0s autopkgtest [20:25:27]: starting date and time: 2025-10-20 20:25:27+0000 0s autopkgtest [20:25:27]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [20:25:27]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.kc26x8xh/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:pytest,src:python-pluggy --apt-upgrade paleomix --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=pytest/8.4.2-1 python-pluggy/1.6.0-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-14.secgroup --name adt-resolute-arm64-paleomix-20251020-202526-juju-7f2275-prod-proposed-migration-environment-15-ebba0cd5-b205-4949-9258-7b8d809566cb --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-arm64-paleomix-20251020-202526-juju-7f2275-prod-proposed-migration-environment-15-ebba0cd5-b205-4949-9258-7b8d809566cb from image adt/ubuntu-resolute-arm64-server-20251020.img (UUID 53f7e888-0b33-40b7-be7f-09b2db152d64)... 65s autopkgtest [20:26:32]: testbed dpkg architecture: arm64 65s autopkgtest [20:26:32]: testbed apt version: 3.1.8ubuntu1 65s autopkgtest [20:26:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup 66s autopkgtest [20:26:33]: testbed release detected to be: None 67s autopkgtest [20:26:34]: updating testbed package index (apt update) 67s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 67s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 67s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 67s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 67s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [59.3 kB] 67s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [646 kB] 68s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [14.3 kB] 68s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 68s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [115 kB] 68s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [43.8 kB] 68s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [409 kB] 68s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [5672 B] 68s Fetched 1382 kB in 1s (1251 kB/s) 70s Reading package lists... 70s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 70s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 71s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 71s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 72s Reading package lists... 72s Reading package lists... 73s Building dependency tree... 73s Reading state information... 73s Calculating upgrade... 74s The following packages will be upgraded: 74s libbrotli1 libjson-c5 python3-inflect python3-oauthlib python3-zipp 74s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 74s Need to get 512 kB of archives. 74s After this operation, 31.7 kB of additional disk space will be used. 74s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libjson-c5 arm64 0.18+ds-1.1 [37.5 kB] 74s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libbrotli1 arm64 1.1.0-2build6 [336 kB] 74s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-inflect all 7.5.0-1 [33.9 kB] 74s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-oauthlib all 3.3.1-1 [93.5 kB] 74s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-zipp all 3.23.0-1 [10.4 kB] 75s dpkg-preconfigure: unable to re-open stdin: No such file or directory 75s Fetched 512 kB in 1s (823 kB/s) 75s (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 ... 83364 files and directories currently installed.) 75s Preparing to unpack .../libjson-c5_0.18+ds-1.1_arm64.deb ... 75s Unpacking libjson-c5:arm64 (0.18+ds-1.1) over (0.18+ds-1) ... 76s Preparing to unpack .../libbrotli1_1.1.0-2build6_arm64.deb ... 76s Unpacking libbrotli1:arm64 (1.1.0-2build6) over (1.1.0-2build5) ... 76s Preparing to unpack .../python3-inflect_7.5.0-1_all.deb ... 76s Unpacking python3-inflect (7.5.0-1) over (7.3.1-2) ... 76s Preparing to unpack .../python3-oauthlib_3.3.1-1_all.deb ... 76s Unpacking python3-oauthlib (3.3.1-1) over (3.2.2-3) ... 76s Preparing to unpack .../python3-zipp_3.23.0-1_all.deb ... 77s Unpacking python3-zipp (3.23.0-1) over (3.21.0-1) ... 77s Setting up libbrotli1:arm64 (1.1.0-2build6) ... 77s Setting up python3-zipp (3.23.0-1) ... 77s Setting up python3-inflect (7.5.0-1) ... 77s Setting up python3-oauthlib (3.3.1-1) ... 78s Setting up libjson-c5:arm64 (0.18+ds-1.1) ... 78s Processing triggers for libc-bin (2.42-0ubuntu3) ... 78s autopkgtest [20:26:45]: upgrading testbed (apt dist-upgrade and autopurge) 78s Reading package lists... 79s Building dependency tree... 79s Reading state information... 79s Calculating upgrade... 80s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 80s Reading package lists... 80s Building dependency tree... 80s Reading state information... 81s Solving dependencies... 81s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 84s autopkgtest [20:26:51]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 09:50:31 UTC 2025 84s autopkgtest [20:26:51]: @@@@@@@@@@@@@@@@@@@@ apt-source paleomix 87s Get:1 http://ftpmaster.internal/ubuntu resolute/universe paleomix 1.3.8-2 (dsc) [2466 B] 87s Get:2 http://ftpmaster.internal/ubuntu resolute/universe paleomix 1.3.8-2 (tar) [1137 kB] 87s Get:3 http://ftpmaster.internal/ubuntu resolute/universe paleomix 1.3.8-2 (diff) [11.3 kB] 87s gpgv: Signature made Wed Oct 9 16:08:04 2024 UTC 87s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 87s gpgv: issuer "emollier@debian.org" 87s gpgv: Can't check signature: No public key 87s dpkg-source: warning: cannot verify inline signature for ./paleomix_1.3.8-2.dsc: no acceptable signature found 87s autopkgtest [20:26:54]: testing package paleomix version 1.3.8-2 88s autopkgtest [20:26:55]: build not needed 89s autopkgtest [20:26:56]: test run-unit-test: preparing testbed 89s Reading package lists... 90s Building dependency tree... 90s Reading state information... 90s Solving dependencies... 91s The following NEW packages will be installed: 91s adapterremoval adwaita-icon-theme at-spi2-common bcftools bedtools bowtie2 91s bwa ca-certificates-java dconf-gsettings-backend dconf-service default-jre 91s default-jre-headless examl fontconfig fontconfig-config fonts-dejavu-core 91s fonts-dejavu-mono gtk-update-icon-cache hicolor-icon-theme java-common 91s junit4 libamd-comgr2 libamdhip64-5 libapache-pom-java libasound2-data 91s libasound2t64 libatk-bridge2.0-0t64 libatk1.0-0t64 libatspi2.0-0t64 91s libavahi-client3 libavahi-common-data libavahi-common3 libbarclay-java 91s libblas3 libcairo-gobject2 libcairo2 libcolord2 libcommons-beanutils-java 91s libcommons-codec-java libcommons-collections3-java 91s libcommons-collections4-java libcommons-compress-java libcommons-io-java 91s libcommons-jexl2-java libcommons-lang3-java libcommons-logging-java 91s libcommons-math3-java libcommons-parent-java libcups2t64 libdatrie1 91s libdconf1 libdeflate0 libdrm-amdgpu1 libepoxy0 libevent-core-2.1-7t64 91s libevent-pthreads-2.1-7t64 libezmorph-java libfabric1 libfontconfig1 91s libfreemarker-java libgatk-native-bindings-java libgbm1 libgdk-pixbuf-2.0-0 91s libgdk-pixbuf2.0-common libgfortran5 libgif7 libgkl-java libgl1 91s libgl1-mesa-dri libglvnd0 libglx-mesa0 libglx0 libgomp1 libgoogle-gson-java 91s libgraphite2-3 libgsl-dev libgsl28 libgslcblas0 libgtk-3-0t64 91s libgtk-3-common libhamcrest-java libharfbuzz0b libhsa-runtime64-1 libhsakmt1 91s libhts3t64 libhtscodecs2 libhtsjdk-java libhttpclient-java libhttpcore-java 91s libhwloc-plugins libhwloc15 libibmad5 libibumad3 libice6 libicu76 91s libjaxen-java libjbig0 libjoptsimple-java libjpeg-turbo8 libjpeg8 91s libjson-java liblapack3 liblcms2-2 liblerc4 liblightcouch-java libllvm17t64 91s liblog4j2-java libmbedcrypto16 libmbedtls21 libmbedx509-7 libmongodb-java 91s libncbi-ngs3 libncbi-vdb3 libngs-java libngs-jni libnspr4 libnss3 91s libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread 91s libopenmpi40 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 91s libpaper-utils libpaper2 libpciaccess0 libpcsclite1 libpicard-java 91s libpixman-1-0 librdmacm1t64 librhino-java libsharpyuv0 libslf4j-java libsm6 91s libsnappy-java libsnappy-jni libsnappy1v5 libtcl8.6 libthai-data libthai0 91s libtiff6 libtk8.6 libucx0 libvulkan1 libwayland-client0 libwayland-cursor0 91s libwayland-egl1 libwebp7 libx11-xcb1 libxcb-dri3-0 libxcb-glx0 91s libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 91s libxcb-xfixes0 libxcomposite1 libxcursor1 libxdamage1 libxerces2-java 91s libxfixes3 libxft2 libxi6 libxinerama1 libxml-commons-external-java 91s libxml-commons-resolver1.1-java libxnvctrl0 libxom-java libxrandr2 91s libxrender1 libxshmfence1 libxss1 libxt6t64 libxtst6 libxxf86vm1 mafft 91s mapdamage mesa-libgallium mpi-default-bin ncbi-vdb-data ocl-icd-libopencl1 91s openjdk-21-jre openjdk-21-jre-headless openmpi-bin openmpi-common paleomix 91s phylip picard-tools python3-coloredlogs python3-configargparse 91s python3-humanfriendly python3-iniconfig python3-packaging python3-pluggy 91s python3-pysam python3-pytest python3-ruamel.yaml python3-ruamel.yaml.clib 91s python3-setproctitle r-base-core r-cran-cli r-cran-codetools 91s r-cran-colorspace r-cran-fansi r-cran-farver r-cran-foreach r-cran-gam 91s r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-inline r-cran-isoband 91s r-cran-iterators r-cran-labeling r-cran-lattice r-cran-lifecycle 91s r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv 91s r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten 91s r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rcppgsl r-cran-rlang 91s r-cran-scales r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite 91s r-cran-withr radiant raxml samtools seqtk unzip x11-common xdg-utils zip 91s 0 upgraded, 248 newly installed, 0 to remove and 0 not upgraded. 91s Need to get 255 MB of archives. 91s After this operation, 891 MB of additional disk space will be used. 91s Get:1 http://ftpmaster.internal/ubuntu resolute/universe arm64 adapterremoval arm64 2.3.4-1 [154 kB] 91s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-5 [8326 B] 91s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu2 [165 kB] 91s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 91s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 91s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 91s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 91s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 91s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 91s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB] 91s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.12+dfsg-5 [156 kB] 92s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 gtk-update-icon-cache arm64 4.20.1+ds-2 [54.4 kB] 92s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 hicolor-icon-theme all 0.18-2 [13.3 kB] 92s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 adwaita-icon-theme all 49.0-1 [581 kB] 92s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 at-spi2-common all 2.57.1-1 [9432 B] 92s Get:16 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhtscodecs2 arm64 1.6.1-2 [82.7 kB] 92s Get:17 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhts3t64 arm64 1.21+ds-1 [441 kB] 92s Get:18 http://ftpmaster.internal/ubuntu resolute/universe arm64 bcftools arm64 1.21-1 [804 kB] 92s Get:19 http://ftpmaster.internal/ubuntu resolute/universe arm64 bedtools arm64 2.31.1+dfsg-2 [636 kB] 92s Get:20 http://ftpmaster.internal/ubuntu resolute/universe arm64 bwa arm64 0.7.18-1 [201 kB] 92s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 ca-certificates-java all 20240118 [11.6 kB] 92s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 libdconf1 arm64 0.40.0-5willsync1 [42.3 kB] 92s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 dconf-service arm64 0.40.0-5willsync1 [28.8 kB] 92s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 dconf-gsettings-backend arm64 0.40.0-5willsync1 [23.8 kB] 92s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 java-common all 0.76 [6852 B] 92s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 92s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 libnspr4 arm64 2:4.36-1ubuntu2 [115 kB] 92s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 libnss3 arm64 2:3.114-1 [1453 kB] 92s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcsclite1 arm64 2.3.3-1 [24.7 kB] 