.2.0-9ubuntu1 [3071 kB] 65s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsan0 amd64 15.2.0-9ubuntu1 [1360 kB] 65s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libtsan2 amd64 15.2.0-9ubuntu1 [2757 kB] 65s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libubsan1 amd64 15.2.0-9ubuntu1 [1210 kB] 65s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libhwasan0 amd64 15.2.0-9ubuntu1 [1685 kB] 65s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libquadmath0 amd64 15.2.0-9ubuntu1 [153 kB] 65s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-15-dev amd64 15.2.0-9ubuntu1 [2863 kB] 65s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-9ubuntu1 [25.4 MB] 70s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15 amd64 15.2.0-9ubuntu1 [527 kB] 70s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1208 B] 70s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc amd64 4:15.2.0-4ubuntu1 [5024 B] 70s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-9ubuntu1 [939 kB] 70s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran-15-dev amd64 15.2.0-9ubuntu1 [972 kB] 71s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.2.0-9ubuntu1 [13.6 MB] 73s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-15 amd64 15.2.0-9ubuntu1 [17.9 kB] 73s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1014 B] 73s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran amd64 4:15.2.0-4ubuntu1 [1172 B] 73s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7 [259 kB] 73s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB] 73s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2build1 [17.4 kB] 73s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2build1 [6120 B] 73s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 73s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-1build1 [611 kB] 73s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libdatrie1 amd64 0.2.14-1 [19.8 kB] 73s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 73s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 73s Get:41 http://ftpmaster.internal/ubuntu resolute/universe amd64 libgslcblas0 amd64 2.8+dfsg-5.1ubuntu1 [133 kB] 74s Get:42 http://ftpmaster.internal/ubuntu resolute/universe amd64 libgsl28 amd64 2.8+dfsg-5.1ubuntu1 [1104 kB] 74s Get:43 http://ftpmaster.internal/ubuntu resolute/universe amd64 libgsl-dev amd64 2.8+dfsg-5.1ubuntu1 [1433 kB] 74s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.1.0-1 [535 kB] 74s Get:45 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhtscodecs2 amd64 1.6.1-2 [132 kB] 74s Get:46 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhts3t64 amd64 1.22.1+ds2-1 [461 kB] 74s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 74s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 74s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB] 74s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 74s Get:51 http://ftpmaster.internal/ubuntu resolute/universe amd64 libopenblas0-pthread amd64 0.3.30+ds-3 [5382 kB] 75s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7 [2739 kB] 75s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 75s Get:54 http://ftpmaster.internal/ubuntu resolute/universe amd64 libopenblas0 amd64 0.3.30+ds-3 [6304 B] 75s Get:55 http://ftpmaster.internal/ubuntu resolute/universe amd64 libopenblas-pthread-dev amd64 0.3.30+ds-3 [5107 kB] 76s Get:56 http://ftpmaster.internal/ubuntu resolute/universe amd64 libopenblas-dev amd64 0.3.30+ds-3 [21.3 kB] 76s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai-data all 0.1.29-2build2 [153 kB] 76s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai0 amd64 0.1.29-2build2 [19.2 kB] 76s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libpango-1.0-0 amd64 1.56.3-2 [239 kB] 76s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoft2-1.0-0 amd64 1.56.3-2 [52.5 kB] 76s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangocairo-1.0-0 amd64 1.56.3-2 [29.0 kB] 76s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB] 76s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB] 76s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 76s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 libsm6 amd64 2:1.2.6-1 [16.4 kB] 76s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1036 kB] 76s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 76s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 76s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 76s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 76s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 76s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB] 76s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libxt6t64 amd64 1:1.2.1-1.3 [173 kB] 76s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 zip amd64 3.0-15ubuntu2 [178 kB] 76s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 unzip amd64 6.0-28ubuntu7 [180 kB] 76s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 76s Get:77 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-core amd64 4.5.2-1 [28.8 MB] 82s Get:78 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-codetools all 0.2-20-1 [90.5 kB] 82s Get:79 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-iterators all 1.0.14-1build1 [336 kB] 82s Get:80 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-foreach all 1.5.2-1build1 [124 kB] 82s Get:81 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gam amd64 1.22-5-1 [394 kB] 82s Get:82 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB] 82s Get:83 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB] 82s Get:84 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rlang amd64 1.1.5-3 [1721 kB] 82s Get:85 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 83s Get:86 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 83s Get:87 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-isoband amd64 0.2.7-1 [1481 kB] 83s Get:88 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mass amd64 7.3-65-1 [1116 kB] 83s Get:89 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lattice amd64 0.22-7-1 [1367 kB] 83s Get:90 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-nlme amd64 3.1.168-1 [2320 kB] 84s Get:91 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrix amd64 1.7-4-1 [4220 kB] 84s Get:92 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mgcv amd64 1.9-3-1 [3414 kB] 85s Get:93 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-farver amd64 2.1.2-1 [1355 kB] 85s Get:94 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-labeling all 0.4.3-1 [62.1 kB] 85s Get:95 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1563 kB] 85s Get:96 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-munsell all 0.5.1-1 [213 kB] 85s Get:97 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r6 all 2.6.1-1 [101 kB] 85s Get:98 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 85s Get:99 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-viridislite all 0.4.2-2 [1088 kB] 85s Get:100 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-scales all 1.3.0-1 [603 kB] 85s Get:101 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fansi amd64 1.0.6-2 [626 kB] 86s Get:102 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB] 86s Get:103 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-utf8 amd64 1.2.4-1 [140 kB] 86s Get:104 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB] 86s Get:105 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pillar all 1.10.1+dfsg-1 [453 kB] 86s Get:106 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 86s Get:107 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [419 kB] 86s Get:108 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 86s Get:109 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB] 86s Get:110 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-inline all 0.3.21-1 [131 kB] 86s Get:111 http://ftpmaster.internal/ubuntu resolute/universe amd64 seqtk amd64 1.4-2 [34.6 kB] 86s Get:112 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pysam amd64 0.23.3+ds-2 [4536 kB] 87s Get:113 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-littler amd64 0.3.21-2 [84.4 kB] 87s Get:114 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 87s Get:115 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcpp amd64 1.1.0-1 [2021 kB] 87s Get:116 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcppgsl amd64 0.3.13-1build1 [199 kB] 87s Get:117 http://ftpmaster.internal/ubuntu resolute/universe amd64 mapdamage all 2.2.2+dfsg-1 [43.3 kB] 87s Get:118 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-runit all 0.4.33.1-1 [250 kB] 87s Preconfiguring packages ... 87s Fetched 160 MB in 23s (6822 kB/s) 87s Selecting previously unselected package libisl23:amd64. 87s (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 ... 83537 files and directories currently installed.) 87s Preparing to unpack .../000-libisl23_0.27-1_amd64.deb ... 87s Unpacking libisl23:amd64 (0.27-1) ... 87s Selecting previously unselected package libmpc3:amd64. 87s Preparing to unpack .../001-libmpc3_1.3.1-2_amd64.deb ... 87s Unpacking libmpc3:amd64 (1.3.1-2) ... 