92s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 openjdk-21-jre-headless arm64 21.0.9~8ea-1 [45.9 MB] 93s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 default-jre-headless arm64 2:1.21-76 [3176 B] 93s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 libatk1.0-0t64 arm64 2.57.1-1 [55.5 kB] 93s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 libxi6 arm64 2:1.8.2-1 [32.4 kB] 93s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 libatspi2.0-0t64 arm64 2.57.1-1 [84.7 kB] 93s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libatk-bridge2.0-0t64 arm64 2.57.1-1 [66.0 kB] 93s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 93s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 93s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.15.0-2.3ubuntu1 [38.1 kB] 93s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.15.0-2.3ubuntu1 [144 kB] 93s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 94s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-render0 arm64 1.17.0-2build1 [18.1 kB] 94s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-shm0 arm64 1.17.0-2build1 [6234 B] 94s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 94s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo2 arm64 1.18.4-1build1 [592 kB] 94s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo-gobject2 arm64 1.18.4-1build1 [128 kB] 94s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 libcolord2 arm64 1.4.7-3build1 [148 kB] 94s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 libavahi-common-data arm64 0.8-16ubuntu3 [31.1 kB] 94s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 libavahi-common3 arm64 0.8-16ubuntu3 [24.5 kB] 94s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 libavahi-client3 arm64 0.8-16ubuntu3 [28.4 kB] 94s Get:50 http://ftpmaster.internal/ubuntu resolute/main arm64 libcups2t64 arm64 2.4.12-0ubuntu3 [269 kB] 94s Get:51 http://ftpmaster.internal/ubuntu resolute/main arm64 libepoxy0 arm64 1.5.10-2 [236 kB] 94s Get:52 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 94s Get:53 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.1.0-1 [523 kB] 94s Get:54 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig arm64 2.15.0-2.3ubuntu1 [191 kB] 94s Get:55 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 94s Get:56 http://ftpmaster.internal/ubuntu resolute/main arm64 libdatrie1 arm64 0.2.13-4 [19.1 kB] 94s Get:57 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 94s Get:58 http://ftpmaster.internal/ubuntu resolute/main arm64 libpango-1.0-0 arm64 1.56.3-1build1 [247 kB] 94s Get:59 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangoft2-1.0-0 arm64 1.56.3-1build1 [53.5 kB] 94s Get:60 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangocairo-1.0-0 arm64 1.56.3-1build1 [29.6 kB] 94s Get:61 http://ftpmaster.internal/ubuntu resolute/main arm64 libwayland-client0 arm64 1.24.0-1build1 [28.9 kB] 94s Get:62 http://ftpmaster.internal/ubuntu resolute/main arm64 libwayland-cursor0 arm64 1.24.0-1build1 [11.1 kB] 94s Get:63 http://ftpmaster.internal/ubuntu resolute/main arm64 libwayland-egl1 arm64 1.24.0-1build1 [6500 B] 94s Get:64 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcomposite1 arm64 1:0.4.6-1 [6626 B] 94s Get:65 http://ftpmaster.internal/ubuntu resolute/main arm64 libxfixes3 arm64 1:6.0.0-2build1 [11.2 kB] 94s Get:66 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcursor1 arm64 1:1.2.3-1 [22.2 kB] 94s Get:67 http://ftpmaster.internal/ubuntu resolute/main arm64 libxdamage1 arm64 1:1.1.6-1build1 [6236 B] 94s Get:68 http://ftpmaster.internal/ubuntu resolute/main arm64 libxinerama1 arm64 2:1.1.4-3build1 [6394 B] 94s Get:69 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrandr2 arm64 2:1.5.4-1 [19.6 kB] 94s Get:70 http://ftpmaster.internal/ubuntu resolute/main arm64 libgtk-3-common all 3.24.50-1ubuntu2 [1425 kB] 94s Get:71 http://ftpmaster.internal/ubuntu resolute/main arm64 libgtk-3-0t64 arm64 3.24.50-1ubuntu2 [3229 kB] 94s Get:72 http://ftpmaster.internal/ubuntu resolute/main arm64 libglvnd0 arm64 1.7.0-1build2 [59.2 kB] 94s Get:73 http://ftpmaster.internal/ubuntu resolute/main arm64 libx11-xcb1 arm64 2:1.8.12-1build1 [8216 B] 94s Get:74 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-dri3-0 arm64 1.17.0-2build1 [8120 B] 94s Get:75 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-glx0 arm64 1.17.0-2build1 [27.8 kB] 94s Get:76 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-present0 arm64 1.17.0-2build1 [6560 B] 94s Get:77 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-xfixes0 arm64 1.17.0-2build1 [11.4 kB] 94s Get:78 http://ftpmaster.internal/ubuntu resolute/main arm64 libxxf86vm1 arm64 1:1.1.4-1build4 [9130 B] 94s Get:79 http://ftpmaster.internal/ubuntu resolute/main arm64 libdrm-amdgpu1 arm64 2.4.125-1 [21.6 kB] 94s Get:80 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-randr0 arm64 1.17.0-2build1 [20.2 kB] 94s Get:81 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-sync1 arm64 1.17.0-2build1 [10.4 kB] 94s Get:82 http://ftpmaster.internal/ubuntu resolute/main arm64 libxshmfence1 arm64 1.3.3-1 [5378 B] 94s Get:83 http://ftpmaster.internal/ubuntu resolute/main arm64 mesa-libgallium arm64 25.2.3-1ubuntu1 [12.1 MB] 94s Get:84 http://ftpmaster.internal/ubuntu resolute/main arm64 libgbm1 arm64 25.2.3-1ubuntu1 [34.4 kB] 94s Get:85 http://ftpmaster.internal/ubuntu resolute/main arm64 libvulkan1 arm64 1.4.321.0-1 [169 kB] 94s Get:86 http://ftpmaster.internal/ubuntu resolute/main arm64 libgl1-mesa-dri arm64 25.2.3-1ubuntu1 [34.9 kB] 94s Get:87 http://ftpmaster.internal/ubuntu resolute/main arm64 libglx-mesa0 arm64 25.2.3-1ubuntu1 [110 kB] 94s Get:88 http://ftpmaster.internal/ubuntu resolute/main arm64 libglx0 arm64 1.7.0-1build2 [34.5 kB] 94s Get:89 http://ftpmaster.internal/ubuntu resolute/main arm64 libgl1 arm64 1.7.0-1build2 [104 kB] 94s Get:90 http://ftpmaster.internal/ubuntu resolute/main arm64 libasound2-data all 1.2.14-1ubuntu1 [21.2 kB] 94s Get:91 http://ftpmaster.internal/ubuntu resolute/main arm64 libasound2t64 arm64 1.2.14-1ubuntu1 [394 kB] 94s Get:92 http://ftpmaster.internal/ubuntu resolute/main arm64 libgif7 arm64 5.2.2-1ubuntu2 [36.1 kB] 95s Get:93 http://ftpmaster.internal/ubuntu resolute/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 95s Get:94 http://ftpmaster.internal/ubuntu resolute/main arm64 libxtst6 arm64 2:1.2.5-1 [13.2 kB] 95s Get:95 http://ftpmaster.internal/ubuntu resolute/main arm64 openjdk-21-jre arm64 21.0.9~8ea-1 [224 kB] 95s Get:96 http://ftpmaster.internal/ubuntu resolute/main arm64 default-jre arm64 2:1.21-76 [918 B] 95s Get:97 http://ftpmaster.internal/ubuntu resolute/main arm64 libevent-core-2.1-7t64 arm64 2.1.12-stable-10build1 [97.5 kB] 95s Get:98 http://ftpmaster.internal/ubuntu resolute/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10build1 [8272 B] 95s Get:99 http://ftpmaster.internal/ubuntu resolute/main arm64 librdmacm1t64 arm64 56.1-1ubuntu1 [71.4 kB] 95s Get:100 http://ftpmaster.internal/ubuntu resolute/universe arm64 libfabric1 arm64 2.1.0-1.1 [622 kB] 95s Get:101 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhwloc15 arm64 2.12.2-1 [169 kB] 95s Get:102 http://ftpmaster.internal/ubuntu resolute/universe arm64 libllvm17t64 arm64 1:17.0.6-22build1 [24.8 MB] 100s Get:103 http://ftpmaster.internal/ubuntu resolute/universe arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3build3 [14.0 MB] 100s Get:104 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhsakmt1 arm64 6.2.4+ds-1 [64.7 kB] 100s Get:105 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhsa-runtime64-1 arm64 6.1.2-3 [305 kB] 100s Get:106 http://ftpmaster.internal/ubuntu resolute/universe arm64 libamdhip64-5 arm64 5.7.1-6 [9707 kB] 101s Get:107 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-5ubuntu1 [148 kB] 101s Get:108 http://ftpmaster.internal/ubuntu resolute/main arm64 libibumad3 arm64 56.1-1ubuntu1 [31.3 kB] 101s Get:109 http://ftpmaster.internal/ubuntu resolute/main arm64 libibmad5 arm64 56.1-1ubuntu1 [44.1 kB] 101s Get:110 http://ftpmaster.internal/ubuntu resolute/universe arm64 libucx0 arm64 1.19.0+ds-1 [1242 kB] 101s Get:111 http://ftpmaster.internal/ubuntu resolute/main arm64 libpciaccess0 arm64 0.18.1-1ubuntu2 [19.4 kB] 101s Get:112 http://ftpmaster.internal/ubuntu resolute/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu4 [12.4 kB] 101s Get:113 http://ftpmaster.internal/ubuntu resolute/main arm64 ocl-icd-libopencl1 arm64 2.3.3-1 [42.2 kB] 101s Get:114 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhwloc-plugins arm64 2.12.2-1 [16.6 kB] 101s Get:115 http://ftpmaster.internal/ubuntu resolute/universe arm64 libopenmpi40 arm64 5.0.8-8ubuntu1 [3274 kB] 101s Get:116 http://ftpmaster.internal/ubuntu resolute/universe arm64 openmpi-common all 5.0.8-8ubuntu1 [108 kB] 101s Get:117 http://ftpmaster.internal/ubuntu resolute/universe arm64 openmpi-bin arm64 5.0.8-8ubuntu1 [209 kB] 101s Get:118 http://ftpmaster.internal/ubuntu resolute/universe arm64 mpi-default-bin arm64 1.18 [2510 B] 101s Get:119 http://ftpmaster.internal/ubuntu resolute/universe arm64 examl arm64 3.0.22-6build1 [828 kB] 101s Get:120 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhamcrest-java all 2.2-2 [117 kB] 101s Get:121 http://ftpmaster.internal/ubuntu resolute/universe arm64 junit4 all 4.13.2-5 [348 kB] 101s Get:122 http://ftpmaster.internal/ubuntu resolute/universe arm64 libapache-pom-java all 33-2 [5874 B] 101s Get:123 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-parent-java all 56-1 [10.7 kB] 101s Get:124 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-lang3-java all 3.17.0-1 [603 kB] 101s Get:125 http://ftpmaster.internal/ubuntu resolute/universe arm64 libfreemarker-java all 2.3.32-2.1 [1517 kB] 101s Get:126 http://ftpmaster.internal/ubuntu resolute/universe arm64 libgoogle-gson-java all 2.10.1-1 [252 kB] 101s Get:127 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjoptsimple-java all 5.0.4-7 [73.2 kB] 101s Get:128 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-codec-java all 1.18.0-1 [303 kB] 101s Get:129 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 101s Get:130 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhttpcore-java all 4.4.16-1 [612 kB] 101s Get:131 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhttpclient-java all 4.5.14-1 [1241 kB] 101s Get:132 http://ftpmaster.internal/ubuntu resolute/universe arm64 liblightcouch-java all 0.2.0-1 [74.2 kB] 101s Get:133 http://ftpmaster.internal/ubuntu resolute/universe arm64 libmongodb-java all 3.6.3-2 [1899 kB] 101s Get:134 http://ftpmaster.internal/ubuntu resolute/universe arm64 libslf4j-java all 1.7.32-2 [141 kB] 101s Get:135 http://ftpmaster.internal/ubuntu resolute/universe arm64 liblog4j2-java all 2.19.0-2 [2294 kB] 101s Get:136 http://ftpmaster.internal/ubuntu resolute/universe arm64 libbarclay-java all 5.0.0+dfsg-1 [108 kB] 101s Get:137 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-6build1 [186 kB] 101s Get:138 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-collections3-java all 3.2.2-3 [526 kB] 101s Get:139 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-beanutils-java all 1.10.1-1.1 [224 kB] 101s Get:140 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-collections4-java all 4.4-2 [670 kB] 101s Get:141 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-io-java all 2.19.0-1 [491 kB] 101s Get:142 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-compress-java all 1.27.1-2 [610 kB] 101s Get:143 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-jexl2-java all 2.1.1-6 [250 kB] 101s Get:144 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-math3-java all 3.6.1-4 [2029 kB] 101s Get:145 http://ftpmaster.internal/ubuntu resolute/universe arm64 libezmorph-java all 1.0.6-4 [76.0 kB] 101s Get:146 http://ftpmaster.internal/ubuntu resolute/universe arm64 libgatk-native-bindings-java all 1.0.0+dfsg-2 [8014 B] 101s Get:147 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-5ubuntu1 [450 kB] 101s Get:148 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjaxen-java all 1.1.6-5 [213 kB] 101s Get:149 http://ftpmaster.internal/ubuntu resolute/universe arm64 libxml-commons-external-java all 1.4.01-6 [240 kB] 101s Get:150 http://ftpmaster.internal/ubuntu resolute/universe arm64 libxml-commons-resolver1.1-java all 1.2-11 [97.6 kB] 101s Get:151 http://ftpmaster.internal/ubuntu resolute/universe arm64 libxerces2-java all 2.12.2-1 [1430 kB] 101s Get:152 http://ftpmaster.internal/ubuntu resolute/universe arm64 libxom-java all 1.3.9-1 [174 kB] 101s Get:153 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjson-java all 3.1.0+dfsg-2 [141 kB] 101s Get:154 http://ftpmaster.internal/ubuntu resolute/universe arm64 libmbedcrypto16 arm64 3.6.2-3ubuntu1 [258 kB] 101s Get:155 http://ftpmaster.internal/ubuntu resolute/universe arm64 libmbedx509-7 arm64 3.6.2-3ubuntu1 [35.7 kB] 101s Get:156 http://ftpmaster.internal/ubuntu resolute/universe arm64 libmbedtls21 arm64 3.6.2-3ubuntu1 [122 kB] 101s Get:157 http://ftpmaster.internal/ubuntu resolute/universe arm64 ncbi-vdb-data all 3.2.1+dfsg-2 [81.3 kB] 102s Get:158 http://ftpmaster.internal/ubuntu resolute/universe arm64 libncbi-vdb3 arm64 3.2.1+dfsg-2 [1259 kB] 102s Get:159 http://ftpmaster.internal/ubuntu resolute/universe arm64 libncbi-ngs3 arm64 3.2.1+dfsg-4ubuntu5 [147 kB] 102s Get:160 http://ftpmaster.internal/ubuntu resolute/universe arm64 libngs-jni arm64 3.2.1+dfsg-4ubuntu5 [4808 B] 102s Get:161 http://ftpmaster.internal/ubuntu resolute/universe arm64 libngs-java arm64 3.2.1+dfsg-4ubuntu5 [91.1 kB] 102s Get:162 http://ftpmaster.internal/ubuntu resolute/universe arm64 librhino-java all 1.7.15-1 [1354 kB] 102s Get:163 http://ftpmaster.internal/ubuntu resolute/main arm64 libsnappy1v5 arm64 1.2.2-1 [30.5 kB] 102s Get:164 http://ftpmaster.internal/ubuntu resolute/universe arm64 libsnappy-jni arm64 1.1.10.7-1 [6672 B] 102s Get:165 http://ftpmaster.internal/ubuntu resolute/universe arm64 libsnappy-java all 1.1.10.7-1 [83.6 kB] 102s Get:166 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhtsjdk-java all 4.1.3+dfsg-2 [1829 kB] 102s Get:167 http://ftpmaster.internal/ubuntu resolute/universe arm64 libgkl-java all 0.8.11+dfsg-2build1 [24.9 kB] 102s Get:168 http://ftpmaster.internal/ubuntu resolute/universe arm64 libgslcblas0 arm64 2.8+dfsg-5.1ubuntu1 [96.3 kB] 102s Get:169 http://ftpmaster.internal/ubuntu resolute/universe arm64 libgsl28 arm64 2.8+dfsg-5.1ubuntu1 [1029 kB] 102s Get:170 http://ftpmaster.internal/ubuntu resolute/universe arm64 libgsl-dev arm64 2.8+dfsg-5.1ubuntu1 [1350 kB] 102s Get:171 http://ftpmaster.internal/ubuntu resolute/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 102s Get:172 http://ftpmaster.internal/ubuntu resolute/main arm64 libicu76 arm64 76.1-4ubuntu2 [11.2 MB] 102s Get:173 http://ftpmaster.internal/ubuntu resolute/universe arm64 libopenblas0-pthread arm64 0.3.30+ds-3 [4307 kB] 102s Get:174 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-6build1 [2340 kB] 102s Get:175 http://ftpmaster.internal/ubuntu resolute/universe arm64 libopenblas0 arm64 0.3.30+ds-3 [6306 B] 102s Get:176 http://ftpmaster.internal/ubuntu resolute/universe arm64 libopenblas-pthread-dev arm64 0.3.30+ds-3 [4259 kB] 102s Get:177 http://ftpmaster.internal/ubuntu resolute/universe arm64 libopenblas-dev arm64 0.3.30+ds-3 [21.3 kB] 102s Get:178 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 102s Get:179 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 102s Get:180 http://ftpmaster.internal/ubuntu resolute/universe arm64 libpicard-java all 3.3.0+dfsg-2 [1765 kB] 102s Get:181 http://ftpmaster.internal/ubuntu resolute/main arm64 libsm6 arm64 2:1.2.6-1 [16.6 kB] 102s Get:182 http://ftpmaster.internal/ubuntu resolute/main arm64 libtcl8.6 arm64 8.6.17+dfsg-1 [1024 kB] 102s Get:183 http://ftpmaster.internal/ubuntu resolute/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 102s Get:184 http://ftpmaster.internal/ubuntu resolute/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 102s Get:185 http://ftpmaster.internal/ubuntu resolute/main arm64 libtk8.6 arm64 8.6.17-1 [811 kB] 102s Get:186 http://ftpmaster.internal/ubuntu resolute/main arm64 libxt6t64 arm64 1:1.2.1-1.3 [168 kB] 103s Get:187 http://ftpmaster.internal/ubuntu resolute/universe arm64 mafft arm64 7.525-1 [826 kB] 103s Get:188 http://ftpmaster.internal/ubuntu resolute/main arm64 zip arm64 3.0-15ubuntu2 [175 kB] 103s Get:189 http://ftpmaster.internal/ubuntu resolute/main arm64 unzip arm64 6.0-28ubuntu7 [176 kB] 103s Get:190 http://ftpmaster.internal/ubuntu resolute/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 103s Get:191 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-base-core arm64 4.5.1-1 [28.7 MB] 103s Get:192 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-codetools all 0.2-20-1 [90.5 kB] 103s Get:193 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-iterators all 1.0.14-1 [336 kB] 103s Get:194 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-foreach all 1.5.2-1 [124 kB] 103s Get:195 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-gam arm64 1.22-5-1 [393 kB] 103s Get:196 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cli arm64 3.6.4-1 [1374 kB] 103s Get:197 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-glue arm64 1.8.0-1 [163 kB] 103s Get:198 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rlang arm64 1.1.5-3 [1706 kB] 104s Get:199 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 104s Get:200 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 104s Get:201 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-isoband arm64 0.2.7-1 [1481 kB] 104s Get:202 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-mass arm64 7.3-65-1 [1109 kB] 104s Get:203 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lattice arm64 0.22-7-1 [1365 kB] 105s Get:204 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-nlme arm64 3.1.168-1 [2310 kB] 105s Get:205 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-matrix arm64 1.7-3-1 [4045 kB] 106s Get:206 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-mgcv arm64 1.9-3-1 [3324 kB] 106s Get:207 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-farver arm64 2.1.2-1 [1344 kB] 106s Get:208 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-labeling all 0.4.3-1 [62.1 kB] 106s Get:209 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-colorspace arm64 2.1-1+dfsg-1 [1563 kB] 107s Get:210 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-munsell all 0.5.1-1 [213 kB] 107s Get:211 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-r6 all 2.6.1-1 [101 kB] 107s Get:212 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 107s Get:213 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-viridislite all 0.4.2-2 [1088 kB] 107s Get:214 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-scales all 1.3.0-1 [603 kB] 107s Get:215 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-fansi arm64 1.0.6-2 [627 kB] 107s Get:216 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 107s Get:217 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-utf8 arm64 1.2.4-1 [140 kB] 107s Get:218 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB] 107s Get:219 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pillar all 1.10.1+dfsg-1 [453 kB] 107s Get:220 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 107s Get:221 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tibble arm64 3.2.1+dfsg-3 [420 kB] 107s Get:222 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 107s Get:223 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB] 107s Get:224 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-inline all 0.3.21-1 [131 kB] 107s Get:225 http://ftpmaster.internal/ubuntu resolute/universe arm64 seqtk arm64 1.4-2 [34.5 kB] 107s Get:226 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pysam arm64 0.23.0+ds-1build1 [3621 kB] 107s Get:227 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-littler arm64 0.3.21-1 [99.7 kB] 107s Get:228 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 107s Get:229 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcpp arm64 1.1.0-1 [2011 kB] 108s Get:230 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcppgsl arm64 0.3.13-1build1 [198 kB] 108s Get:231 http://ftpmaster.internal/ubuntu resolute/universe arm64 mapdamage all 2.2.2+dfsg-1 [43.3 kB] 108s Get:232 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-humanfriendly all 10.0-6 [70.8 kB] 108s Get:233 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-coloredlogs all 15.0.1-1 [38.2 kB] 108s Get:234 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-configargparse all 1.7-2 [31.7 kB] 108s Get:235 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-ruamel.yaml.clib arm64 0.2.12+ds-1build1 [138 kB] 108s Get:236 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-ruamel.yaml all 0.18.10+ds-1 [127 kB] 108s Get:237 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-setproctitle arm64 1.3.7-1 [19.4 kB] 108s Get:238 http://ftpmaster.internal/ubuntu resolute/universe arm64 bowtie2 arm64 2.5.4-1 [1380 kB] 108s Get:239 http://ftpmaster.internal/ubuntu resolute/universe arm64 phylip arm64 1:3.697+dfsg-4build1 [843 kB] 108s Get:240 http://ftpmaster.internal/ubuntu resolute/universe arm64 picard-tools all 3.3.0+dfsg-2 [308 kB] 108s Get:241 http://ftpmaster.internal/ubuntu resolute/universe arm64 radiant all 2.8.1+dfsg-2 [184 kB] 108s Get:242 http://ftpmaster.internal/ubuntu resolute/universe arm64 raxml arm64 8.2.13+dfsg-2 [1009 kB] 108s Get:243 http://ftpmaster.internal/ubuntu resolute/universe arm64 samtools arm64 1.21-1 [609 kB] 108s Get:244 http://ftpmaster.internal/ubuntu resolute/universe arm64 paleomix arm64 1.3.8-2 [971 kB] 108s Get:245 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 108s Get:246 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-packaging all 25.0-1 [52.8 kB] 108s Get:247 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 python3-pluggy all 1.6.0-1 [21.0 kB] 108s Get:248 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 python3-pytest all 8.4.2-1 [268 kB] 109s Preconfiguring packages ... 109s Fetched 255 MB in 17s (14.8 MB/s) 109s Selecting previously unselected package adapterremoval. 109s (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 ... 83374 files and directories currently installed.) 109s Preparing to unpack .../000-adapterremoval_2.3.4-1_arm64.deb ... 109s Unpacking adapterremoval (2.3.4-1) ... 109s Selecting previously unselected package libgdk-pixbuf2.0-common. 109s Preparing to unpack .../001-libgdk-pixbuf2.0-common_2.42.12+dfsg-5_all.deb ... 109s Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-5) ... 109s Selecting previously unselected package libjpeg-turbo8:arm64. 109s Preparing to unpack .../002-libjpeg-turbo8_2.1.5-4ubuntu2_arm64.deb ... 109s Unpacking libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 109s Selecting previously unselected package libjpeg8:arm64. 109s Preparing to unpack .../003-libjpeg8_8c-2ubuntu11_arm64.deb ... 109s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 109s Selecting previously unselected package libdeflate0:arm64. 109s Preparing to unpack .../004-libdeflate0_1.23-2_arm64.deb ... 109s Unpacking libdeflate0:arm64 (1.23-2) ... 110s Selecting previously unselected package libjbig0:arm64. 110s Preparing to unpack .../005-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 110s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 110s Selecting previously unselected package liblerc4:arm64. 110s Preparing to unpack .../006-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 110s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 110s Selecting previously unselected package libsharpyuv0:arm64. 110s Preparing to unpack .../007-libsharpyuv0_1.5.0-0.1_arm64.deb ... 110s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 110s Selecting previously unselected package libwebp7:arm64. 110s Preparing to unpack .../008-libwebp7_1.5.0-0.1_arm64.deb ... 110s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 110s Selecting previously unselected package libtiff6:arm64. 110s Preparing to unpack .../009-libtiff6_4.7.0-3ubuntu3_arm64.deb ... 110s Unpacking libtiff6:arm64 (4.7.0-3ubuntu3) ... 110s Selecting previously unselected package libgdk-pixbuf-2.0-0:arm64. 110s Preparing to unpack .../010-libgdk-pixbuf-2.0-0_2.42.12+dfsg-5_arm64.deb ... 110s Unpacking libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-5) ... 