87s Selecting previously unselected package cpp-15-x86-64-linux-gnu. 87s Preparing to unpack .../002-cpp-15-x86-64-linux-gnu_15.2.0-9ubuntu1_amd64.deb ... 87s Unpacking cpp-15-x86-64-linux-gnu (15.2.0-9ubuntu1) ... 87s Selecting previously unselected package cpp-15. 87s Preparing to unpack .../003-cpp-15_15.2.0-9ubuntu1_amd64.deb ... 87s Unpacking cpp-15 (15.2.0-9ubuntu1) ... 87s Selecting previously unselected package cpp-x86-64-linux-gnu. 88s Preparing to unpack .../004-cpp-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 88s Unpacking cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 88s Selecting previously unselected package cpp. 88s Preparing to unpack .../005-cpp_4%3a15.2.0-4ubuntu1_amd64.deb ... 88s Unpacking cpp (4:15.2.0-4ubuntu1) ... 88s Selecting previously unselected package fonts-dejavu-mono. 88s Preparing to unpack .../006-fonts-dejavu-mono_2.37-8_all.deb ... 88s Unpacking fonts-dejavu-mono (2.37-8) ... 88s Selecting previously unselected package fonts-dejavu-core. 88s Preparing to unpack .../007-fonts-dejavu-core_2.37-8_all.deb ... 88s Unpacking fonts-dejavu-core (2.37-8) ... 88s Selecting previously unselected package fontconfig-config. 88s Preparing to unpack .../008-fontconfig-config_2.15.0-2.3ubuntu1_amd64.deb ... 88s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 88s Selecting previously unselected package libfontconfig1:amd64. 88s Preparing to unpack .../009-libfontconfig1_2.15.0-2.3ubuntu1_amd64.deb ... 88s Unpacking libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 88s Selecting previously unselected package fontconfig. 88s Preparing to unpack .../010-fontconfig_2.15.0-2.3ubuntu1_amd64.deb ... 88s Unpacking fontconfig (2.15.0-2.3ubuntu1) ... 88s Selecting previously unselected package libcc1-0:amd64. 88s Preparing to unpack .../011-libcc1-0_15.2.0-9ubuntu1_amd64.deb ... 88s Unpacking libcc1-0:amd64 (15.2.0-9ubuntu1) ... 88s Selecting previously unselected package libgomp1:amd64. 88s Preparing to unpack .../012-libgomp1_15.2.0-9ubuntu1_amd64.deb ... 88s Unpacking libgomp1:amd64 (15.2.0-9ubuntu1) ... 88s Selecting previously unselected package libitm1:amd64. 88s Preparing to unpack .../013-libitm1_15.2.0-9ubuntu1_amd64.deb ... 88s Unpacking libitm1:amd64 (15.2.0-9ubuntu1) ... 88s Selecting previously unselected package libasan8:amd64. 88s Preparing to unpack .../014-libasan8_15.2.0-9ubuntu1_amd64.deb ... 88s Unpacking libasan8:amd64 (15.2.0-9ubuntu1) ... 88s Selecting previously unselected package liblsan0:amd64. 88s Preparing to unpack .../015-liblsan0_15.2.0-9ubuntu1_amd64.deb ... 88s Unpacking liblsan0:amd64 (15.2.0-9ubuntu1) ... 88s Selecting previously unselected package libtsan2:amd64. 88s Preparing to unpack .../016-libtsan2_15.2.0-9ubuntu1_amd64.deb ... 88s Unpacking libtsan2:amd64 (15.2.0-9ubuntu1) ... 88s Selecting previously unselected package libubsan1:amd64. 88s Preparing to unpack .../017-libubsan1_15.2.0-9ubuntu1_amd64.deb ... 88s Unpacking libubsan1:amd64 (15.2.0-9ubuntu1) ... 88s Selecting previously unselected package libhwasan0:amd64. 88s Preparing to unpack .../018-libhwasan0_15.2.0-9ubuntu1_amd64.deb ... 88s Unpacking libhwasan0:amd64 (15.2.0-9ubuntu1) ... 88s Selecting previously unselected package libquadmath0:amd64. 88s Preparing to unpack .../019-libquadmath0_15.2.0-9ubuntu1_amd64.deb ... 88s Unpacking libquadmath0:amd64 (15.2.0-9ubuntu1) ... 88s Selecting previously unselected package libgcc-15-dev:amd64. 88s Preparing to unpack .../020-libgcc-15-dev_15.2.0-9ubuntu1_amd64.deb ... 88s Unpacking libgcc-15-dev:amd64 (15.2.0-9ubuntu1) ... 88s Selecting previously unselected package gcc-15-x86-64-linux-gnu. 88s Preparing to unpack .../021-gcc-15-x86-64-linux-gnu_15.2.0-9ubuntu1_amd64.deb ... 88s Unpacking gcc-15-x86-64-linux-gnu (15.2.0-9ubuntu1) ... 88s Selecting previously unselected package gcc-15. 88s Preparing to unpack .../022-gcc-15_15.2.0-9ubuntu1_amd64.deb ... 88s Unpacking gcc-15 (15.2.0-9ubuntu1) ... 88s Selecting previously unselected package gcc-x86-64-linux-gnu. 88s Preparing to unpack .../023-gcc-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 88s Unpacking gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 88s Selecting previously unselected package gcc. 88s Preparing to unpack .../024-gcc_4%3a15.2.0-4ubuntu1_amd64.deb ... 88s Unpacking gcc (4:15.2.0-4ubuntu1) ... 88s Selecting previously unselected package libgfortran5:amd64. 88s Preparing to unpack .../025-libgfortran5_15.2.0-9ubuntu1_amd64.deb ... 88s Unpacking libgfortran5:amd64 (15.2.0-9ubuntu1) ... 88s Selecting previously unselected package libgfortran-15-dev:amd64. 88s Preparing to unpack .../026-libgfortran-15-dev_15.2.0-9ubuntu1_amd64.deb ... 88s Unpacking libgfortran-15-dev:amd64 (15.2.0-9ubuntu1) ... 88s Selecting previously unselected package gfortran-15-x86-64-linux-gnu. 88s Preparing to unpack .../027-gfortran-15-x86-64-linux-gnu_15.2.0-9ubuntu1_amd64.deb ... 88s Unpacking gfortran-15-x86-64-linux-gnu (15.2.0-9ubuntu1) ... 88s Selecting previously unselected package gfortran-15. 88s Preparing to unpack .../028-gfortran-15_15.2.0-9ubuntu1_amd64.deb ... 88s Unpacking gfortran-15 (15.2.0-9ubuntu1) ... 88s Selecting previously unselected package gfortran-x86-64-linux-gnu. 88s Preparing to unpack .../029-gfortran-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 88s Unpacking gfortran-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 88s Selecting previously unselected package gfortran. 88s Preparing to unpack .../030-gfortran_4%3a15.2.0-4ubuntu1_amd64.deb ... 88s Unpacking gfortran (4:15.2.0-4ubuntu1) ... 88s Selecting previously unselected package libblas3:amd64. 88s Preparing to unpack .../031-libblas3_3.12.1-7_amd64.deb ... 88s Unpacking libblas3:amd64 (3.12.1-7) ... 88s Selecting previously unselected package libpixman-1-0:amd64. 88s Preparing to unpack .../032-libpixman-1-0_0.46.4-1_amd64.deb ... 88s Unpacking libpixman-1-0:amd64 (0.46.4-1) ... 88s Selecting previously unselected package libxcb-render0:amd64. 88s Preparing to unpack .../033-libxcb-render0_1.17.0-2build1_amd64.deb ... 88s Unpacking libxcb-render0:amd64 (1.17.0-2build1) ... 88s Selecting previously unselected package libxcb-shm0:amd64. 88s Preparing to unpack .../034-libxcb-shm0_1.17.0-2build1_amd64.deb ... 88s Unpacking libxcb-shm0:amd64 (1.17.0-2build1) ... 88s Selecting previously unselected package libxrender1:amd64. 88s Preparing to unpack .../035-libxrender1_1%3a0.9.12-1_amd64.deb ... 88s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 88s Selecting previously unselected package libcairo2:amd64. 88s Preparing to unpack .../036-libcairo2_1.18.4-1build1_amd64.deb ... 88s Unpacking libcairo2:amd64 (1.18.4-1build1) ... 89s Selecting previously unselected package libdatrie1:amd64. 89s Preparing to unpack .../037-libdatrie1_0.2.14-1_amd64.deb ... 89s Unpacking libdatrie1:amd64 (0.2.14-1) ... 89s Selecting previously unselected package libdeflate0:amd64. 89s Preparing to unpack .../038-libdeflate0_1.23-2_amd64.deb ... 89s Unpacking libdeflate0:amd64 (1.23-2) ... 89s Selecting previously unselected package libgraphite2-3:amd64. 89s Preparing to unpack .../039-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 89s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 89s Selecting previously unselected package libgslcblas0:amd64. 89s Preparing to unpack .../040-libgslcblas0_2.8+dfsg-5.1ubuntu1_amd64.deb ... 89s Unpacking libgslcblas0:amd64 (2.8+dfsg-5.1ubuntu1) ... 89s Selecting previously unselected package libgsl28:amd64. 89s Preparing to unpack .../041-libgsl28_2.8+dfsg-5.1ubuntu1_amd64.deb ... 89s Unpacking libgsl28:amd64 (2.8+dfsg-5.1ubuntu1) ... 89s Selecting previously unselected package libgsl-dev. 89s Preparing to unpack .../042-libgsl-dev_2.8+dfsg-5.1ubuntu1_amd64.deb ... 89s Unpacking libgsl-dev (2.8+dfsg-5.1ubuntu1) ... 89s Selecting previously unselected package libharfbuzz0b:amd64. 89s Preparing to unpack .../043-libharfbuzz0b_12.1.0-1_amd64.deb ... 89s Unpacking libharfbuzz0b:amd64 (12.1.0-1) ... 89s Selecting previously unselected package libhtscodecs2:amd64. 89s Preparing to unpack .../044-libhtscodecs2_1.6.1-2_amd64.deb ... 89s Unpacking libhtscodecs2:amd64 (1.6.1-2) ... 89s Selecting previously unselected package libhts3t64:amd64. 89s Preparing to unpack .../045-libhts3t64_1.22.1+ds2-1_amd64.deb ... 89s Unpacking libhts3t64:amd64 (1.22.1+ds2-1) ... 89s Selecting previously unselected package x11-common. 89s Preparing to unpack .../046-x11-common_1%3a7.7+24ubuntu1_all.deb ... 89s Unpacking x11-common (1:7.7+24ubuntu1) ... 89s Selecting previously unselected package libice6:amd64. 89s Preparing to unpack .../047-libice6_2%3a1.1.1-1_amd64.deb ... 89s Unpacking libice6:amd64 (2:1.1.1-1) ... 89s Selecting previously unselected package libjpeg-turbo8:amd64. 89s Preparing to unpack .../048-libjpeg-turbo8_2.1.5-4ubuntu2_amd64.deb ... 89s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 89s Selecting previously unselected package libjpeg8:amd64. 89s Preparing to unpack .../049-libjpeg8_8c-2ubuntu11_amd64.deb ... 89s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 89s Selecting previously unselected package libopenblas0-pthread:amd64. 89s Preparing to unpack .../050-libopenblas0-pthread_0.3.30+ds-3_amd64.deb ... 