110s Selecting previously unselected package gtk-update-icon-cache. 110s Preparing to unpack .../011-gtk-update-icon-cache_4.20.1+ds-2_arm64.deb ... 110s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. 110s No diversion 'diversion of /usr/share/man/man8/update-icon-caches.8.gz to /usr/share/man/man8/update-icon-caches.gtk2.8.gz by libgtk-3-bin', none removed. 110s Unpacking gtk-update-icon-cache (4.20.1+ds-2) ... 110s Selecting previously unselected package hicolor-icon-theme. 110s Preparing to unpack .../012-hicolor-icon-theme_0.18-2_all.deb ... 110s Unpacking hicolor-icon-theme (0.18-2) ... 110s Selecting previously unselected package adwaita-icon-theme. 110s Preparing to unpack .../013-adwaita-icon-theme_49.0-1_all.deb ... 110s Unpacking adwaita-icon-theme (49.0-1) ... 110s Selecting previously unselected package at-spi2-common. 110s Preparing to unpack .../014-at-spi2-common_2.57.1-1_all.deb ... 110s Unpacking at-spi2-common (2.57.1-1) ... 110s Selecting previously unselected package libhtscodecs2:arm64. 110s Preparing to unpack .../015-libhtscodecs2_1.6.1-2_arm64.deb ... 110s Unpacking libhtscodecs2:arm64 (1.6.1-2) ... 110s Selecting previously unselected package libhts3t64:arm64. 110s Preparing to unpack .../016-libhts3t64_1.21+ds-1_arm64.deb ... 110s Unpacking libhts3t64:arm64 (1.21+ds-1) ... 110s Selecting previously unselected package bcftools. 111s Preparing to unpack .../017-bcftools_1.21-1_arm64.deb ... 111s Unpacking bcftools (1.21-1) ... 111s Selecting previously unselected package bedtools. 111s Preparing to unpack .../018-bedtools_2.31.1+dfsg-2_arm64.deb ... 111s Unpacking bedtools (2.31.1+dfsg-2) ... 111s Selecting previously unselected package bwa. 111s Preparing to unpack .../019-bwa_0.7.18-1_arm64.deb ... 111s Unpacking bwa (0.7.18-1) ... 111s Selecting previously unselected package ca-certificates-java. 111s Preparing to unpack .../020-ca-certificates-java_20240118_all.deb ... 111s Unpacking ca-certificates-java (20240118) ... 111s Selecting previously unselected package libdconf1:arm64. 111s Preparing to unpack .../021-libdconf1_0.40.0-5willsync1_arm64.deb ... 111s Unpacking libdconf1:arm64 (0.40.0-5willsync1) ... 111s Selecting previously unselected package dconf-service. 111s Preparing to unpack .../022-dconf-service_0.40.0-5willsync1_arm64.deb ... 111s Unpacking dconf-service (0.40.0-5willsync1) ... 111s Selecting previously unselected package dconf-gsettings-backend:arm64. 111s Preparing to unpack .../023-dconf-gsettings-backend_0.40.0-5willsync1_arm64.deb ... 111s Unpacking dconf-gsettings-backend:arm64 (0.40.0-5willsync1) ... 111s Selecting previously unselected package java-common. 111s Preparing to unpack .../024-java-common_0.76_all.deb ... 111s Unpacking java-common (0.76) ... 111s Selecting previously unselected package liblcms2-2:arm64. 111s Preparing to unpack .../025-liblcms2-2_2.16-2_arm64.deb ... 111s Unpacking liblcms2-2:arm64 (2.16-2) ... 111s Selecting previously unselected package libnspr4:arm64. 111s Preparing to unpack .../026-libnspr4_2%3a4.36-1ubuntu2_arm64.deb ... 111s Unpacking libnspr4:arm64 (2:4.36-1ubuntu2) ... 111s Selecting previously unselected package libnss3:arm64. 111s Preparing to unpack .../027-libnss3_2%3a3.114-1_arm64.deb ... 111s Unpacking libnss3:arm64 (2:3.114-1) ... 111s Selecting previously unselected package libpcsclite1:arm64. 111s Preparing to unpack .../028-libpcsclite1_2.3.3-1_arm64.deb ... 111s Unpacking libpcsclite1:arm64 (2.3.3-1) ... 111s Selecting previously unselected package openjdk-21-jre-headless:arm64. 111s Preparing to unpack .../029-openjdk-21-jre-headless_21.0.9~8ea-1_arm64.deb ... 111s Unpacking openjdk-21-jre-headless:arm64 (21.0.9~8ea-1) ... 113s Selecting previously unselected package default-jre-headless. 113s Preparing to unpack .../030-default-jre-headless_2%3a1.21-76_arm64.deb ... 113s Unpacking default-jre-headless (2:1.21-76) ... 113s Selecting previously unselected package libatk1.0-0t64:arm64. 113s Preparing to unpack .../031-libatk1.0-0t64_2.57.1-1_arm64.deb ... 113s Unpacking libatk1.0-0t64:arm64 (2.57.1-1) ... 113s Selecting previously unselected package libxi6:arm64. 113s Preparing to unpack .../032-libxi6_2%3a1.8.2-1_arm64.deb ... 113s Unpacking libxi6:arm64 (2:1.8.2-1) ... 114s Selecting previously unselected package libatspi2.0-0t64:arm64. 114s Preparing to unpack .../033-libatspi2.0-0t64_2.57.1-1_arm64.deb ... 114s Unpacking libatspi2.0-0t64:arm64 (2.57.1-1) ... 114s Selecting previously unselected package libatk-bridge2.0-0t64:arm64. 114s Preparing to unpack .../034-libatk-bridge2.0-0t64_2.57.1-1_arm64.deb ... 114s Unpacking libatk-bridge2.0-0t64:arm64 (2.57.1-1) ... 114s Selecting previously unselected package fonts-dejavu-mono. 114s Preparing to unpack .../035-fonts-dejavu-mono_2.37-8_all.deb ... 114s Unpacking fonts-dejavu-mono (2.37-8) ... 114s Selecting previously unselected package fonts-dejavu-core. 114s Preparing to unpack .../036-fonts-dejavu-core_2.37-8_all.deb ... 114s Unpacking fonts-dejavu-core (2.37-8) ... 114s Selecting previously unselected package fontconfig-config. 114s Preparing to unpack .../037-fontconfig-config_2.15.0-2.3ubuntu1_arm64.deb ... 114s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 114s Selecting previously unselected package libfontconfig1:arm64. 114s Preparing to unpack .../038-libfontconfig1_2.15.0-2.3ubuntu1_arm64.deb ... 114s Unpacking libfontconfig1:arm64 (2.15.0-2.3ubuntu1) ... 114s Selecting previously unselected package libpixman-1-0:arm64. 114s Preparing to unpack .../039-libpixman-1-0_0.44.0-3_arm64.deb ... 114s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 115s Selecting previously unselected package libxcb-render0:arm64. 115s Preparing to unpack .../040-libxcb-render0_1.17.0-2build1_arm64.deb ... 115s Unpacking libxcb-render0:arm64 (1.17.0-2build1) ... 115s Selecting previously unselected package libxcb-shm0:arm64. 115s Preparing to unpack .../041-libxcb-shm0_1.17.0-2build1_arm64.deb ... 115s Unpacking libxcb-shm0:arm64 (1.17.0-2build1) ... 115s Selecting previously unselected package libxrender1:arm64. 115s Preparing to unpack .../042-libxrender1_1%3a0.9.12-1_arm64.deb ... 115s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 115s Selecting previously unselected package libcairo2:arm64. 115s Preparing to unpack .../043-libcairo2_1.18.4-1build1_arm64.deb ... 115s Unpacking libcairo2:arm64 (1.18.4-1build1) ... 115s Selecting previously unselected package libcairo-gobject2:arm64. 115s Preparing to unpack .../044-libcairo-gobject2_1.18.4-1build1_arm64.deb ... 115s Unpacking libcairo-gobject2:arm64 (1.18.4-1build1) ... 115s Selecting previously unselected package libcolord2:arm64. 115s Preparing to unpack .../045-libcolord2_1.4.7-3build1_arm64.deb ... 115s Unpacking libcolord2:arm64 (1.4.7-3build1) ... 115s Selecting previously unselected package libavahi-common-data:arm64. 115s Preparing to unpack .../046-libavahi-common-data_0.8-16ubuntu3_arm64.deb ... 115s Unpacking libavahi-common-data:arm64 (0.8-16ubuntu3) ... 115s Selecting previously unselected package libavahi-common3:arm64. 115s Preparing to unpack .../047-libavahi-common3_0.8-16ubuntu3_arm64.deb ... 115s Unpacking libavahi-common3:arm64 (0.8-16ubuntu3) ... 115s Selecting previously unselected package libavahi-client3:arm64. 115s Preparing to unpack .../048-libavahi-client3_0.8-16ubuntu3_arm64.deb ... 115s Unpacking libavahi-client3:arm64 (0.8-16ubuntu3) ... 115s Selecting previously unselected package libcups2t64:arm64. 115s Preparing to unpack .../049-libcups2t64_2.4.12-0ubuntu3_arm64.deb ... 115s Unpacking libcups2t64:arm64 (2.4.12-0ubuntu3) ... 115s Selecting previously unselected package libepoxy0:arm64. 115s Preparing to unpack .../050-libepoxy0_1.5.10-2_arm64.deb ... 115s Unpacking libepoxy0:arm64 (1.5.10-2) ... 115s Selecting previously unselected package libgraphite2-3:arm64. 115s Preparing to unpack .../051-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 115s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 115s Selecting previously unselected package libharfbuzz0b:arm64. 115s Preparing to unpack .../052-libharfbuzz0b_12.1.0-1_arm64.deb ... 115s Unpacking libharfbuzz0b:arm64 (12.1.0-1) ... 115s Selecting previously unselected package fontconfig. 115s Preparing to unpack .../053-fontconfig_2.15.0-2.3ubuntu1_arm64.deb ... 115s Unpacking fontconfig (2.15.0-2.3ubuntu1) ... 116s Selecting previously unselected package libthai-data. 116s Preparing to unpack .../054-libthai-data_0.1.29-2build1_all.deb ... 116s Unpacking libthai-data (0.1.29-2build1) ... 116s Selecting previously unselected package libdatrie1:arm64. 116s Preparing to unpack .../055-libdatrie1_0.2.13-4_arm64.deb ... 116s Unpacking libdatrie1:arm64 (0.2.13-4) ... 116s Selecting previously unselected package libthai0:arm64. 116s Preparing to unpack .../056-libthai0_0.1.29-2build1_arm64.deb ... 116s Unpacking libthai0:arm64 (0.1.29-2build1) ... 116s Selecting previously unselected package libpango-1.0-0:arm64. 116s Preparing to unpack .../057-libpango-1.0-0_1.56.3-1build1_arm64.deb ... 116s Unpacking libpango-1.0-0:arm64 (1.56.3-1build1) ... 116s Selecting previously unselected package libpangoft2-1.0-0:arm64. 116s Preparing to unpack .../058-libpangoft2-1.0-0_1.56.3-1build1_arm64.deb ... 116s Unpacking libpangoft2-1.0-0:arm64 (1.56.3-1build1) ... 116s Selecting previously unselected package libpangocairo-1.0-0:arm64. 116s Preparing to unpack .../059-libpangocairo-1.0-0_1.56.3-1build1_arm64.deb ... 116s Unpacking libpangocairo-1.0-0:arm64 (1.56.3-1build1) ... 116s Selecting previously unselected package libwayland-client0:arm64. 116s Preparing to unpack .../060-libwayland-client0_1.24.0-1build1_arm64.deb ... 116s Unpacking libwayland-client0:arm64 (1.24.0-1build1) ... 116s Selecting previously unselected package libwayland-cursor0:arm64. 116s Preparing to unpack .../061-libwayland-cursor0_1.24.0-1build1_arm64.deb ... 116s Unpacking libwayland-cursor0:arm64 (1.24.0-1build1) ... 116s Selecting previously unselected package libwayland-egl1:arm64. 116s Preparing to unpack .../062-libwayland-egl1_1.24.0-1build1_arm64.deb ... 116s Unpacking libwayland-egl1:arm64 (1.24.0-1build1) ... 116s Selecting previously unselected package libxcomposite1:arm64. 116s Preparing to unpack .../063-libxcomposite1_1%3a0.4.6-1_arm64.deb ... 116s Unpacking libxcomposite1:arm64 (1:0.4.6-1) ... 116s Selecting previously unselected package libxfixes3:arm64. 116s Preparing to unpack .../064-libxfixes3_1%3a6.0.0-2build1_arm64.deb ... 116s Unpacking libxfixes3:arm64 (1:6.0.0-2build1) ... 116s Selecting previously unselected package libxcursor1:arm64. 116s Preparing to unpack .../065-libxcursor1_1%3a1.2.3-1_arm64.deb ... 116s Unpacking libxcursor1:arm64 (1:1.2.3-1) ... 116s Selecting previously unselected package libxdamage1:arm64. 116s Preparing to unpack .../066-libxdamage1_1%3a1.1.6-1build1_arm64.deb ... 116s Unpacking libxdamage1:arm64 (1:1.1.6-1build1) ... 116s Selecting previously unselected package libxinerama1:arm64. 116s Preparing to unpack .../067-libxinerama1_2%3a1.1.4-3build1_arm64.deb ... 116s Unpacking libxinerama1:arm64 (2:1.1.4-3build1) ... 116s Selecting previously unselected package libxrandr2:arm64. 116s Preparing to unpack .../068-libxrandr2_2%3a1.5.4-1_arm64.deb ... 116s Unpacking libxrandr2:arm64 (2:1.5.4-1) ... 116s Selecting previously unselected package libgtk-3-common. 116s Preparing to unpack .../069-libgtk-3-common_3.24.50-1ubuntu2_all.deb ... 116s Unpacking libgtk-3-common (3.24.50-1ubuntu2) ... 117s Selecting previously unselected package libgtk-3-0t64:arm64. 117s Preparing to unpack .../070-libgtk-3-0t64_3.24.50-1ubuntu2_arm64.deb ... 117s Unpacking libgtk-3-0t64:arm64 (3.24.50-1ubuntu2) ... 117s Selecting previously unselected package libglvnd0:arm64. 117s Preparing to unpack .../071-libglvnd0_1.7.0-1build2_arm64.deb ... 117s Unpacking libglvnd0:arm64 (1.7.0-1build2) ... 117s Selecting previously unselected package libx11-xcb1:arm64. 117s Preparing to unpack .../072-libx11-xcb1_2%3a1.8.12-1build1_arm64.deb ... 117s Unpacking libx11-xcb1:arm64 (2:1.8.12-1build1) ... 117s Selecting previously unselected package libxcb-dri3-0:arm64. 117s Preparing to unpack .../073-libxcb-dri3-0_1.17.0-2build1_arm64.deb ... 117s Unpacking libxcb-dri3-0:arm64 (1.17.0-2build1) ... 117s Selecting previously unselected package libxcb-glx0:arm64. 117s Preparing to unpack .../074-libxcb-glx0_1.17.0-2build1_arm64.deb ... 117s Unpacking libxcb-glx0:arm64 (1.17.0-2build1) ... 117s Selecting previously unselected package libxcb-present0:arm64. 117s Preparing to unpack .../075-libxcb-present0_1.17.0-2build1_arm64.deb ... 117s Unpacking libxcb-present0:arm64 (1.17.0-2build1) ... 117s Selecting previously unselected package libxcb-xfixes0:arm64. 117s Preparing to unpack .../076-libxcb-xfixes0_1.17.0-2build1_arm64.deb ... 117s Unpacking libxcb-xfixes0:arm64 (1.17.0-2build1) ... 117s Selecting previously unselected package libxxf86vm1:arm64. 117s Preparing to unpack .../077-libxxf86vm1_1%3a1.1.4-1build4_arm64.deb ... 117s Unpacking libxxf86vm1:arm64 (1:1.1.4-1build4) ... 117s Selecting previously unselected package libdrm-amdgpu1:arm64. 117s Preparing to unpack .../078-libdrm-amdgpu1_2.4.125-1_arm64.deb ... 117s Unpacking libdrm-amdgpu1:arm64 (2.4.125-1) ... 117s Selecting previously unselected package libxcb-randr0:arm64. 117s Preparing to unpack .../079-libxcb-randr0_1.17.0-2build1_arm64.deb ... 117s Unpacking libxcb-randr0:arm64 (1.17.0-2build1) ... 117s Selecting previously unselected package libxcb-sync1:arm64. 117s Preparing to unpack .../080-libxcb-sync1_1.17.0-2build1_arm64.deb ... 117s Unpacking libxcb-sync1:arm64 (1.17.0-2build1) ... 117s Selecting previously unselected package libxshmfence1:arm64. 117s Preparing to unpack .../081-libxshmfence1_1.3.3-1_arm64.deb ... 117s Unpacking libxshmfence1:arm64 (1.3.3-1) ... 117s Selecting previously unselected package mesa-libgallium:arm64. 117s Preparing to unpack .../082-mesa-libgallium_25.2.3-1ubuntu1_arm64.deb ... 117s Unpacking mesa-libgallium:arm64 (25.2.3-1ubuntu1) ... 118s Selecting previously unselected package libgbm1:arm64. 118s Preparing to unpack .../083-libgbm1_25.2.3-1ubuntu1_arm64.deb ... 118s Unpacking libgbm1:arm64 (25.2.3-1ubuntu1) ... 118s Selecting previously unselected package libvulkan1:arm64. 118s Preparing to unpack .../084-libvulkan1_1.4.321.0-1_arm64.deb ... 118s Unpacking libvulkan1:arm64 (1.4.321.0-1) ... 118s Selecting previously unselected package libgl1-mesa-dri:arm64. 118s Preparing to unpack .../085-libgl1-mesa-dri_25.2.3-1ubuntu1_arm64.deb ... 118s Unpacking libgl1-mesa-dri:arm64 (25.2.3-1ubuntu1) ... 118s Selecting previously unselected package libglx-mesa0:arm64. 118s Preparing to unpack .../086-libglx-mesa0_25.2.3-1ubuntu1_arm64.deb ... 118s Unpacking libglx-mesa0:arm64 (25.2.3-1ubuntu1) ... 118s Selecting previously unselected package libglx0:arm64. 118s Preparing to unpack .../087-libglx0_1.7.0-1build2_arm64.deb ... 118s Unpacking libglx0:arm64 (1.7.0-1build2) ... 118s Selecting previously unselected package libgl1:arm64. 118s Preparing to unpack .../088-libgl1_1.7.0-1build2_arm64.deb ... 118s Unpacking libgl1:arm64 (1.7.0-1build2) ... 118s Selecting previously unselected package libasound2-data. 118s Preparing to unpack .../089-libasound2-data_1.2.14-1ubuntu1_all.deb ... 118s Unpacking libasound2-data (1.2.14-1ubuntu1) ... 118s Selecting previously unselected package libasound2t64:arm64. 118s Preparing to unpack .../090-libasound2t64_1.2.14-1ubuntu1_arm64.deb ... 118s Unpacking libasound2t64:arm64 (1.2.14-1ubuntu1) ... 118s Selecting previously unselected package libgif7:arm64. 119s Preparing to unpack .../091-libgif7_5.2.2-1ubuntu2_arm64.deb ... 119s Unpacking libgif7:arm64 (5.2.2-1ubuntu2) ... 119s Selecting previously unselected package x11-common. 119s Preparing to unpack .../092-x11-common_1%3a7.7+24ubuntu1_all.deb ... 119s Unpacking x11-common (1:7.7+24ubuntu1) ... 119s Selecting previously unselected package libxtst6:arm64. 119s Preparing to unpack .../093-libxtst6_2%3a1.2.5-1_arm64.deb ... 119s Unpacking libxtst6:arm64 (2:1.2.5-1) ... 119s Selecting previously unselected package openjdk-21-jre:arm64. 119s Preparing to unpack .../094-openjdk-21-jre_21.0.9~8ea-1_arm64.deb ... 119s Unpacking openjdk-21-jre:arm64 (21.0.9~8ea-1) ... 119s Selecting previously unselected package default-jre. 119s Preparing to unpack .../095-default-jre_2%3a1.21-76_arm64.deb ... 119s Unpacking default-jre (2:1.21-76) ... 119s Selecting previously unselected package libevent-core-2.1-7t64:arm64. 119s Preparing to unpack .../096-libevent-core-2.1-7t64_2.1.12-stable-10build1_arm64.deb ... 119s Unpacking libevent-core-2.1-7t64:arm64 (2.1.12-stable-10build1) ... 119s Selecting previously unselected package libevent-pthreads-2.1-7t64:arm64. 119s Preparing to unpack .../097-libevent-pthreads-2.1-7t64_2.1.12-stable-10build1_arm64.deb ... 119s Unpacking libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10build1) ... 119s Selecting previously unselected package librdmacm1t64:arm64. 119s Preparing to unpack .../098-librdmacm1t64_56.1-1ubuntu1_arm64.deb ... 119s Unpacking librdmacm1t64:arm64 (56.1-1ubuntu1) ... 119s Selecting previously unselected package libfabric1:arm64. 119s Preparing to unpack .../099-libfabric1_2.1.0-1.1_arm64.deb ... 119s Unpacking libfabric1:arm64 (2.1.0-1.1) ... 119s Selecting previously unselected package libhwloc15:arm64. 119s Preparing to unpack .../100-libhwloc15_2.12.2-1_arm64.deb ... 119s Unpacking libhwloc15:arm64 (2.12.2-1) ... 119s Selecting previously unselected package libllvm17t64:arm64. 119s Preparing to unpack .../101-libllvm17t64_1%3a17.0.6-22build1_arm64.deb ... 119s Unpacking libllvm17t64:arm64 (1:17.0.6-22build1) ... 120s Selecting previously unselected package libamd-comgr2:arm64. 120s Preparing to unpack .../102-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build3_arm64.deb ... 120s Unpacking libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3build3) ... 121s Selecting previously unselected package libhsakmt1:arm64. 121s Preparing to unpack .../103-libhsakmt1_6.2.4+ds-1_arm64.deb ... 121s Unpacking libhsakmt1:arm64 (6.2.4+ds-1) ... 121s Selecting previously unselected package libhsa-runtime64-1:arm64. 121s Preparing to unpack .../104-libhsa-runtime64-1_6.1.2-3_arm64.deb ... 121s Unpacking libhsa-runtime64-1:arm64 (6.1.2-3) ... 121s Selecting previously unselected package libamdhip64-5:arm64. 121s Preparing to unpack .../105-libamdhip64-5_5.7.1-6_arm64.deb ... 121s Unpacking libamdhip64-5:arm64 (5.7.1-6) ... 121s Selecting previously unselected package libgomp1:arm64. 122s Preparing to unpack .../106-libgomp1_15.2.0-5ubuntu1_arm64.deb ... 122s Unpacking libgomp1:arm64 (15.2.0-5ubuntu1) ... 122s Selecting previously unselected package libibumad3:arm64. 122s Preparing to unpack .../107-libibumad3_56.1-1ubuntu1_arm64.deb ... 122s Unpacking libibumad3:arm64 (56.1-1ubuntu1) ... 122s Selecting previously unselected package libibmad5:arm64. 122s Preparing to unpack .../108-libibmad5_56.1-1ubuntu1_arm64.deb ... 122s Unpacking libibmad5:arm64 (56.1-1ubuntu1) ... 122s Selecting previously unselected package libucx0:arm64. 122s Preparing to unpack .../109-libucx0_1.19.0+ds-1_arm64.deb ... 122s Unpacking libucx0:arm64 (1.19.0+ds-1) ... 122s Selecting previously unselected package libpciaccess0:arm64. 122s Preparing to unpack .../110-libpciaccess0_0.18.1-1ubuntu2_arm64.deb ... 122s Unpacking libpciaccess0:arm64 (0.18.1-1ubuntu2) ... 122s Selecting previously unselected package libxnvctrl0:arm64. 122s Preparing to unpack .../111-libxnvctrl0_510.47.03-0ubuntu4_arm64.deb ... 122s Unpacking libxnvctrl0:arm64 (510.47.03-0ubuntu4) ... 122s Selecting previously unselected package ocl-icd-libopencl1:arm64. 122s Preparing to unpack .../112-ocl-icd-libopencl1_2.3.3-1_arm64.deb ... 122s Unpacking ocl-icd-libopencl1:arm64 (2.3.3-1) ... 122s Selecting previously unselected package libhwloc-plugins:arm64. 122s Preparing to unpack .../113-libhwloc-plugins_2.12.2-1_arm64.deb ... 122s Unpacking libhwloc-plugins:arm64 (2.12.2-1) ... 122s Selecting previously unselected package libopenmpi40:arm64. 122s Preparing to unpack .../114-libopenmpi40_5.0.8-8ubuntu1_arm64.deb ... 122s Unpacking libopenmpi40:arm64 (5.0.8-8ubuntu1) ... 122s Selecting previously unselected package openmpi-common. 122s Preparing to unpack .../115-openmpi-common_5.0.8-8ubuntu1_all.deb ... 122s Unpacking openmpi-common (5.0.8-8ubuntu1) ... 122s Selecting previously unselected package openmpi-bin. 122s Preparing to unpack .../116-openmpi-bin_5.0.8-8ubuntu1_arm64.deb ... 122s Unpacking openmpi-bin (5.0.8-8ubuntu1) ... 122s Selecting previously unselected package mpi-default-bin. 122s Preparing to unpack .../117-mpi-default-bin_1.18_arm64.deb ... 122s Unpacking mpi-default-bin (1.18) ... 122s Selecting previously unselected package examl. 123s Preparing to unpack .../118-examl_3.0.22-6build1_arm64.deb ... 123s Unpacking examl (3.0.22-6build1) ... 123s Selecting previously unselected package libhamcrest-java. 123s Preparing to unpack .../119-libhamcrest-java_2.2-2_all.deb ... 123s Unpacking libhamcrest-java (2.2-2) ... 123s Selecting previously unselected package junit4. 123s Preparing to unpack .../120-junit4_4.13.2-5_all.deb ... 123s Unpacking junit4 (4.13.2-5) ... 123s Selecting previously unselected package libapache-pom-java. 123s Preparing to unpack .../121-libapache-pom-java_33-2_all.deb ... 123s Unpacking libapache-pom-java (33-2) ... 123s Selecting previously unselected package libcommons-parent-java. 123s Preparing to unpack .../122-libcommons-parent-java_56-1_all.deb ... 123s Unpacking libcommons-parent-java (56-1) ... 123s Selecting previously unselected package libcommons-lang3-java. 123s Preparing to unpack .../123-libcommons-lang3-java_3.17.0-1_all.deb ... 123s Unpacking libcommons-lang3-java (3.17.0-1) ... 123s Selecting previously unselected package libfreemarker-java. 123s Preparing to unpack .../124-libfreemarker-java_2.3.32-2.1_all.deb ... 123s Unpacking libfreemarker-java (2.3.32-2.1) ... 123s Selecting previously unselected package libgoogle-gson-java. 123s Preparing to unpack .../125-libgoogle-gson-java_2.10.1-1_all.deb ... 123s Unpacking libgoogle-gson-java (2.10.1-1) ... 123s Selecting previously unselected package libjoptsimple-java. 123s Preparing to unpack .../126-libjoptsimple-java_5.0.4-7_all.deb ... 123s Unpacking libjoptsimple-java (5.0.4-7) ... 123s Selecting previously unselected package libcommons-codec-java. 123s Preparing to unpack .../127-libcommons-codec-java_1.18.0-1_all.deb ... 123s Unpacking libcommons-codec-java (1.18.0-1) ... 123s Selecting previously unselected package libcommons-logging-java. 123s Preparing to unpack .../128-libcommons-logging-java_1.3.0-1ubuntu1_all.deb ... 123s Unpacking libcommons-logging-java (1.3.0-1ubuntu1) ... 123s Selecting previously unselected package libhttpcore-java. 123s Preparing to unpack .../129-libhttpcore-java_4.4.16-1_all.deb ... 123s Unpacking libhttpcore-java (4.4.16-1) ... 123s Selecting previously unselected package libhttpclient-java. 123s Preparing to unpack .../130-libhttpclient-java_4.5.14-1_all.deb ... 123s Unpacking libhttpclient-java (4.5.14-1) ... 123s Selecting previously unselected package liblightcouch-java. 123s Preparing to unpack .../131-liblightcouch-java_0.2.0-1_all.deb ... 123s Unpacking liblightcouch-java (0.2.0-1) ... 124s Selecting previously unselected package libmongodb-java. 124s Preparing to unpack .../132-libmongodb-java_3.6.3-2_all.deb ... 124s Unpacking libmongodb-java (3.6.3-2) ... 124s Selecting previously unselected package libslf4j-java. 124s Preparing to unpack .../133-libslf4j-java_1.7.32-2_all.deb ... 124s Unpacking libslf4j-java (1.7.32-2) ... 124s Selecting previously unselected package liblog4j2-java. 124s Preparing to unpack .../134-liblog4j2-java_2.19.0-2_all.deb ... 124s Unpacking liblog4j2-java (2.19.0-2) ... 124s Selecting previously unselected package libbarclay-java. 124s Preparing to unpack .../135-libbarclay-java_5.0.0+dfsg-1_all.deb ... 124s Unpacking libbarclay-java (5.0.0+dfsg-1) ... 124s Selecting previously unselected package libblas3:arm64. 124s Preparing to unpack .../136-libblas3_3.12.1-6build1_arm64.deb ... 124s Unpacking libblas3:arm64 (3.12.1-6build1) ... 124s Selecting previously unselected package libcommons-collections3-java. 124s Preparing to unpack .../137-libcommons-collections3-java_3.2.2-3_all.deb ... 124s Unpacking libcommons-collections3-java (3.2.2-3) ... 