89s Unpacking libopenblas0-pthread:amd64 (0.3.30+ds-3) ... 89s Selecting previously unselected package liblapack3:amd64. 89s Preparing to unpack .../051-liblapack3_3.12.1-7_amd64.deb ... 89s Unpacking liblapack3:amd64 (3.12.1-7) ... 89s Selecting previously unselected package liblerc4:amd64. 89s Preparing to unpack .../052-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 89s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 89s Selecting previously unselected package libopenblas0:amd64. 89s Preparing to unpack .../053-libopenblas0_0.3.30+ds-3_amd64.deb ... 89s Unpacking libopenblas0:amd64 (0.3.30+ds-3) ... 89s Selecting previously unselected package libopenblas-pthread-dev:amd64. 89s Preparing to unpack .../054-libopenblas-pthread-dev_0.3.30+ds-3_amd64.deb ... 89s Unpacking libopenblas-pthread-dev:amd64 (0.3.30+ds-3) ... 89s Selecting previously unselected package libopenblas-dev:amd64. 89s Preparing to unpack .../055-libopenblas-dev_0.3.30+ds-3_amd64.deb ... 89s Unpacking libopenblas-dev:amd64 (0.3.30+ds-3) ... 89s Selecting previously unselected package libthai-data. 89s Preparing to unpack .../056-libthai-data_0.1.29-2build2_all.deb ... 89s Unpacking libthai-data (0.1.29-2build2) ... 89s Selecting previously unselected package libthai0:amd64. 89s Preparing to unpack .../057-libthai0_0.1.29-2build2_amd64.deb ... 89s Unpacking libthai0:amd64 (0.1.29-2build2) ... 89s Selecting previously unselected package libpango-1.0-0:amd64. 89s Preparing to unpack .../058-libpango-1.0-0_1.56.3-2_amd64.deb ... 89s Unpacking libpango-1.0-0:amd64 (1.56.3-2) ... 89s Selecting previously unselected package libpangoft2-1.0-0:amd64. 89s Preparing to unpack .../059-libpangoft2-1.0-0_1.56.3-2_amd64.deb ... 89s Unpacking libpangoft2-1.0-0:amd64 (1.56.3-2) ... 89s Selecting previously unselected package libpangocairo-1.0-0:amd64. 89s Preparing to unpack .../060-libpangocairo-1.0-0_1.56.3-2_amd64.deb ... 89s Unpacking libpangocairo-1.0-0:amd64 (1.56.3-2) ... 89s Selecting previously unselected package libpaper2:amd64. 89s Preparing to unpack .../061-libpaper2_2.2.5-0.3_amd64.deb ... 89s Unpacking libpaper2:amd64 (2.2.5-0.3) ... 89s Selecting previously unselected package libpaper-utils. 89s Preparing to unpack .../062-libpaper-utils_2.2.5-0.3_amd64.deb ... 89s Unpacking libpaper-utils (2.2.5-0.3) ... 89s Selecting previously unselected package libsharpyuv0:amd64. 89s Preparing to unpack .../063-libsharpyuv0_1.5.0-0.1_amd64.deb ... 89s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 89s Selecting previously unselected package libsm6:amd64. 89s Preparing to unpack .../064-libsm6_2%3a1.2.6-1_amd64.deb ... 89s Unpacking libsm6:amd64 (2:1.2.6-1) ... 89s Selecting previously unselected package libtcl8.6:amd64. 89s Preparing to unpack .../065-libtcl8.6_8.6.17+dfsg-1_amd64.deb ... 89s Unpacking libtcl8.6:amd64 (8.6.17+dfsg-1) ... 89s Selecting previously unselected package libjbig0:amd64. 89s Preparing to unpack .../066-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 89s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 89s Selecting previously unselected package libwebp7:amd64. 89s Preparing to unpack .../067-libwebp7_1.5.0-0.1_amd64.deb ... 89s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 89s Selecting previously unselected package libtiff6:amd64. 89s Preparing to unpack .../068-libtiff6_4.7.0-3ubuntu3_amd64.deb ... 89s Unpacking libtiff6:amd64 (4.7.0-3ubuntu3) ... 89s Selecting previously unselected package libxft2:amd64. 89s Preparing to unpack .../069-libxft2_2.3.6-1build1_amd64.deb ... 89s Unpacking libxft2:amd64 (2.3.6-1build1) ... 89s Selecting previously unselected package libxss1:amd64. 89s Preparing to unpack .../070-libxss1_1%3a1.2.3-1build3_amd64.deb ... 89s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 89s Selecting previously unselected package libtk8.6:amd64. 89s Preparing to unpack .../071-libtk8.6_8.6.17-1_amd64.deb ... 89s Unpacking libtk8.6:amd64 (8.6.17-1) ... 89s Selecting previously unselected package libxt6t64:amd64. 89s Preparing to unpack .../072-libxt6t64_1%3a1.2.1-1.3_amd64.deb ... 89s Unpacking libxt6t64:amd64 (1:1.2.1-1.3) ... 89s Selecting previously unselected package zip. 89s Preparing to unpack .../073-zip_3.0-15ubuntu2_amd64.deb ... 89s Unpacking zip (3.0-15ubuntu2) ... 89s Selecting previously unselected package unzip. 89s Preparing to unpack .../074-unzip_6.0-28ubuntu7_amd64.deb ... 89s Unpacking unzip (6.0-28ubuntu7) ... 89s Selecting previously unselected package xdg-utils. 89s Preparing to unpack .../075-xdg-utils_1.2.1-2ubuntu1_all.deb ... 89s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 89s Selecting previously unselected package r-base-core. 89s Preparing to unpack .../076-r-base-core_4.5.2-1_amd64.deb ... 89s Unpacking r-base-core (4.5.2-1) ... 89s Selecting previously unselected package r-cran-codetools. 89s Preparing to unpack .../077-r-cran-codetools_0.2-20-1_all.deb ... 89s Unpacking r-cran-codetools (0.2-20-1) ... 89s Selecting previously unselected package r-cran-iterators. 89s Preparing to unpack .../078-r-cran-iterators_1.0.14-1build1_all.deb ... 90s Unpacking r-cran-iterators (1.0.14-1build1) ... 90s Selecting previously unselected package r-cran-foreach. 90s Preparing to unpack .../079-r-cran-foreach_1.5.2-1build1_all.deb ... 90s Unpacking r-cran-foreach (1.5.2-1build1) ... 90s Selecting previously unselected package r-cran-gam. 90s Preparing to unpack .../080-r-cran-gam_1.22-5-1_amd64.deb ... 90s Unpacking r-cran-gam (1.22-5-1) ... 90s Selecting previously unselected package r-cran-cli. 90s Preparing to unpack .../081-r-cran-cli_3.6.4-1_amd64.deb ... 90s Unpacking r-cran-cli (3.6.4-1) ... 90s Selecting previously unselected package r-cran-glue. 90s Preparing to unpack .../082-r-cran-glue_1.8.0-1_amd64.deb ... 90s Unpacking r-cran-glue (1.8.0-1) ... 90s Selecting previously unselected package r-cran-rlang. 90s Preparing to unpack .../083-r-cran-rlang_1.1.5-3_amd64.deb ... 90s Unpacking r-cran-rlang (1.1.5-3) ... 90s Selecting previously unselected package r-cran-lifecycle. 90s Preparing to unpack .../084-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 90s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 90s Selecting previously unselected package r-cran-gtable. 90s Preparing to unpack .../085-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 90s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 90s Selecting previously unselected package r-cran-isoband. 90s Preparing to unpack .../086-r-cran-isoband_0.2.7-1_amd64.deb ... 90s Unpacking r-cran-isoband (0.2.7-1) ... 90s Selecting previously unselected package r-cran-mass. 90s Preparing to unpack .../087-r-cran-mass_7.3-65-1_amd64.deb ... 90s Unpacking r-cran-mass (7.3-65-1) ... 90s Selecting previously unselected package r-cran-lattice. 90s Preparing to unpack .../088-r-cran-lattice_0.22-7-1_amd64.deb ... 90s Unpacking r-cran-lattice (0.22-7-1) ... 90s Selecting previously unselected package r-cran-nlme. 90s Preparing to unpack .../089-r-cran-nlme_3.1.168-1_amd64.deb ... 90s Unpacking r-cran-nlme (3.1.168-1) ... 90s Selecting previously unselected package r-cran-matrix. 90s Preparing to unpack .../090-r-cran-matrix_1.7-4-1_amd64.deb ... 90s Unpacking r-cran-matrix (1.7-4-1) ... 90s Selecting previously unselected package r-cran-mgcv. 90s Preparing to unpack .../091-r-cran-mgcv_1.9-3-1_amd64.deb ... 90s Unpacking r-cran-mgcv (1.9-3-1) ... 90s Selecting previously unselected package r-cran-farver. 90s Preparing to unpack .../092-r-cran-farver_2.1.2-1_amd64.deb ... 90s Unpacking r-cran-farver (2.1.2-1) ... 90s Selecting previously unselected package r-cran-labeling. 90s Preparing to unpack .../093-r-cran-labeling_0.4.3-1_all.deb ... 90s Unpacking r-cran-labeling (0.4.3-1) ... 90s Selecting previously unselected package r-cran-colorspace. 90s Preparing to unpack .../094-r-cran-colorspace_2.1-1+dfsg-1_amd64.deb ... 90s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ... 90s Selecting previously unselected package r-cran-munsell. 90s Preparing to unpack .../095-r-cran-munsell_0.5.1-1_all.deb ... 90s Unpacking r-cran-munsell (0.5.1-1) ... 90s Selecting previously unselected package r-cran-r6. 90s Preparing to unpack .../096-r-cran-r6_2.6.1-1_all.deb ... 90s Unpacking r-cran-r6 (2.6.1-1) ... 90s Selecting previously unselected package r-cran-rcolorbrewer. 90s Preparing to unpack .../097-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ... 90s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ... 90s Selecting previously unselected package r-cran-viridislite. 90s Preparing to unpack .../098-r-cran-viridislite_0.4.2-2_all.deb ... 90s Unpacking r-cran-viridislite (0.4.2-2) ... 90s Selecting previously unselected package r-cran-scales. 90s Preparing to unpack .../099-r-cran-scales_1.3.0-1_all.deb ... 90s Unpacking r-cran-scales (1.3.0-1) ... 90s Selecting previously unselected package r-cran-fansi. 90s Preparing to unpack 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r-cran-tibble. 90s Preparing to unpack .../106-r-cran-tibble_3.2.1+dfsg-3_amd64.deb ... 90s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 90s Selecting previously unselected package r-cran-withr. 