124s Selecting previously unselected package libcommons-beanutils-java. 124s Preparing to unpack .../138-libcommons-beanutils-java_1.10.1-1.1_all.deb ... 124s Unpacking libcommons-beanutils-java (1.10.1-1.1) ... 124s Selecting previously unselected package libcommons-collections4-java. 125s Preparing to unpack .../139-libcommons-collections4-java_4.4-2_all.deb ... 125s Unpacking libcommons-collections4-java (4.4-2) ... 125s Selecting previously unselected package libcommons-io-java. 125s Preparing to unpack .../140-libcommons-io-java_2.19.0-1_all.deb ... 125s Unpacking libcommons-io-java (2.19.0-1) ... 125s Selecting previously unselected package libcommons-compress-java. 125s Preparing to unpack .../141-libcommons-compress-java_1.27.1-2_all.deb ... 125s Unpacking libcommons-compress-java (1.27.1-2) ... 125s Selecting previously unselected package libcommons-jexl2-java. 125s Preparing to unpack .../142-libcommons-jexl2-java_2.1.1-6_all.deb ... 125s Unpacking libcommons-jexl2-java (2.1.1-6) ... 125s Selecting previously unselected package libcommons-math3-java. 125s Preparing to unpack .../143-libcommons-math3-java_3.6.1-4_all.deb ... 125s Unpacking libcommons-math3-java (3.6.1-4) ... 125s Selecting previously unselected package libezmorph-java. 125s Preparing to unpack .../144-libezmorph-java_1.0.6-4_all.deb ... 125s Unpacking libezmorph-java (1.0.6-4) ... 125s Selecting previously unselected package libgatk-native-bindings-java. 125s Preparing to unpack .../145-libgatk-native-bindings-java_1.0.0+dfsg-2_all.deb ... 125s Unpacking libgatk-native-bindings-java (1.0.0+dfsg-2) ... 125s Selecting previously unselected package libgfortran5:arm64. 125s Preparing to unpack .../146-libgfortran5_15.2.0-5ubuntu1_arm64.deb ... 125s Unpacking libgfortran5:arm64 (15.2.0-5ubuntu1) ... 125s Selecting previously unselected package libjaxen-java. 125s Preparing to unpack .../147-libjaxen-java_1.1.6-5_all.deb ... 125s Unpacking libjaxen-java (1.1.6-5) ... 125s Selecting previously unselected package libxml-commons-external-java. 125s Preparing to unpack .../148-libxml-commons-external-java_1.4.01-6_all.deb ... 125s Unpacking libxml-commons-external-java (1.4.01-6) ... 125s Selecting previously unselected package libxml-commons-resolver1.1-java. 125s Preparing to unpack .../149-libxml-commons-resolver1.1-java_1.2-11_all.deb ... 125s Unpacking libxml-commons-resolver1.1-java (1.2-11) ... 125s Selecting previously unselected package libxerces2-java. 125s Preparing to unpack .../150-libxerces2-java_2.12.2-1_all.deb ... 125s Unpacking libxerces2-java (2.12.2-1) ... 125s Selecting previously unselected package libxom-java. 125s Preparing to unpack .../151-libxom-java_1.3.9-1_all.deb ... 125s Unpacking libxom-java (1.3.9-1) ... 125s Selecting previously unselected package libjson-java. 125s Preparing to unpack .../152-libjson-java_3.1.0+dfsg-2_all.deb ... 125s Unpacking libjson-java (3.1.0+dfsg-2) ... 125s Selecting previously unselected package libmbedcrypto16:arm64. 126s Preparing to unpack .../153-libmbedcrypto16_3.6.2-3ubuntu1_arm64.deb ... 126s Unpacking libmbedcrypto16:arm64 (3.6.2-3ubuntu1) ... 126s Selecting previously unselected package libmbedx509-7:arm64. 126s Preparing to unpack .../154-libmbedx509-7_3.6.2-3ubuntu1_arm64.deb ... 126s Unpacking libmbedx509-7:arm64 (3.6.2-3ubuntu1) ... 126s Selecting previously unselected package libmbedtls21:arm64. 126s Preparing to unpack .../155-libmbedtls21_3.6.2-3ubuntu1_arm64.deb ... 126s Unpacking libmbedtls21:arm64 (3.6.2-3ubuntu1) ... 126s Selecting previously unselected package ncbi-vdb-data. 126s Preparing to unpack .../156-ncbi-vdb-data_3.2.1+dfsg-2_all.deb ... 126s Unpacking ncbi-vdb-data (3.2.1+dfsg-2) ... 126s Selecting previously unselected package libncbi-vdb3:arm64. 126s Preparing to unpack .../157-libncbi-vdb3_3.2.1+dfsg-2_arm64.deb ... 126s Unpacking libncbi-vdb3:arm64 (3.2.1+dfsg-2) ... 126s Selecting previously unselected package libncbi-ngs3:arm64. 126s Preparing to unpack .../158-libncbi-ngs3_3.2.1+dfsg-4ubuntu5_arm64.deb ... 126s Unpacking libncbi-ngs3:arm64 (3.2.1+dfsg-4ubuntu5) ... 126s Selecting previously unselected package libngs-jni:arm64. 126s Preparing to unpack .../159-libngs-jni_3.2.1+dfsg-4ubuntu5_arm64.deb ... 126s Unpacking libngs-jni:arm64 (3.2.1+dfsg-4ubuntu5) ... 126s Selecting previously unselected package libngs-java:arm64. 126s Preparing to unpack .../160-libngs-java_3.2.1+dfsg-4ubuntu5_arm64.deb ... 126s Unpacking libngs-java:arm64 (3.2.1+dfsg-4ubuntu5) ... 126s Selecting previously unselected package librhino-java. 126s Preparing to unpack .../161-librhino-java_1.7.15-1_all.deb ... 126s Unpacking librhino-java (1.7.15-1) ... 126s Selecting previously unselected package libsnappy1v5:arm64. 126s Preparing to unpack .../162-libsnappy1v5_1.2.2-1_arm64.deb ... 126s Unpacking libsnappy1v5:arm64 (1.2.2-1) ... 126s Selecting previously unselected package libsnappy-jni. 126s Preparing to unpack .../163-libsnappy-jni_1.1.10.7-1_arm64.deb ... 126s Unpacking libsnappy-jni (1.1.10.7-1) ... 126s Selecting previously unselected package libsnappy-java. 126s Preparing to unpack .../164-libsnappy-java_1.1.10.7-1_all.deb ... 126s Unpacking libsnappy-java (1.1.10.7-1) ... 126s Selecting previously unselected package libhtsjdk-java. 126s Preparing to unpack .../165-libhtsjdk-java_4.1.3+dfsg-2_all.deb ... 126s Unpacking libhtsjdk-java (4.1.3+dfsg-2) ... 126s Selecting previously unselected package libgkl-java. 126s Preparing to unpack .../166-libgkl-java_0.8.11+dfsg-2build1_all.deb ... 126s Unpacking libgkl-java (0.8.11+dfsg-2build1) ... 126s Selecting previously unselected package libgslcblas0:arm64. 126s Preparing to unpack .../167-libgslcblas0_2.8+dfsg-5.1ubuntu1_arm64.deb ... 126s Unpacking libgslcblas0:arm64 (2.8+dfsg-5.1ubuntu1) ... 127s Selecting previously unselected package libgsl28:arm64. 127s Preparing to unpack .../168-libgsl28_2.8+dfsg-5.1ubuntu1_arm64.deb ... 127s Unpacking libgsl28:arm64 (2.8+dfsg-5.1ubuntu1) ... 127s Selecting previously unselected package libgsl-dev. 127s Preparing to unpack .../169-libgsl-dev_2.8+dfsg-5.1ubuntu1_arm64.deb ... 127s Unpacking libgsl-dev (2.8+dfsg-5.1ubuntu1) ... 127s Selecting previously unselected package libice6:arm64. 127s Preparing to unpack .../170-libice6_2%3a1.1.1-1_arm64.deb ... 127s Unpacking libice6:arm64 (2:1.1.1-1) ... 127s Selecting previously unselected package libicu76:arm64. 127s Preparing to unpack .../171-libicu76_76.1-4ubuntu2_arm64.deb ... 127s Unpacking libicu76:arm64 (76.1-4ubuntu2) ... 127s Selecting previously unselected package libopenblas0-pthread:arm64. 127s Preparing to unpack .../172-libopenblas0-pthread_0.3.30+ds-3_arm64.deb ... 127s Unpacking libopenblas0-pthread:arm64 (0.3.30+ds-3) ... 128s Selecting previously unselected package liblapack3:arm64. 128s Preparing to unpack .../173-liblapack3_3.12.1-6build1_arm64.deb ... 128s Unpacking liblapack3:arm64 (3.12.1-6build1) ... 128s Selecting previously unselected package libopenblas0:arm64. 128s Preparing to unpack .../174-libopenblas0_0.3.30+ds-3_arm64.deb ... 128s Unpacking libopenblas0:arm64 (0.3.30+ds-3) ... 128s Selecting previously unselected package libopenblas-pthread-dev:arm64. 128s Preparing to unpack .../175-libopenblas-pthread-dev_0.3.30+ds-3_arm64.deb ... 128s Unpacking libopenblas-pthread-dev:arm64 (0.3.30+ds-3) ... 128s Selecting previously unselected package libopenblas-dev:arm64. 128s Preparing to unpack .../176-libopenblas-dev_0.3.30+ds-3_arm64.deb ... 128s Unpacking libopenblas-dev:arm64 (0.3.30+ds-3) ... 128s Selecting previously unselected package libpaper2:arm64. 128s Preparing to unpack .../177-libpaper2_2.2.5-0.3_arm64.deb ... 128s Unpacking libpaper2:arm64 (2.2.5-0.3) ... 128s Selecting previously unselected package libpaper-utils. 128s Preparing to unpack .../178-libpaper-utils_2.2.5-0.3_arm64.deb ... 128s Unpacking libpaper-utils (2.2.5-0.3) ... 128s Selecting previously unselected package libpicard-java. 128s Preparing to unpack .../179-libpicard-java_3.3.0+dfsg-2_all.deb ... 128s Unpacking libpicard-java (3.3.0+dfsg-2) ... 129s Selecting previously unselected package libsm6:arm64. 129s Preparing to unpack .../180-libsm6_2%3a1.2.6-1_arm64.deb ... 129s Unpacking libsm6:arm64 (2:1.2.6-1) ... 129s Selecting previously unselected package libtcl8.6:arm64. 129s Preparing to unpack .../181-libtcl8.6_8.6.17+dfsg-1_arm64.deb ... 129s Unpacking libtcl8.6:arm64 (8.6.17+dfsg-1) ... 129s Selecting previously unselected package libxft2:arm64. 129s Preparing to unpack .../182-libxft2_2.3.6-1build1_arm64.deb ... 129s Unpacking libxft2:arm64 (2.3.6-1build1) ... 129s Selecting previously unselected package libxss1:arm64. 129s Preparing to unpack .../183-libxss1_1%3a1.2.3-1build3_arm64.deb ... 129s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 129s Selecting previously unselected package libtk8.6:arm64. 129s Preparing to unpack .../184-libtk8.6_8.6.17-1_arm64.deb ... 129s Unpacking libtk8.6:arm64 (8.6.17-1) ... 129s Selecting previously unselected package libxt6t64:arm64. 129s Preparing to unpack .../185-libxt6t64_1%3a1.2.1-1.3_arm64.deb ... 129s Unpacking libxt6t64:arm64 (1:1.2.1-1.3) ... 129s Selecting previously unselected package mafft. 129s Preparing to unpack .../186-mafft_7.525-1_arm64.deb ... 129s Unpacking mafft (7.525-1) ... 129s Selecting previously unselected package zip. 129s Preparing to unpack .../187-zip_3.0-15ubuntu2_arm64.deb ... 129s Unpacking zip (3.0-15ubuntu2) ... 129s Selecting previously unselected package unzip. 129s Preparing to unpack .../188-unzip_6.0-28ubuntu7_arm64.deb ... 129s Unpacking unzip (6.0-28ubuntu7) ... 129s Selecting previously unselected package xdg-utils. 129s Preparing to unpack .../189-xdg-utils_1.2.1-2ubuntu1_all.deb ... 129s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 129s Selecting previously unselected package r-base-core. 129s Preparing to unpack .../190-r-base-core_4.5.1-1_arm64.deb ... 129s Unpacking r-base-core (4.5.1-1) ... 130s Selecting previously unselected package r-cran-codetools. 130s Preparing to unpack .../191-r-cran-codetools_0.2-20-1_all.deb ... 130s Unpacking r-cran-codetools (0.2-20-1) ... 130s Selecting previously unselected package r-cran-iterators. 130s Preparing to unpack .../192-r-cran-iterators_1.0.14-1_all.deb ... 130s Unpacking r-cran-iterators (1.0.14-1) ... 130s Selecting previously unselected package r-cran-foreach. 130s Preparing to unpack .../193-r-cran-foreach_1.5.2-1_all.deb ... 130s Unpacking r-cran-foreach (1.5.2-1) ... 130s Selecting previously unselected package r-cran-gam. 130s Preparing to unpack .../194-r-cran-gam_1.22-5-1_arm64.deb ... 130s Unpacking r-cran-gam (1.22-5-1) ... 130s Selecting previously unselected package r-cran-cli. 130s Preparing to unpack .../195-r-cran-cli_3.6.4-1_arm64.deb ... 130s Unpacking r-cran-cli (3.6.4-1) ... 130s Selecting previously unselected package r-cran-glue. 130s Preparing to unpack .../196-r-cran-glue_1.8.0-1_arm64.deb ... 130s Unpacking r-cran-glue (1.8.0-1) ... 130s Selecting previously unselected package r-cran-rlang. 130s Preparing to unpack .../197-r-cran-rlang_1.1.5-3_arm64.deb ... 130s Unpacking r-cran-rlang (1.1.5-3) ... 131s Selecting previously unselected package r-cran-lifecycle. 131s Preparing to unpack .../198-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 131s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 131s Selecting previously unselected package r-cran-gtable. 131s Preparing to unpack .../199-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 131s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 131s Selecting previously unselected package r-cran-isoband. 131s Preparing to unpack .../200-r-cran-isoband_0.2.7-1_arm64.deb ... 131s Unpacking r-cran-isoband (0.2.7-1) ... 131s Selecting previously unselected package r-cran-mass. 131s Preparing to unpack .../201-r-cran-mass_7.3-65-1_arm64.deb ... 131s Unpacking r-cran-mass (7.3-65-1) ... 131s Selecting previously unselected package r-cran-lattice. 131s Preparing to unpack .../202-r-cran-lattice_0.22-7-1_arm64.deb ... 131s Unpacking r-cran-lattice (0.22-7-1) ... 131s Selecting previously unselected package r-cran-nlme. 131s Preparing to unpack .../203-r-cran-nlme_3.1.168-1_arm64.deb ... 131s Unpacking r-cran-nlme (3.1.168-1) ... 131s Selecting previously unselected package r-cran-matrix. 131s Preparing to unpack .../204-r-cran-matrix_1.7-3-1_arm64.deb ... 131s Unpacking r-cran-matrix (1.7-3-1) ... 131s Selecting previously unselected package r-cran-mgcv. 131s Preparing to unpack .../205-r-cran-mgcv_1.9-3-1_arm64.deb ... 131s Unpacking r-cran-mgcv (1.9-3-1) ... 131s Selecting previously unselected package r-cran-farver. 131s Preparing to unpack .../206-r-cran-farver_2.1.2-1_arm64.deb ... 131s Unpacking r-cran-farver (2.1.2-1) ... 131s Selecting previously unselected package r-cran-labeling. 131s Preparing to unpack .../207-r-cran-labeling_0.4.3-1_all.deb ... 131s Unpacking r-cran-labeling (0.4.3-1) ... 131s Selecting previously unselected package r-cran-colorspace. 131s Preparing to unpack .../208-r-cran-colorspace_2.1-1+dfsg-1_arm64.deb ... 131s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ... 132s Selecting previously unselected package r-cran-munsell. 132s Preparing to unpack .../209-r-cran-munsell_0.5.1-1_all.deb ... 132s Unpacking r-cran-munsell (0.5.1-1) ... 132s Selecting previously unselected package r-cran-r6. 132s Preparing to unpack .../210-r-cran-r6_2.6.1-1_all.deb ... 132s Unpacking r-cran-r6 (2.6.1-1) ... 132s Selecting previously unselected package r-cran-rcolorbrewer. 132s Preparing to unpack .../211-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ... 132s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ... 132s Selecting previously unselected package r-cran-viridislite. 132s Preparing to unpack .../212-r-cran-viridislite_0.4.2-2_all.deb ... 132s Unpacking r-cran-viridislite (0.4.2-2) ... 132s Selecting previously unselected package r-cran-scales. 132s Preparing to unpack .../213-r-cran-scales_1.3.0-1_all.deb ... 132s Unpacking r-cran-scales (1.3.0-1) ... 132s Selecting previously unselected package r-cran-fansi. 132s Preparing to unpack .../214-r-cran-fansi_1.0.6-2_arm64.deb ... 132s Unpacking r-cran-fansi (1.0.6-2) ... 132s Selecting previously unselected package r-cran-magrittr. 132s Preparing to unpack .../215-r-cran-magrittr_2.0.3-1_arm64.deb ... 132s Unpacking r-cran-magrittr (2.0.3-1) ... 132s Selecting previously unselected package r-cran-utf8. 132s Preparing to unpack .../216-r-cran-utf8_1.2.4-1_arm64.deb ... 132s Unpacking r-cran-utf8 (1.2.4-1) ... 132s Selecting previously unselected package r-cran-vctrs. 132s Preparing to unpack .../217-r-cran-vctrs_0.6.5-1_arm64.deb ... 132s Unpacking r-cran-vctrs (0.6.5-1) ... 132s Selecting previously unselected package r-cran-pillar. 132s Preparing to unpack .../218-r-cran-pillar_1.10.1+dfsg-1_all.deb ... 132s Unpacking r-cran-pillar (1.10.1+dfsg-1) ... 132s Selecting previously unselected package r-cran-pkgconfig. 132s Preparing to unpack .../219-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 132s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 132s Selecting previously unselected package r-cran-tibble. 132s Preparing to unpack .../220-r-cran-tibble_3.2.1+dfsg-3_arm64.deb ... 132s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 133s Selecting previously unselected package r-cran-withr. 133s Preparing to unpack .../221-r-cran-withr_3.0.2+dfsg-1_all.deb ... 133s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 133s Selecting previously unselected package r-cran-ggplot2. 133s Preparing to unpack .../222-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ... 133s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ... 133s Selecting previously unselected package r-cran-inline. 133s Preparing to unpack .../223-r-cran-inline_0.3.21-1_all.deb ... 133s Unpacking r-cran-inline (0.3.21-1) ... 133s Selecting previously unselected package seqtk. 133s Preparing to unpack .../224-seqtk_1.4-2_arm64.deb ... 133s Unpacking seqtk (1.4-2) ... 133s Selecting previously unselected package python3-pysam. 133s Preparing to unpack .../225-python3-pysam_0.23.0+ds-1build1_arm64.deb ... 133s Unpacking python3-pysam (0.23.0+ds-1build1) ... 133s Selecting previously unselected package r-cran-littler. 133s Preparing to unpack .../226-r-cran-littler_0.3.21-1_arm64.deb ... 133s Unpacking r-cran-littler (0.3.21-1) ... 133s Selecting previously unselected package r-cran-pkgkitten. 133s Preparing to unpack .../227-r-cran-pkgkitten_0.2.4-1_all.deb ... 133s Unpacking r-cran-pkgkitten (0.2.4-1) ... 133s Selecting previously unselected package r-cran-rcpp. 133s Preparing to unpack .../228-r-cran-rcpp_1.1.0-1_arm64.deb ... 133s Unpacking r-cran-rcpp (1.1.0-1) ... 134s Selecting previously unselected package r-cran-rcppgsl. 134s Preparing to unpack .../229-r-cran-rcppgsl_0.3.13-1build1_arm64.deb ... 134s Unpacking r-cran-rcppgsl (0.3.13-1build1) ... 134s Selecting previously unselected package mapdamage. 134s Preparing to unpack .../230-mapdamage_2.2.2+dfsg-1_all.deb ... 134s Unpacking mapdamage (2.2.2+dfsg-1) ... 134s Selecting previously unselected package python3-humanfriendly. 134s Preparing to unpack .../231-python3-humanfriendly_10.0-6_all.deb ... 134s Unpacking python3-humanfriendly (10.0-6) ... 134s Selecting previously unselected package python3-coloredlogs. 134s Preparing to unpack .../232-python3-coloredlogs_15.0.1-1_all.deb ... 134s Unpacking python3-coloredlogs (15.0.1-1) ... 134s Selecting previously unselected package python3-configargparse. 134s Preparing to unpack .../233-python3-configargparse_1.7-2_all.deb ... 134s Unpacking python3-configargparse (1.7-2) ... 134s Selecting previously unselected package python3-ruamel.yaml.clib. 134s Preparing to unpack .../234-python3-ruamel.yaml.clib_0.2.12+ds-1build1_arm64.deb ... 134s Unpacking python3-ruamel.yaml.clib (0.2.12+ds-1build1) ... 134s Selecting previously unselected package python3-ruamel.yaml. 134s Preparing to unpack .../235-python3-ruamel.yaml_0.18.10+ds-1_all.deb ... 134s Unpacking python3-ruamel.yaml (0.18.10+ds-1) ... 134s Selecting previously unselected package python3-setproctitle:arm64. 134s Preparing to unpack .../236-python3-setproctitle_1.3.7-1_arm64.deb ... 134s Unpacking python3-setproctitle:arm64 (1.3.7-1) ... 134s Selecting previously unselected package bowtie2. 134s Preparing to unpack .../237-bowtie2_2.5.4-1_arm64.deb ... 134s Unpacking bowtie2 (2.5.4-1) ... 134s Selecting previously unselected package phylip. 134s Preparing to unpack .../238-phylip_1%3a3.697+dfsg-4build1_arm64.deb ... 134s Unpacking phylip (1:3.697+dfsg-4build1) ... 134s Selecting previously unselected package picard-tools. 134s Preparing to unpack .../239-picard-tools_3.3.0+dfsg-2_all.deb ... 134s Unpacking picard-tools (3.3.0+dfsg-2) ... 134s Selecting previously unselected package radiant. 135s Preparing to unpack .../240-radiant_2.8.1+dfsg-2_all.deb ... 135s Unpacking radiant (2.8.1+dfsg-2) ... 135s Selecting previously unselected package raxml. 135s Preparing to unpack .../241-raxml_8.2.13+dfsg-2_arm64.deb ... 135s Unpacking raxml (8.2.13+dfsg-2) ... 135s Selecting previously unselected package samtools. 135s Preparing to unpack .../242-samtools_1.21-1_arm64.deb ... 135s Unpacking samtools (1.21-1) ... 135s Selecting previously unselected package paleomix. 135s Preparing to unpack .../243-paleomix_1.3.8-2_arm64.deb ... 135s Unpacking paleomix (1.3.8-2) ... 135s Selecting previously unselected package python3-iniconfig. 135s Preparing to unpack .../244-python3-iniconfig_1.1.1-2_all.deb ... 135s Unpacking python3-iniconfig (1.1.1-2) ... 135s Selecting previously unselected package python3-packaging. 135s Preparing to unpack .../245-python3-packaging_25.0-1_all.deb ... 135s Unpacking python3-packaging (25.0-1) ... 135s Selecting previously unselected package python3-pluggy. 135s Preparing to unpack .../246-python3-pluggy_1.6.0-1_all.deb ... 135s Unpacking python3-pluggy (1.6.0-1) ... 135s Selecting previously unselected package python3-pytest. 135s Preparing to unpack .../247-python3-pytest_8.4.2-1_all.deb ... 135s Unpacking python3-pytest (8.4.2-1) ... 135s Setting up libhtscodecs2:arm64 (1.6.1-2) ... 135s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 135s Setting up python3-configargparse (1.7-2) ... 135s Setting up libxcb-dri3-0:arm64 (1.17.0-2build1) ... 135s Setting up liblcms2-2:arm64 (2.16-2) ... 135s Setting up python3-iniconfig (1.1.1-2) ... 136s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 136s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 136s Setting up libx11-xcb1:arm64 (2:1.8.12-1build1) ... 136s Setting up libpciaccess0:arm64 (0.18.1-1ubuntu2) ... 136s Setting up libslf4j-java (1.7.32-2) ... 136s Setting up adapterremoval (2.3.4-1) ... 136s Setting up libxdamage1:arm64 (1:1.1.6-1build1) ... 136s Setting up libxcb-xfixes0:arm64 (1.17.0-2build1) ... 136s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 136s Setting up seqtk (1.4-2) ... 136s Setting up hicolor-icon-theme (0.18-2) ... 136s Setting up libxi6:arm64 (2:1.8.2-1) ... 136s Setting up libgatk-native-bindings-java (1.0.0+dfsg-2) ... 136s Setting up java-common (0.76) ... 136s Setting up libxrender1:arm64 (1:0.9.12-1) ... 136s Setting up libdatrie1:arm64 (0.2.13-4) ... 136s Setting up libgslcblas0:arm64 (2.8+dfsg-5.1ubuntu1) ... 136s Setting up libxcb-render0:arm64 (1.17.0-2build1) ... 136s Setting up mafft (7.525-1) ... 136s Setting up bwa (0.7.18-1) ... 136s Setting up libglvnd0:arm64 (1.7.0-1build2) ... 136s Setting up libgoogle-gson-java (2.10.1-1) ... 136s Setting up radiant (2.8.1+dfsg-2) ... 136s Setting up libxcb-glx0:arm64 (1.17.0-2build1) ... 136s Setting up unzip (6.0-28ubuntu7) ... 136s Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-5) ... 136s Setting up phylip (1:3.697+dfsg-4build1) ... 136s Setting up python3-ruamel.yaml.clib (0.2.12+ds-1build1) ... 136s Setting up x11-common (1:7.7+24ubuntu1) ... 136s Setting up libibumad3:arm64 (56.1-1ubuntu1) ... 136s Setting up libdeflate0:arm64 (1.23-2) ... 136s Setting up libxcb-shm0:arm64 (1.17.0-2build1) ... 136s Setting up libibmad5:arm64 (56.1-1ubuntu1) ... 136s Setting up libgomp1:arm64 (15.2.0-5ubuntu1) ... 136s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 136s Setting up libcolord2:arm64 (1.4.7-3build1) ... 136s Setting up libxxf86vm1:arm64 (1:1.1.4-1build4) ... 136s Setting up libsnappy1v5:arm64 (1.2.2-1) ... 136s Setting up bowtie2 (2.5.4-1) ... 136s Setting up libxnvctrl0:arm64 (510.47.03-0ubuntu4) ... 136s Setting up libxcb-present0:arm64 (1.17.0-2build1) ... 136s Setting up libdconf1:arm64 (0.40.0-5willsync1) ... 136s Setting up libcommons-collections3-java (3.2.2-3) ... 136s Setting up libasound2-data (1.2.14-1ubuntu1) ... 136s Setting up zip (3.0-15ubuntu2) ... 136s Setting up librhino-java (1.7.15-1) ... 136s Setting up libblas3:arm64 (3.12.1-6build1) ... 136s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 136s Setting up python3-packaging (25.0-1) ... 137s Setting up libasound2t64:arm64 (1.2.14-1ubuntu1) ... 137s Setting up libllvm17t64:arm64 (1:17.0.6-22build1) ... 137s Setting up libjaxen-java (1.1.6-5) ... 137s Setting up python3-humanfriendly (10.0-6) ... 137s Setting up libepoxy0:arm64 (1.5.10-2) ... 137s Setting up libnspr4:arm64 (2:4.36-1ubuntu2) ... 137s Setting up libxfixes3:arm64 (1:6.0.0-2build1) ... 137s Setting up libxcb-sync1:arm64 (1.17.0-2build1) ... 137s Setting up libapache-pom-java (33-2) ... 137s Setting up libavahi-common-data:arm64 (0.8-16ubuntu3) ... 137s Setting up libatspi2.0-0t64:arm64 (2.57.1-1) ... 137s Setting up libxinerama1:arm64 (2:1.1.4-3build1) ... 137s Setting up fonts-dejavu-mono (2.37-8) ... 137s Setting up libhwloc15:arm64 (2.12.2-1) ... 137s Setting up libxml-commons-resolver1.1-java (1.2-11) ... 137s Setting up python3-setproctitle:arm64 (1.3.7-1) ... 137s Setting up libxrandr2:arm64 (2:1.5.4-1) ... 137s Setting up libtcl8.6:arm64 (8.6.17+dfsg-1) ... 137s Setting up fonts-dejavu-core (2.37-8) ... 137s Setting up libpcsclite1:arm64 (2.3.3-1) ... 137s Setting up libmongodb-java (3.6.3-2) ... 137s Setting up libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 137s Setting up libhamcrest-java (2.2-2) ... 137s Setting up libgfortran5:arm64 (15.2.0-5ubuntu1) ... 137s Setting up libvulkan1:arm64 (1.4.321.0-1) ... 137s Setting up python3-pluggy (1.6.0-1) ... 138s Setting up libwebp7:arm64 (1.5.0-0.1) ... 138s Setting up python3-ruamel.yaml (0.18.10+ds-1) ... 138s Setting up libgif7:arm64 (5.2.2-1ubuntu2) ... 