90s Preparing to unpack .../107-r-cran-withr_3.0.2+dfsg-1_all.deb ... 90s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 90s Selecting previously unselected package r-cran-ggplot2. 90s Preparing to unpack .../108-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ... 90s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ... 90s Selecting previously unselected package r-cran-inline. 90s Preparing to unpack .../109-r-cran-inline_0.3.21-1_all.deb ... 90s Unpacking r-cran-inline (0.3.21-1) ... 90s Selecting previously unselected package seqtk. 90s Preparing to unpack .../110-seqtk_1.4-2_amd64.deb ... 90s Unpacking seqtk (1.4-2) ... 90s Selecting previously unselected package python3-pysam. 90s Preparing to unpack .../111-python3-pysam_0.23.3+ds-2_amd64.deb ... 90s Unpacking python3-pysam (0.23.3+ds-2) ... 90s Selecting previously unselected package r-cran-littler. 90s Preparing to unpack .../112-r-cran-littler_0.3.21-2_amd64.deb ... 90s Unpacking r-cran-littler (0.3.21-2) ... 90s Selecting previously unselected package r-cran-pkgkitten. 90s Preparing to unpack .../113-r-cran-pkgkitten_0.2.4-1_all.deb ... 90s Unpacking r-cran-pkgkitten (0.2.4-1) ... 90s Selecting previously unselected package r-cran-rcpp. 90s Preparing to unpack .../114-r-cran-rcpp_1.1.0-1_amd64.deb ... 90s Unpacking r-cran-rcpp (1.1.0-1) ... 90s Selecting previously unselected package r-cran-rcppgsl. 90s Preparing to unpack .../115-r-cran-rcppgsl_0.3.13-1build1_amd64.deb ... 90s Unpacking r-cran-rcppgsl (0.3.13-1build1) ... 90s Selecting previously unselected package mapdamage. 90s Preparing to unpack .../116-mapdamage_2.2.2+dfsg-1_all.deb ... 90s Unpacking mapdamage (2.2.2+dfsg-1) ... 90s Selecting previously unselected package r-cran-runit. 90s Preparing to unpack .../117-r-cran-runit_0.4.33.1-1_all.deb ... 90s Unpacking r-cran-runit (0.4.33.1-1) ... 90s Setting up libhtscodecs2:amd64 (1.6.1-2) ... 90s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 90s Setting up libpixman-1-0:amd64 (0.46.4-1) ... 90s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... 90s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 90s Setting up seqtk (1.4-2) ... 90s Setting up libxrender1:amd64 (1:0.9.12-1) ... 90s Setting up libdatrie1:amd64 (0.2.14-1) ... 90s Setting up libgslcblas0:amd64 (2.8+dfsg-5.1ubuntu1) ... 90s Setting up libxcb-render0:amd64 (1.17.0-2build1) ... 90s Setting up unzip (6.0-28ubuntu7) ... 90s Setting up x11-common (1:7.7+24ubuntu1) ... 91s Setting up libdeflate0:amd64 (1.23-2) ... 91s Setting up libxcb-shm0:amd64 (1.17.0-2build1) ... 91s Setting up libgomp1:amd64 (15.2.0-9ubuntu1) ... 91s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 91s Setting up zip (3.0-15ubuntu2) ... 91s Setting up libblas3:amd64 (3.12.1-7) ... 91s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide 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up libgsl28:amd64 (2.8+dfsg-5.1ubuntu1) ... 91s Setting up xdg-utils (1.2.1-2ubuntu1) ... 91s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 91s Setting up libcc1-0:amd64 (15.2.0-9ubuntu1) ... 91s Setting up liblsan0:amd64 (15.2.0-9ubuntu1) ... 91s Setting up libitm1:amd64 (15.2.0-9ubuntu1) ... 91s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 91s Setting up libice6:amd64 (2:1.1.1-1) ... 91s Setting up liblapack3:amd64 (3.12.1-7) ... 91s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 91s Setting up libgsl-dev (2.8+dfsg-5.1ubuntu1) ... 91s Setting up libopenblas0-pthread:amd64 (0.3.30+ds-3) ... 91s update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 91s update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 91s update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-x86_64-linux-gnu) in auto mode 91s Setting up python3-pysam (0.23.3+ds-2) ... 91s Setting up libgcc-15-dev:amd64 (15.2.0-9ubuntu1) ... 91s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 91s Setting up libpaper-utils (2.2.5-0.3) ... 91s Setting up cpp-15-x86-64-linux-gnu (15.2.0-9ubuntu1) ... 91s Setting up libgfortran-15-dev:amd64 (15.2.0-9ubuntu1) ... 91s Setting up gcc-15-x86-64-linux-gnu (15.2.0-9ubuntu1) ... 91s Setting up libthai0:amd64 (0.1.29-2build2) ... 91s Setting up libopenblas0:amd64 (0.3.30+ds-3) ... 91s Setting up cpp-15 (15.2.0-9ubuntu1) ... 91s Setting up libtiff6:amd64 (4.7.0-3ubuntu3) ... 91s Setting up libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 91s Setting up libsm6:amd64 (2:1.2.6-1) ... 91s Setting up cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 91s Setting up libopenblas-pthread-dev:amd64 (0.3.30+ds-3) ... 91s update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode 91s update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode 91s update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/x86_64-linux-gnu/libopenblas.so (libopenblas.so-x86_64-linux-gnu) in auto mode 91s Setting up gfortran-15-x86-64-linux-gnu (15.2.0-9ubuntu1) ... 91s Setting up fontconfig (2.15.0-2.3ubuntu1) ... 93s Regenerating fonts cache... done. 93s Setting up libxft2:amd64 (2.3.6-1build1) ... 93s Setting up gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 93s Setting up libtk8.6:amd64 (8.6.17-1) ... 93s Setting up libpango-1.0-0:amd64 (1.56.3-2) ... 93s Setting up gfortran-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 93s Setting up libcairo2:amd64 (1.18.4-1build1) ... 93s Setting up gcc-15 (15.2.0-9ubuntu1) ... 93s Setting up libopenblas-dev:amd64 (0.3.30+ds-3) ... 93s Setting up libxt6t64:amd64 (1:1.2.1-1.3) ... 93s Setting up cpp (4:15.2.0-4ubuntu1) ... 93s Setting up libpangoft2-1.0-0:amd64 (1.56.3-2) ... 93s Setting up gfortran-15 (15.2.0-9ubuntu1) ... 93s Setting up libpangocairo-1.0-0:amd64 (1.56.3-2) ... 93s Setting up gcc (4:15.2.0-4ubuntu1) ... 93s Setting up r-base-core (4.5.2-1) ... 93s Creating config file /etc/R/Renviron with new version 93s Setting up r-cran-labeling (0.4.3-1) ... 93s Setting up r-cran-lattice (0.22-7-1) ... 93s Setting up r-cran-nlme (3.1.168-1) ... 93s Setting up r-cran-farver (2.1.2-1) ... 93s Setting up r-cran-viridislite (0.4.2-2) ... 93s Setting up r-cran-r6 (2.6.1-1) ... 93s Setting up r-cran-pkgkitten (0.2.4-1) ... 93s Setting up r-cran-magrittr (2.0.3-1) ... 93s Setting up r-cran-littler (0.3.21-2) ... 93s Setting up r-cran-rcpp (1.1.0-1) ... 93s Setting up r-cran-codetools (0.2-20-1) ... 93s Setting up r-cran-inline (0.3.21-1) ... 93s Setting up r-cran-rlang (1.1.5-3) ... 93s Setting up r-cran-withr (3.0.2+dfsg-1) ... 93s Setting up r-cran-iterators (1.0.14-1build1) ... 93s Setting up r-cran-foreach (1.5.2-1build1) ... 93s Setting up r-cran-fansi (1.0.6-2) ... 93s Setting up r-cran-mass (7.3-65-1) ... 93s Setting up r-cran-glue (1.8.0-1) ... 93s Setting up r-cran-gam (1.22-5-1) ... 93s Setting up r-cran-cli (3.6.4-1) ... 93s Setting up gfortran (4:15.2.0-4ubuntu1) ... 93s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 93s update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist 93s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 93s update-alternatives: warning: skip creation of /usr/share/man/man1/f77.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f77) doesn't exist 93s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... 93s Setting up r-cran-pkgconfig (2.0.3-2build2) ... 93s Setting up r-cran-utf8 (1.2.4-1) ... 93s Setting up r-cran-colorspace (2.1-1+dfsg-1) ... 93s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ... 93s Setting up r-cran-isoband (0.2.7-1) ... 93s Setting up r-cran-runit (0.4.33.1-1) ... 93s Setting up r-cran-gtable (0.3.6+dfsg-1) ... 93s Setting up r-cran-matrix (1.7-4-1) ... 93s Setting up r-cran-mgcv (1.9-3-1) ... 93s Setting up r-cran-rcppgsl (0.3.13-1build1) ... 93s Setting up r-cran-vctrs (0.6.5-1) ... 93s Setting up r-cran-pillar (1.10.1+dfsg-1) ... 93s Setting up r-cran-munsell (0.5.1-1) ... 93s Setting up r-cran-tibble (3.2.1+dfsg-3) ... 93s Setting up r-cran-scales (1.3.0-1) ... 93s Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... 93s Setting up mapdamage (2.2.2+dfsg-1) ... 93s Processing triggers for install-info (7.2-5) ... 93s Processing triggers for libc-bin (2.42-2ubuntu2) ... 93s Processing triggers for man-db (2.13.1-1) ... 95s autopkgtest [06:53:38]: test run-unit-test: [----------------------- 96s Started with the command: /usr/bin/mapDamage -i tests/test.bam -r tests/fake1.fasta -d tests/results --no-stats 96s additional tests/results/Length_plot.pdf generated 96s Successful run 96s Reading from 'tests/test.bam' 96s Writing results to 'tests/results/' 96s pdf tests/results/Fragmisincorporation_plot.pdf generated 96s .. 96s ---------------------------------------------------------------------- 96s Ran 2 tests in 1.429s 96s 96s OK 97s autopkgtest [06:53:40]: test run-unit-test: -----------------------] 97s autopkgtest [06:53:40]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 97s run-unit-test PASS 97s autopkgtest [06:53:40]: test run-r-packages-check: preparing testbed 117s Creating nova instance adt-resolute-amd64-mapdamage-20251204-065202-juju-7f2275-prod-proposed-migration-environment-2-094d6249-aced-4fc3-8dcd-0a591a0de282 from image adt/ubuntu-resolute-amd64-server-20251204.img (UUID 51c52a3c-b973-44be-bcc8-3a3ff6355fda)... 167s autopkgtest [06:54:50]: testbed dpkg architecture: amd64 167s autopkgtest [06:54:50]: testbed apt version: 3.1.12 167s autopkgtest [06:54:50]: @@@@@@@@@@@@@@@@@@@@ test bed setup 167s autopkgtest [06:54:50]: testbed release detected to be: resolute 168s autopkgtest [06:54:51]: updating testbed package index (apt update) 168s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 168s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 168s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 168s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 168s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [23.1 kB] 168s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [152 kB] 168s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [928 kB] 169s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [162 kB] 169s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [218 kB] 169s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [6652 B] 169s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [120 B] 169s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [752 kB] 169s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [344 kB] 169s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [24.1 kB] 169s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4040 B] 169s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [9636 B] 169s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [748 B] 170s Fetched 2749 kB in 1s (2852 kB/s) 170s Reading package lists... 171s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 171s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 171s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 171s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 171s Reading package lists... 171s Reading package lists... 172s Building dependency tree... 172s Reading state information... 172s Calculating upgrade... 172s The following packages will be upgraded: 172s libpython3-stdlib python3 python3-gdbm python3-minimal 172s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 172s Need to get 72.9 kB of archives. 172s After this operation, 2048 B of additional disk space will be used. 172s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.13.9-2 [28.1 kB] 172s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.13.9-2 [23.0 kB] 172s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.13.9-2 [10.8 kB] 172s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-gdbm amd64 3.13.9-2 [11.0 kB] 172s dpkg-preconfigure: unable to re-open stdin: No such file or directory 172s Fetched 72.9 kB in 0s (0 B/s) 172s (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 ... 83537 files and directories currently installed.) 172s Preparing to unpack .../python3-minimal_3.13.9-2_amd64.deb ... 172s Unpacking python3-minimal (3.13.9-2) over (3.13.7-1) ... 172s Setting up python3-minimal (3.13.9-2) ... 172s (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 ... 83537 files and directories currently installed.) 172s Preparing to unpack .../python3_3.13.9-2_amd64.deb ... 172s running python pre-rtupdate hooks for python3.13... 172s Unpacking python3 (3.13.9-2) over (3.13.7-1) ... 172s Preparing to unpack .../libpython3-stdlib_3.13.9-2_amd64.deb ... 172s Unpacking libpython3-stdlib:amd64 (3.13.9-2) over (3.13.7-1) ... 172s Preparing to unpack .../python3-gdbm_3.13.9-2_amd64.deb ... 172s Unpacking python3-gdbm (3.13.9-2) over (3.13.9-1) ... 172s Setting up python3-gdbm (3.13.9-2) ... 172s Setting up libpython3-stdlib:amd64 (3.13.9-2) ... 172s Setting up python3 (3.13.9-2) ... 172s running python rtupdate hooks for python3.13... 172s running python post-rtupdate hooks for python3.13... 172s Processing triggers for man-db (2.13.1-1) ... 173s autopkgtest [06:54:56]: upgrading testbed (apt dist-upgrade and autopurge) 173s Reading package lists... 173s Building dependency tree... 173s Reading state information... 173s Calculating upgrade... 173s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 173s Reading package lists... 174s Building dependency tree... 174s Reading state information... 174s Solving dependencies... 174s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 176s Reading package lists... 176s Building dependency tree... 176s Reading state information... 176s Solving dependencies... 176s The following NEW packages will be installed: 176s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 176s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 176s libgraphite2-3 libgsl-dev libgsl28 libgslcblas0 libharfbuzz0b libhts3t64 176s libhtscodecs2 libice6 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 176s libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread 176s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 176s libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 176s libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 176s libxss1 libxt6t64 mapdamage python3-pysam r-base-core r-cran-cli 176s r-cran-codetools r-cran-colorspace r-cran-fansi r-cran-farver r-cran-foreach 176s r-cran-gam r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-inline 176s r-cran-isoband r-cran-iterators r-cran-labeling r-cran-lattice 176s r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix 176s r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig 176s r-cran-pkgkitten r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rcppgsl 176s r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8 r-cran-vctrs 176s r-cran-viridislite r-cran-withr seqtk unzip x11-common xdg-utils zip 176s 0 upgraded, 93 newly installed, 0 to remove and 0 not upgraded. 176s Need to get 92.1 MB of archives. 176s After this operation, 305 MB of additional disk space will be used. 176s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 176s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 177s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.15.0-2.3ubuntu1 [38.0 kB] 177s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.15.0-2.3ubuntu1 [141 kB] 177s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig amd64 2.15.0-2.3ubuntu1 [180 kB] 177s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7 [259 kB] 177s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB] 177s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2build1 [17.4 kB] 177s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2build1 [6120 B] 177s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 177s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-1build1 [611 kB] 177s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libdatrie1 amd64 0.2.14-1 [19.8 kB] 177s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 177s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-9ubuntu1 [939 kB] 177s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-9ubuntu1 [151 kB] 177s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 177s Get:17 http://ftpmaster.internal/ubuntu resolute/universe amd64 libgslcblas0 amd64 2.8+dfsg-5.1ubuntu1 [133 kB] 177s Get:18 http://ftpmaster.internal/ubuntu resolute/universe amd64 libgsl28 amd64 2.8+dfsg-5.1ubuntu1 [1104 kB] 177s Get:19 http://ftpmaster.internal/ubuntu resolute/universe amd64 libgsl-dev amd64 2.8+dfsg-5.1ubuntu1 [1433 kB] 177s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.1.0-1 [535 kB] 177s Get:21 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhtscodecs2 amd64 1.6.1-2 [132 kB] 177s Get:22 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhts3t64 amd64 1.22.1+ds2-1 [461 kB] 177s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 177s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 177s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB] 177s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 177s Get:27 http://ftpmaster.internal/ubuntu resolute/universe amd64 libopenblas0-pthread amd64 0.3.30+ds-3 [5382 kB] 177s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7 [2739 kB] 177s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 177s Get:30 http://ftpmaster.internal/ubuntu resolute/universe amd64 libopenblas0 amd64 0.3.30+ds-3 [6304 B] 177s Get:31 http://ftpmaster.internal/ubuntu resolute/universe amd64 libopenblas-pthread-dev amd64 0.3.30+ds-3 [5107 kB] 178s Get:32 http://ftpmaster.internal/ubuntu resolute/universe amd64 libopenblas-dev amd64 0.3.30+ds-3 [21.3 kB] 178s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai-data all 0.1.29-2build2 [153 kB] 178s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai0 amd64 0.1.29-2build2 [19.2 kB] 178s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libpango-1.0-0 amd64 1.56.3-2 [239 kB] 178s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoft2-1.0-0 amd64 1.56.3-2 [52.5 kB] 178s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangocairo-1.0-0 amd64 1.56.3-2 [29.0 kB] 178s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB] 178s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB] 178s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 178s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libsm6 amd64 2:1.2.6-1 [16.4 kB] 178s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1036 kB] 178s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 178s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 178s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 178s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 178s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 178s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB] 178s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libxt6t64 amd64 1:1.2.1-1.3 [173 kB] 178s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 zip amd64 3.0-15ubuntu2 [178 kB] 178s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 unzip amd64 6.0-28ubuntu7 [180 kB] 178s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 178s Get:53 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-core amd64 4.5.2-1 [28.8 MB] 178s Get:54 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-codetools all 0.2-20-1 [90.5 kB] 178s Get:55 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-iterators all 1.0.14-1build1 [336 kB] 179s Get:56 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-foreach all 1.5.2-1build1 [124 kB] 179s Get:57 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gam amd64 1.22-5-1 [394 kB] 179s Get:58 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB] 179s Get:59 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB] 179s Get:60 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rlang amd64 1.1.5-3 [1721 kB] 179s Get:61 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 179s Get:62 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 179s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-isoband amd64 0.2.7-1 [1481 kB] 179s Get:64 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mass amd64 7.3-65-1 [1116 kB] 179s Get:65 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lattice amd64 0.22-7-1 [1367 kB] 179s Get:66 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-nlme amd64 3.1.168-1 [2320 kB] 179s Get:67 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrix amd64 1.7-4-1 [4220 kB] 179s Get:68 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mgcv amd64 1.9-3-1 [3414 kB] 179s Get:69 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-farver amd64 2.1.2-1 [1355 kB] 179s Get:70 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-labeling all 0.4.3-1 [62.1 kB] 179s Get:71 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1563 kB] 179s Get:72 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-munsell all 0.5.1-1 [213 kB] 179s Get:73 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r6 all 2.6.1-1 [101 kB] 179s Get:74 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 179s Get:75 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-viridislite all 0.4.2-2 [1088 kB] 179s Get:76 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-scales all 1.3.0-1 [603 kB] 179s Get:77 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fansi amd64 1.0.6-2 [626 kB] 179s Get:78 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB] 179s Get:79 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-utf8 amd64 1.2.4-1 [140 kB] 179s Get:80 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB] 179s Get:81 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pillar all 1.10.1+dfsg-1 [453 kB] 179s Get:82 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 179s Get:83 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [419 kB] 179s Get:84 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 179s Get:85 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB] 180s Get:86 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-inline all 0.3.21-1 [131 kB] 180s Get:87 http://ftpmaster.internal/ubuntu resolute/universe amd64 seqtk amd64 1.4-2 [34.6 kB] 180s Get:88 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pysam amd64 0.23.3+ds-2 [4536 kB] 180s Get:89 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-littler amd64 0.3.21-2 [84.4 kB] 180s Get:90 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 180s Get:91 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcpp amd64 1.1.0-1 [2021 kB] 180s Get:92 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcppgsl amd64 0.3.13-1build1 [199 kB] 180s Get:93 http://ftpmaster.internal/ubuntu resolute/universe amd64 mapdamage all 2.2.2+dfsg-1 [43.3 kB] 180s Preconfiguring packages ... 180s Fetched 92.1 MB in 3s (26.7 MB/s) 180s Selecting previously unselected package fonts-dejavu-mono. 180s (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 ... 83537 files and directories currently installed.) 180s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 180s Unpacking fonts-dejavu-mono (2.37-8) ... 180s Selecting previously unselected package fonts-dejavu-core. 180s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 180s Unpacking fonts-dejavu-core (2.37-8) ... 180s Selecting previously unselected package fontconfig-config. 180s Preparing to unpack .../02-fontconfig-config_2.15.0-2.3ubuntu1_amd64.deb ... 180s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 180s Selecting previously unselected package libfontconfig1:amd64. 180s Preparing to unpack .../03-libfontconfig1_2.15.0-2.3ubuntu1_amd64.deb ... 180s Unpacking libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 180s Selecting previously unselected package fontconfig. 180s Preparing to unpack .../04-fontconfig_2.15.0-2.3ubuntu1_amd64.deb ... 180s Unpacking fontconfig (2.15.0-2.3ubuntu1) ... 180s Selecting previously unselected package libblas3:amd64. 180s Preparing to unpack .../05-libblas3_3.12.1-7_amd64.deb ... 180s Unpacking libblas3:amd64 (3.12.1-7) ... 180s Selecting previously unselected package libpixman-1-0:amd64. 180s Preparing to unpack .../06-libpixman-1-0_0.46.4-1_amd64.deb ... 180s Unpacking libpixman-1-0:amd64 (0.46.4-1) ... 180s Selecting previously unselected package libxcb-render0:amd64. 180s Preparing to unpack .../07-libxcb-render0_1.17.0-2build1_amd64.deb ... 180s Unpacking libxcb-render0:amd64 (1.17.0-2build1) ... 180s Selecting previously unselected package libxcb-shm0:amd64. 180s Preparing to unpack .../08-libxcb-shm0_1.17.0-2build1_amd64.deb ... 180s Unpacking libxcb-shm0:amd64 (1.17.0-2build1) ... 180s Selecting previously unselected package libxrender1:amd64. 180s Preparing to unpack .../09-libxrender1_1%3a0.9.12-1_amd64.deb ... 180s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 180s Selecting previously unselected package libcairo2:amd64. 180s Preparing to unpack .../10-libcairo2_1.18.4-1build1_amd64.deb ... 180s Unpacking libcairo2:amd64 (1.18.4-1build1) ... 180s Selecting previously unselected package libdatrie1:amd64. 180s Preparing to unpack .../11-libdatrie1_0.2.14-1_amd64.deb ... 180s Unpacking libdatrie1:amd64 (0.2.14-1) ... 180s Selecting previously unselected package libdeflate0:amd64. 180s Preparing to unpack .../12-libdeflate0_1.23-2_amd64.deb ... 180s Unpacking libdeflate0:amd64 (1.23-2) ... 180s Selecting previously unselected package libgfortran5:amd64. 180s Preparing to unpack .../13-libgfortran5_15.2.0-9ubuntu1_amd64.deb ... 180s Unpacking libgfortran5:amd64 (15.2.0-9ubuntu1) ... 180s Selecting previously unselected package libgomp1:amd64. 180s Preparing to unpack .../14-libgomp1_15.2.0-9ubuntu1_amd64.deb ... 180s Unpacking libgomp1:amd64 (15.2.0-9ubuntu1) ... 180s Selecting previously unselected package libgraphite2-3:amd64. 180s Preparing to unpack .../15-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 180s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 180s Selecting previously unselected package libgslcblas0:amd64. 180s Preparing to unpack .../16-libgslcblas0_2.8+dfsg-5.1ubuntu1_amd64.deb ... 180s Unpacking libgslcblas0:amd64 (2.8+dfsg-5.1ubuntu1) ... 180s Selecting previously unselected package libgsl28:amd64. 180s Preparing to unpack .../17-libgsl28_2.8+dfsg-5.1ubuntu1_amd64.deb ... 180s Unpacking libgsl28:amd64 (2.8+dfsg-5.1ubuntu1) ... 180s Selecting previously unselected package libgsl-dev. 180s Preparing to unpack .../18-libgsl-dev_2.8+dfsg-5.1ubuntu1_amd64.deb ... 180s Unpacking libgsl-dev (2.8+dfsg-5.1ubuntu1) ... 180s Selecting previously unselected package libharfbuzz0b:amd64. 180s Preparing to unpack .../19-libharfbuzz0b_12.1.0-1_amd64.deb ... 180s Unpacking libharfbuzz0b:amd64 (12.1.0-1) ... 180s Selecting previously unselected package libhtscodecs2:amd64. 180s Preparing to unpack .../20-libhtscodecs2_1.6.1-2_amd64.deb ... 180s Unpacking libhtscodecs2:amd64 (1.6.1-2) ... 180s Selecting previously unselected package libhts3t64:amd64. 180s Preparing to unpack .../21-libhts3t64_1.22.1+ds2-1_amd64.deb ... 180s Unpacking libhts3t64:amd64 (1.22.1+ds2-1) ... 180s Selecting previously unselected package x11-common. 180s Preparing to unpack .../22-x11-common_1%3a7.7+24ubuntu1_all.deb ... 180s Unpacking x11-common (1:7.7+24ubuntu1) ... 180s Selecting previously unselected package libice6:amd64. 180s Preparing to unpack .../23-libice6_2%3a1.1.1-1_amd64.deb ... 180s Unpacking libice6:amd64 (2:1.1.1-1) ... 180s Selecting previously unselected package libjpeg-turbo8:amd64. 180s Preparing to unpack .../24-libjpeg-turbo8_2.1.5-4ubuntu2_amd64.deb ... 180s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 180s Selecting previously unselected package libjpeg8:amd64. 180s Preparing to unpack .../25-libjpeg8_8c-2ubuntu11_amd64.deb ... 180s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 181s Selecting previously unselected package libopenblas0-pthread:amd64. 181s Preparing to unpack .../26-libopenblas0-pthread_0.3.30+ds-3_amd64.deb ... 181s Unpacking libopenblas0-pthread:amd64 (0.3.30+ds-3) ... 181s Selecting previously unselected package liblapack3:amd64. 181s Preparing to unpack .../27-liblapack3_3.12.1-7_amd64.deb ... 181s Unpacking liblapack3:amd64 (3.12.1-7) ... 181s Selecting previously unselected package liblerc4:amd64. 181s Preparing to unpack .../28-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 181s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 181s Selecting previously unselected package libopenblas0:amd64. 181s Preparing to unpack .../29-libopenblas0_0.3.30+ds-3_amd64.deb ... 181s Unpacking libopenblas0:amd64 (0.3.30+ds-3) ... 181s Selecting previously unselected package libopenblas-pthread-dev:amd64. 181s Preparing to unpack .../30-libopenblas-pthread-dev_0.3.30+ds-3_amd64.deb ... 181s Unpacking libopenblas-pthread-dev:amd64 (0.3.30+ds-3) ... 181s Selecting previously unselected package libopenblas-dev:amd64. 181s Preparing to unpack .../31-libopenblas-dev_0.3.30+ds-3_amd64.deb ... 181s Unpacking libopenblas-dev:amd64 (0.3.30+ds-3) ... 181s Selecting previously unselected package libthai-data. 181s Preparing to unpack .../32-libthai-data_0.1.29-2build2_all.deb ... 181s Unpacking libthai-data (0.1.29-2build2) ... 181s Selecting previously unselected package libthai0:amd64. 181s Preparing to unpack .../33-libthai0_0.1.29-2build2_amd64.deb ... 181s Unpacking libthai0:amd64 (0.1.29-2build2) ... 181s Selecting previously unselected package libpango-1.0-0:amd64. 181s Preparing to unpack .../34-libpango-1.0-0_1.56.3-2_amd64.deb ... 181s Unpacking libpango-1.0-0:amd64 (1.56.3-2) ... 181s Selecting previously unselected package libpangoft2-1.0-0:amd64. 181s Preparing to unpack .../35-libpangoft2-1.0-0_1.56.3-2_amd64.deb ... 181s Unpacking libpangoft2-1.0-0:amd64 (1.56.3-2) ... 181s Selecting previously unselected package libpangocairo-1.0-0:amd64. 181s Preparing to unpack .../36-libpangocairo-1.0-0_1.56.3-2_amd64.deb ... 181s Unpacking libpangocairo-1.0-0:amd64 (1.56.3-2) ... 181s Selecting previously unselected package libpaper2:amd64. 181s Preparing to unpack .../37-libpaper2_2.2.5-0.3_amd64.deb ... 181s Unpacking libpaper2:amd64 (2.2.5-0.3) ... 181s Selecting previously unselected package libpaper-utils. 181s Preparing to unpack .../38-libpaper-utils_2.2.5-0.3_amd64.deb ... 181s Unpacking libpaper-utils (2.2.5-0.3) ... 181s Selecting previously unselected package libsharpyuv0:amd64. 181s Preparing to unpack .../39-libsharpyuv0_1.5.0-0.1_amd64.deb ... 181s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 181s Selecting previously unselected package libsm6:amd64. 181s Preparing to unpack .../40-libsm6_2%3a1.2.6-1_amd64.deb ... 181s Unpacking libsm6:amd64 (2:1.2.6-1) ... 181s Selecting previously unselected package libtcl8.6:amd64. 181s Preparing to unpack .../41-libtcl8.6_8.6.17+dfsg-1_amd64.deb ... 181s Unpacking libtcl8.6:amd64 (8.6.17+dfsg-1) ... 181s Selecting previously unselected package libjbig0:amd64. 181s Preparing to unpack .../42-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 181s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 181s Selecting previously unselected package libwebp7:amd64. 181s Preparing to unpack .../43-libwebp7_1.5.0-0.1_amd64.deb ... 181s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 181s Selecting previously unselected package libtiff6:amd64. 181s Preparing to unpack .../44-libtiff6_4.7.0-3ubuntu3_amd64.deb ... 181s Unpacking libtiff6:amd64 (4.7.0-3ubuntu3) ... 181s Selecting previously unselected package libxft2:amd64. 181s Preparing to unpack .../45-libxft2_2.3.6-1build1_amd64.deb ... 181s Unpacking libxft2:amd64 (2.3.6-1build1) ... 181s Selecting previously unselected package libxss1:amd64. 181s Preparing to unpack .../46-libxss1_1%3a1.2.3-1build3_amd64.deb ... 181s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 181s Selecting previously unselected package libtk8.6:amd64. 181s Preparing to unpack .../47-libtk8.6_8.6.17-1_amd64.deb ... 181s Unpacking libtk8.6:amd64 (8.6.17-1) ... 181s Selecting previously unselected package libxt6t64:amd64. 181s Preparing to unpack .../48-libxt6t64_1%3a1.2.1-1.3_amd64.deb ... 181s Unpacking libxt6t64:amd64 (1:1.2.1-1.3) ... 181s Selecting previously unselected package zip. 181s Preparing to unpack .../49-zip_3.0-15ubuntu2_amd64.deb ... 181s Unpacking zip (3.0-15ubuntu2) ... 181s Selecting previously unselected package unzip. 181s Preparing to unpack .../50-unzip_6.0-28ubuntu7_amd64.deb ... 181s Unpacking unzip (6.0-28ubuntu7) ... 181s Selecting previously unselected package xdg-utils. 181s Preparing to unpack .../51-xdg-utils_1.2.1-2ubuntu1_all.deb ... 181s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 181s Selecting previously unselected package r-base-core. 181s Preparing to unpack .../52-r-base-core_4.5.2-1_amd64.deb ... 181s Unpacking r-base-core (4.5.2-1) ... 181s Selecting previously unselected package r-cran-codetools. 181s Preparing to unpack .../53-r-cran-codetools_0.2-20-1_all.deb ... 181s Unpacking r-cran-codetools (0.2-20-1) ... 181s Selecting previously unselected package r-cran-iterators. 181s Preparing to unpack .../54-r-cran-iterators_1.0.14-1build1_all.deb ... 181s Unpacking r-cran-iterators (1.0.14-1build1) ... 181s Selecting previously unselected package r-cran-foreach. 181s Preparing to unpack .../55-r-cran-foreach_1.5.2-1build1_all.deb ... 181s Unpacking r-cran-foreach (1.5.2-1build1) ... 181s Selecting previously unselected package r-cran-gam. 181s Preparing to unpack .../56-r-cran-gam_1.22-5-1_amd64.deb ... 181s Unpacking r-cran-gam (1.22-5-1) ... 181s Selecting previously unselected package r-cran-cli. 181s Preparing to unpack .../57-r-cran-cli_3.6.4-1_amd64.deb ... 181s Unpacking r-cran-cli (3.6.4-1) ... 181s Selecting previously unselected package r-cran-glue. 181s Preparing to unpack .../58-r-cran-glue_1.8.0-1_amd64.deb ... 181s Unpacking r-cran-glue (1.8.0-1) ... 181s Selecting previously unselected package r-cran-rlang. 181s Preparing to unpack .../59-r-cran-rlang_1.1.5-3_amd64.deb ... 181s Unpacking r-cran-rlang (1.1.5-3) ... 181s Selecting previously unselected package r-cran-lifecycle. 181s Preparing to unpack .../60-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 181s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 181s Selecting previously unselected package r-cran-gtable. 181s Preparing to unpack .../61-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 181s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 181s Selecting previously unselected package r-cran-isoband. 181s Preparing to unpack .../62-r-cran-isoband_0.2.7-1_amd64.deb ... 181s Unpacking r-cran-isoband (0.2.7-1) ... 181s Selecting previously unselected package r-cran-mass. 181s Preparing to unpack .../63-r-cran-mass_7.3-65-1_amd64.deb ... 181s Unpacking r-cran-mass (7.3-65-1) ... 181s Selecting previously unselected package r-cran-lattice. 181s Preparing to unpack .../64-r-cran-lattice_0.22-7-1_amd64.deb ... 181s Unpacking r-cran-lattice (0.22-7-1) ... 181s Selecting previously unselected package r-cran-nlme. 181s Preparing to unpack .../65-r-cran-nlme_3.1.168-1_amd64.deb ... 181s Unpacking r-cran-nlme (3.1.168-1) ... 181s Selecting previously unselected package r-cran-matrix. 181s Preparing to unpack .../66-r-cran-matrix_1.7-4-1_amd64.deb ... 181s Unpacking r-cran-matrix (1.7-4-1) ... 181s Selecting previously unselected package r-cran-mgcv. 181s Preparing to unpack .../67-r-cran-mgcv_1.9-3-1_amd64.deb ... 181s Unpacking r-cran-mgcv (1.9-3-1) ... 181s Selecting previously unselected package r-cran-farver. 181s Preparing to unpack .../68-r-cran-farver_2.1.2-1_amd64.deb ... 181s Unpacking r-cran-farver (2.1.2-1) ... 181s Selecting previously unselected package r-cran-labeling. 181s Preparing to unpack .../69-r-cran-labeling_0.4.3-1_all.deb ... 181s Unpacking r-cran-labeling (0.4.3-1) ... 181s Selecting previously unselected package r-cran-colorspace. 181s Preparing to unpack .../70-r-cran-colorspace_2.1-1+dfsg-1_amd64.deb ... 181s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ... 181s Selecting previously unselected package r-cran-munsell. 182s Preparing to unpack .../71-r-cran-munsell_0.5.1-1_all.deb ... 182s Unpacking r-cran-munsell (0.5.1-1) ... 182s Selecting previously unselected package r-cran-r6. 182s Preparing to unpack .../72-r-cran-r6_2.6.1-1_all.deb ... 182s Unpacking r-cran-r6 (2.6.1-1) ... 182s Selecting previously unselected package r-cran-rcolorbrewer. 182s Preparing to unpack .../73-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ... 182s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ... 182s Selecting previously unselected package r-cran-viridislite. 182s Preparing to unpack .../74-r-cran-viridislite_0.4.2-2_all.deb ... 182s Unpacking r-cran-viridislite (0.4.2-2) ... 182s Selecting previously unselected package r-cran-scales. 182s Preparing to unpack .../75-r-cran-scales_1.3.0-1_all.deb ... 182s Unpacking r-cran-scales (1.3.0-1) ... 182s Selecting previously unselected package r-cran-fansi. 182s Preparing to unpack .../76-r-cran-fansi_1.0.6-2_amd64.deb ... 182s Unpacking r-cran-fansi (1.0.6-2) ... 182s Selecting previously unselected package r-cran-magrittr. 182s Preparing to unpack .../77-r-cran-magrittr_2.0.3-1_amd64.deb ... 182s Unpacking r-cran-magrittr (2.0.3-1) ... 182s Selecting previously unselected package r-cran-utf8. 182s Preparing to unpack .../78-r-cran-utf8_1.2.4-1_amd64.deb ... 182s Unpacking r-cran-utf8 (1.2.4-1) ... 182s Selecting previously unselected package r-cran-vctrs. 182s Preparing to unpack .../79-r-cran-vctrs_0.6.5-1_amd64.deb ... 182s Unpacking r-cran-vctrs (0.6.5-1) ... 182s Selecting previously unselected package r-cran-pillar. 182s Preparing to unpack .../80-r-cran-pillar_1.10.1+dfsg-1_all.deb ... 182s Unpacking r-cran-pillar (1.10.1+dfsg-1) ... 182s Selecting previously unselected package r-cran-pkgconfig. 182s Preparing to unpack .../81-r-cran-pkgconfig_2.0.3-2build2_all.deb ... 182s Unpacking r-cran-pkgconfig (2.0.3-2build2) ... 182s Selecting previously unselected package r-cran-tibble. 182s Preparing to unpack .../82-r-cran-tibble_3.2.1+dfsg-3_amd64.deb ... 182s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 182s Selecting previously unselected package r-cran-withr. 182s Preparing to unpack .../83-r-cran-withr_3.0.2+dfsg-1_all.deb ... 182s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 182s Selecting previously unselected package r-cran-ggplot2. 182s Preparing to unpack .../84-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ... 182s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ... 182s Selecting previously unselected package r-cran-inline. 182s Preparing to unpack .../85-r-cran-inline_0.3.21-1_all.deb ... 182s Unpacking r-cran-inline (0.3.21-1) ... 182s Selecting previously unselected package seqtk. 182s Preparing to unpack .../86-seqtk_1.4-2_amd64.deb ... 182s Unpacking seqtk (1.4-2) ... 182s Selecting previously unselected package python3-pysam. 182s Preparing to unpack .../87-python3-pysam_0.23.3+ds-2_amd64.deb ... 182s Unpacking python3-pysam (0.23.3+ds-2) ... 182s Selecting previously unselected package r-cran-littler. 182s Preparing to unpack .../88-r-cran-littler_0.3.21-2_amd64.deb ... 182s Unpacking r-cran-littler (0.3.21-2) ... 182s Selecting previously unselected package r-cran-pkgkitten. 182s Preparing to unpack .../89-r-cran-pkgkitten_0.2.4-1_all.deb ... 182s Unpacking r-cran-pkgkitten (0.2.4-1) ... 182s Selecting previously unselected package r-cran-rcpp. 182s Preparing to unpack .../90-r-cran-rcpp_1.1.0-1_amd64.deb ... 182s Unpacking r-cran-rcpp (1.1.0-1) ... 182s Selecting previously unselected package r-cran-rcppgsl. 182s Preparing to unpack .../91-r-cran-rcppgsl_0.3.13-1build1_amd64.deb ... 182s Unpacking r-cran-rcppgsl (0.3.13-1build1) ... 182s Selecting previously unselected package mapdamage. 182s Preparing to unpack .../92-mapdamage_2.2.2+dfsg-1_all.deb ... 182s Unpacking mapdamage (2.2.2+dfsg-1) ... 182s Setting up libhtscodecs2:amd64 (1.6.1-2) ... 182s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 182s Setting up libpixman-1-0:amd64 (0.46.4-1) ... 182s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... 182s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 182s Setting up seqtk (1.4-2) ... 182s Setting up libxrender1:amd64 (1:0.9.12-1) ... 182s Setting up libdatrie1:amd64 (0.2.14-1) ... 182s Setting up libgslcblas0:amd64 (2.8+dfsg-5.1ubuntu1) ... 182s Setting up libxcb-render0:amd64 (1.17.0-2build1) ... 182s Setting up unzip (6.0-28ubuntu7) ... 182s Setting up x11-common (1:7.7+24ubuntu1) ... 182s Setting up libdeflate0:amd64 (1.23-2) ... 182s Setting up libxcb-shm0:amd64 (1.17.0-2build1) ... 182s Setting up libgomp1:amd64 (15.2.0-9ubuntu1) ... 182s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 182s Setting up zip (3.0-15ubuntu2) ... 182s Setting up libblas3:amd64 (3.12.1-7) ... 182s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 182s Setting up fonts-dejavu-mono (2.37-8) ... 182s Setting up libtcl8.6:amd64 (8.6.17+dfsg-1) ... 182s Setting up fonts-dejavu-core (2.37-8) ... 182s Setting up libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 182s Setting up libgfortran5:amd64 (15.2.0-9ubuntu1) ... 182s Setting up libwebp7:amd64 (1.5.0-0.1) ... 182s Setting up libhts3t64:amd64 (1.22.1+ds2-1) ... 182s Setting up libharfbuzz0b:amd64 (12.1.0-1) ... 182s Setting up libthai-data (0.1.29-2build2) ... 182s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 182s Setting up libpaper2:amd64 (2.2.5-0.3) ... 182s Setting up libgsl28:amd64 (2.8+dfsg-5.1ubuntu1) ... 182s Setting up xdg-utils (1.2.1-2ubuntu1) ... 182s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 182s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 182s Setting up libice6:amd64 (2:1.1.1-1) ... 182s Setting up liblapack3:amd64 (3.12.1-7) ... 182s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 182s Setting up libgsl-dev (2.8+dfsg-5.1ubuntu1) ... 182s Setting up libopenblas0-pthread:amd64 (0.3.30+ds-3) ... 182s update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 182s update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 182s update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-x86_64-linux-gnu) in auto mode 182s Setting up python3-pysam (0.23.3+ds-2) ... 182s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 183s Setting up libpaper-utils (2.2.5-0.3) ... 183s Setting up libthai0:amd64 (0.1.29-2build2) ... 183s Setting up libopenblas0:amd64 (0.3.30+ds-3) ... 183s Setting up libtiff6:amd64 (4.7.0-3ubuntu3) ... 183s Setting up libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 183s Setting up libsm6:amd64 (2:1.2.6-1) ... 183s Setting up libopenblas-pthread-dev:amd64 (0.3.30+ds-3) ... 183s update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode 183s update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode 183s update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/x86_64-linux-gnu/libopenblas.so (libopenblas.so-x86_64-linux-gnu) in auto mode 183s Setting up fontconfig (2.15.0-2.3ubuntu1) ... 185s Regenerating fonts cache... done. 185s Setting up libxft2:amd64 (2.3.6-1build1) ... 185s Setting up libtk8.6:amd64 (8.6.17-1) ... 185s Setting up libpango-1.0-0:amd64 (1.56.3-2) ... 185s Setting up libcairo2:amd64 (1.18.4-1build1) ... 185s Setting up libopenblas-dev:amd64 (0.3.30+ds-3) ... 185s Setting up libxt6t64:amd64 (1:1.2.1-1.3) ... 185s Setting up libpangoft2-1.0-0:amd64 (1.56.3-2) ... 185s Setting up libpangocairo-1.0-0:amd64 (1.56.3-2) ... 185s Setting up r-base-core (4.5.2-1) ... 185s Creating config file /etc/R/Renviron with new version 185s Setting up r-cran-labeling (0.4.3-1) ... 185s Setting up r-cran-lattice (0.22-7-1) ... 185s Setting up r-cran-nlme (3.1.168-1) ... 185s Setting up r-cran-farver (2.1.2-1) ... 185s Setting up r-cran-viridislite (0.4.2-2) ... 185s Setting up r-cran-r6 (2.6.1-1) ... 185s Setting up r-cran-pkgkitten (0.2.4-1) ... 185s Setting up r-cran-magrittr (2.0.3-1) ... 185s Setting up r-cran-littler (0.3.21-2) ... 185s Setting up r-cran-rcpp (1.1.0-1) ... 185s Setting up r-cran-codetools (0.2-20-1) ... 185s Setting up r-cran-inline (0.3.21-1) ... 185s Setting up r-cran-rlang (1.1.5-3) ... 185s Setting up r-cran-withr (3.0.2+dfsg-1) ... 185s Setting up r-cran-iterators (1.0.14-1build1) ... 185s Setting up r-cran-foreach (1.5.2-1build1) ... 185s Setting up r-cran-fansi (1.0.6-2) ... 185s Setting up r-cran-mass (7.3-65-1) ... 185s Setting up r-cran-glue (1.8.0-1) ... 185s Setting up r-cran-gam (1.22-5-1) ... 185s Setting up r-cran-cli (3.6.4-1) ... 185s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... 185s Setting up r-cran-pkgconfig (2.0.3-2build2) ... 185s Setting up r-cran-utf8 (1.2.4-1) ... 185s Setting up r-cran-colorspace (2.1-1+dfsg-1) ... 185s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ... 185s Setting up r-cran-isoband (0.2.7-1) ... 185s Setting up r-cran-gtable (0.3.6+dfsg-1) ... 185s Setting up r-cran-matrix (1.7-4-1) ... 185s Setting up r-cran-mgcv (1.9-3-1) ... 185s Setting up r-cran-rcppgsl (0.3.13-1build1) ... 185s Setting up r-cran-vctrs (0.6.5-1) ... 185s Setting up r-cran-pillar (1.10.1+dfsg-1) ... 185s Setting up r-cran-munsell (0.5.1-1) ... 185s Setting up r-cran-tibble (3.2.1+dfsg-3) ... 185s Setting up r-cran-scales (1.3.0-1) ... 185s Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... 185s Setting up mapdamage (2.2.2+dfsg-1) ... 185s Processing triggers for install-info (7.2-5) ... 185s Processing triggers for libc-bin (2.42-2ubuntu2) ... 185s Processing triggers for man-db (2.13.1-1) ... 187s autopkgtest [06:55:10]: test run-r-packages-check: [----------------------- 188s All R packages are present 188s autopkgtest [06:55:11]: test run-r-packages-check: -----------------------] 189s autopkgtest [06:55:12]: test run-r-packages-check: - - - - - - - - - - results - - - - - - - - - - 189s run-r-packages-check PASS 189s autopkgtest [06:55:12]: @@@@@@@@@@@@@@@@@@@@ summary 189s run-unit-test PASS 189s run-r-packages-check PASS