138s Setting up libfreemarker-java (2.3.32-2.1) ... 138s Setting up ocl-icd-libopencl1:arm64 (2.3.3-1) ... 138s Setting up libxshmfence1:arm64 (1.3.3-1) ... 138s Setting up at-spi2-common (2.57.1-1) ... 138s Setting up libxcb-randr0:arm64 (1.17.0-2build1) ... 138s Setting up libxml-commons-external-java (1.4.01-6) ... 138s Setting up openmpi-common (5.0.8-8ubuntu1) ... 138s Setting up libhts3t64:arm64 (1.21+ds-1) ... 138s Setting up librdmacm1t64:arm64 (56.1-1ubuntu1) ... 138s Setting up libharfbuzz0b:arm64 (12.1.0-1) ... 138s Setting up ncbi-vdb-data (3.2.1+dfsg-2) ... 138s Setting up libthai-data (0.1.29-2build1) ... 138s Setting up libcommons-math3-java (3.6.1-4) ... 138s Setting up libevent-core-2.1-7t64:arm64 (2.1.12-stable-10build1) ... 138s Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3build3) ... 138s Setting up libwayland-egl1:arm64 (1.24.0-1build1) ... 138s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 138s Setting up libicu76:arm64 (76.1-4ubuntu2) ... 138s Setting up libmbedcrypto16:arm64 (3.6.2-3ubuntu1) ... 138s Setting up libpaper2:arm64 (2.2.5-0.3) ... 139s Setting up libhttpcore-java (4.4.16-1) ... 139s Setting up libjoptsimple-java (5.0.4-7) ... 139s Setting up ca-certificates-java (20240118) ... 139s No JRE found. Skipping Java certificates setup. 139s Setting up libxerces2-java (2.12.2-1) ... 139s Setting up libgsl28:arm64 (2.8+dfsg-5.1ubuntu1) ... 139s Setting up python3-coloredlogs (15.0.1-1) ... 139s Setting up libsnappy-jni (1.1.10.7-1) ... 139s Setting up libezmorph-java (1.0.6-4) ... 139s Setting up libxcomposite1:arm64 (1:0.4.6-1) ... 139s Setting up xdg-utils (1.2.1-2ubuntu1) ... 139s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 139s Setting up bedtools (2.31.1+dfsg-2) ... 139s Setting up raxml (8.2.13+dfsg-2) ... 139s Setting up libdrm-amdgpu1:arm64 (2.4.125-1) ... 139s Setting up libwayland-client0:arm64 (1.24.0-1build1) ... 139s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 139s Setting up libfabric1:arm64 (2.1.0-1.1) ... 139s Setting up libice6:arm64 (2:1.1.1-1) ... 139s Setting up mesa-libgallium:arm64 (25.2.3-1ubuntu1) ... 139s Setting up liblapack3:arm64 (3.12.1-6build1) ... 139s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 139s Setting up libgsl-dev (2.8+dfsg-5.1ubuntu1) ... 139s Setting up libopenblas0-pthread:arm64 (0.3.30+ds-3) ... 139s update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 139s update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 139s update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/aarch64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-aarch64-linux-gnu) in auto mode 139s Setting up python3-pysam (0.23.0+ds-1build1) ... 139s Setting up libatk1.0-0t64:arm64 (2.57.1-1) ... 139s Setting up libgbm1:arm64 (25.2.3-1ubuntu1) ... 139s Setting up libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10build1) ... 139s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 140s Setting up python3-pytest (8.4.2-1) ... 140s Setting up libxtst6:arm64 (2:1.2.5-1) ... 140s Setting up libxcursor1:arm64 (1:1.2.3-1) ... 140s Setting up libgl1-mesa-dri:arm64 (25.2.3-1ubuntu1) ... 140s Setting up bcftools (1.21-1) ... 140s Setting up libcommons-parent-java (56-1) ... 140s Setting up libavahi-common3:arm64 (0.8-16ubuntu3) ... 140s Setting up libcommons-logging-java (1.3.0-1ubuntu1) ... 140s Setting up dconf-service (0.40.0-5willsync1) ... 140s Setting up libnss3:arm64 (2:3.114-1) ... 140s Setting up libpaper-utils (2.2.5-0.3) ... 140s Setting up libxom-java (1.3.9-1) ... 140s Setting up libhwloc-plugins:arm64 (2.12.2-1) ... 140s Setting up samtools (1.21-1) ... 140s Setting up libcommons-jexl2-java (2.1.1-6) ... 140s Setting up libthai0:arm64 (0.1.29-2build1) ... 140s Setting up libmbedx509-7:arm64 (3.6.2-3ubuntu1) ... 140s Setting up libcommons-collections4-java (4.4-2) ... 140s Setting up libcommons-lang3-java (3.17.0-1) ... 140s Setting up libmbedtls21:arm64 (3.6.2-3ubuntu1) ... 140s Setting up libopenblas0:arm64 (0.3.30+ds-3) ... 140s Setting up libtiff6:arm64 (4.7.0-3ubuntu3) ... 140s Setting up libwayland-cursor0:arm64 (1.24.0-1build1) ... 140s Setting up libcommons-beanutils-java (1.10.1-1.1) ... 140s Setting up libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-5) ... 140s Setting up libsnappy-java (1.1.10.7-1) ... 140s Setting up libfontconfig1:arm64 (2.15.0-2.3ubuntu1) ... 140s Setting up libcommons-codec-java (1.18.0-1) ... 140s Setting up libsm6:arm64 (2:1.2.6-1) ... 140s Setting up libavahi-client3:arm64 (0.8-16ubuntu3) ... 140s Setting up libhsakmt1:arm64 (6.2.4+ds-1) ... 141s Setting up libopenblas-pthread-dev:arm64 (0.3.30+ds-3) ... 141s update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode 141s update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode 141s update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/aarch64-linux-gnu/libopenblas.so (libopenblas.so-aarch64-linux-gnu) in auto mode 141s Setting up libatk-bridge2.0-0t64:arm64 (2.57.1-1) ... 141s Setting up gtk-update-icon-cache (4.20.1+ds-2) ... 141s Setting up fontconfig (2.15.0-2.3ubuntu1) ... 143s Regenerating fonts cache... done. 143s Setting up libxft2:arm64 (2.3.6-1build1) ... 143s Setting up libglx-mesa0:arm64 (25.2.3-1ubuntu1) ... 143s Setting up openjdk-21-jre-headless:arm64 (21.0.9~8ea-1) ... 143s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode 143s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 143s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 143s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 143s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 143s Setting up libglx0:arm64 (1.7.0-1build2) ... 143s Setting up dconf-gsettings-backend:arm64 (0.40.0-5willsync1) ... 143s Setting up libcommons-io-java (2.19.0-1) ... 143s Setting up libtk8.6:arm64 (8.6.17-1) ... 143s Setting up libpango-1.0-0:arm64 (1.56.3-1build1) ... 143s Setting up libncbi-vdb3:arm64 (3.2.1+dfsg-2) ... 143s Setting up libcairo2:arm64 (1.18.4-1build1) ... 143s Setting up libopenblas-dev:arm64 (0.3.30+ds-3) ... 143s Setting up libgl1:arm64 (1.7.0-1build2) ... 143s Setting up adwaita-icon-theme (49.0-1) ... 143s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode 143s Setting up libxt6t64:arm64 (1:1.2.1-1.3) ... 143s Setting up libhttpclient-java (4.5.14-1) ... 143s Setting up libhsa-runtime64-1:arm64 (6.1.2-3) ... 143s Setting up liblightcouch-java (0.2.0-1) ... 143s Setting up libcairo-gobject2:arm64 (1.18.4-1build1) ... 143s Setting up libpangoft2-1.0-0:arm64 (1.56.3-1build1) ... 143s Setting up libcups2t64:arm64 (2.4.12-0ubuntu3) ... 143s Setting up libgtk-3-common (3.24.50-1ubuntu2) ... 143s Setting up libpangocairo-1.0-0:arm64 (1.56.3-1build1) ... 143s Setting up libncbi-ngs3:arm64 (3.2.1+dfsg-4ubuntu5) ... 143s Setting up libngs-jni:arm64 (3.2.1+dfsg-4ubuntu5) ... 143s Setting up libcommons-compress-java (1.27.1-2) ... 143s Setting up liblog4j2-java (2.19.0-2) ... 143s Setting up libamdhip64-5:arm64 (5.7.1-6) ... 143s Setting up r-base-core (4.5.1-1) ... 143s Creating config file /etc/R/Renviron with new version 143s Setting up r-cran-labeling (0.4.3-1) ... 143s Setting up r-cran-lattice (0.22-7-1) ... 143s Setting up r-cran-nlme (3.1.168-1) ... 143s Setting up r-cran-farver (2.1.2-1) ... 143s Setting up r-cran-viridislite (0.4.2-2) ... 143s Setting up libngs-java:arm64 (3.2.1+dfsg-4ubuntu5) ... 143s Setting up r-cran-r6 (2.6.1-1) ... 143s Setting up r-cran-pkgkitten (0.2.4-1) ... 143s Setting up r-cran-magrittr (2.0.3-1) ... 143s Setting up libbarclay-java (5.0.0+dfsg-1) ... 143s Setting up r-cran-littler (0.3.21-1) ... 143s Setting up r-cran-rcpp (1.1.0-1) ... 143s Setting up r-cran-codetools (0.2-20-1) ... 143s Setting up r-cran-inline (0.3.21-1) ... 143s Setting up libucx0:arm64 (1.19.0+ds-1) ... 143s Setting up r-cran-rlang (1.1.5-3) ... 143s Setting up r-cran-withr (3.0.2+dfsg-1) ... 143s Setting up r-cran-iterators (1.0.14-1) ... 143s Setting up r-cran-foreach (1.5.2-1) ... 143s Setting up r-cran-fansi (1.0.6-2) ... 143s Setting up r-cran-mass (7.3-65-1) ... 143s Setting up r-cran-glue (1.8.0-1) ... 143s Setting up r-cran-gam (1.22-5-1) ... 143s Setting up r-cran-cli (3.6.4-1) ... 143s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... 143s Setting up r-cran-pkgconfig (2.0.3-2build1) ... 143s Setting up r-cran-utf8 (1.2.4-1) ... 143s Setting up r-cran-colorspace (2.1-1+dfsg-1) ... 143s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ... 143s Setting up r-cran-isoband (0.2.7-1) ... 143s Setting up r-cran-gtable (0.3.6+dfsg-1) ... 143s Setting up r-cran-matrix (1.7-3-1) ... 143s Setting up r-cran-mgcv (1.9-3-1) ... 143s Setting up r-cran-rcppgsl (0.3.13-1build1) ... 143s Setting up r-cran-vctrs (0.6.5-1) ... 143s Setting up r-cran-pillar (1.10.1+dfsg-1) ... 143s Setting up libopenmpi40:arm64 (5.0.8-8ubuntu1) ... 143s Setting up r-cran-munsell (0.5.1-1) ... 143s Setting up r-cran-tibble (3.2.1+dfsg-3) ... 143s Setting up r-cran-scales (1.3.0-1) ... 143s Setting up openmpi-bin (5.0.8-8ubuntu1) ... 143s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 143s update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist 143s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 143s Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... 143s Setting up mpi-default-bin (1.18) ... 143s Setting up mapdamage (2.2.2+dfsg-1) ... 144s Setting up examl (3.0.22-6build1) ... 144s Processing triggers for libc-bin (2.42-0ubuntu3) ... 144s Processing triggers for man-db (2.13.1-1) ... 147s Processing triggers for libglib2.0-0t64:arm64 (2.86.0-2) ... 147s Setting up libgtk-3-0t64:arm64 (3.24.50-1ubuntu2) ... 147s Processing triggers for install-info (7.1.1-1ubuntu1) ... 147s Processing triggers for ca-certificates-java (20240118) ... 148s Adding debian:ACCVRAIZ1.pem 148s Adding debian:AC_RAIZ_FNMT-RCM.pem 148s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 148s Adding debian:ANF_Secure_Server_Root_CA.pem 148s Adding debian:Actalis_Authentication_Root_CA.pem 148s Adding debian:AffirmTrust_Commercial.pem 148s Adding debian:AffirmTrust_Networking.pem 148s Adding debian:AffirmTrust_Premium.pem 148s Adding debian:AffirmTrust_Premium_ECC.pem 148s Adding debian:Amazon_Root_CA_1.pem 148s Adding debian:Amazon_Root_CA_2.pem 148s Adding debian:Amazon_Root_CA_3.pem 148s Adding debian:Amazon_Root_CA_4.pem 148s Adding debian:Atos_TrustedRoot_2011.pem 148s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 148s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 148s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 148s Adding debian:BJCA_Global_Root_CA1.pem 149s Adding debian:BJCA_Global_Root_CA2.pem 149s Adding debian:Baltimore_CyberTrust_Root.pem 149s Adding debian:Buypass_Class_2_Root_CA.pem 149s Adding debian:Buypass_Class_3_Root_CA.pem 149s Adding debian:CA_Disig_Root_R2.pem 149s Adding debian:CFCA_EV_ROOT.pem 149s Adding debian:COMODO_Certification_Authority.pem 149s Adding debian:COMODO_ECC_Certification_Authority.pem 149s Adding debian:COMODO_RSA_Certification_Authority.pem 149s Adding debian:Certainly_Root_E1.pem 149s Adding debian:Certainly_Root_R1.pem 149s Adding debian:Certigna.pem 149s Adding debian:Certigna_Root_CA.pem 149s Adding debian:Certum_EC-384_CA.pem 149s Adding debian:Certum_Trusted_Network_CA.pem 149s Adding debian:Certum_Trusted_Network_CA_2.pem 149s Adding debian:Certum_Trusted_Root_CA.pem 149s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 149s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 149s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 149s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 149s Adding debian:Comodo_AAA_Services_root.pem 149s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 149s Adding debian:D-TRUST_BR_Root_CA_2_2023.pem 149s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 149s Adding debian:D-TRUST_EV_Root_CA_2_2023.pem 149s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 149s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 149s Adding debian:DigiCert_Assured_ID_Root_CA.pem 149s Adding debian:DigiCert_Assured_ID_Root_G2.pem 149s Adding debian:DigiCert_Assured_ID_Root_G3.pem 149s Adding debian:DigiCert_Global_Root_CA.pem 149s Adding debian:DigiCert_Global_Root_G2.pem 149s Adding debian:DigiCert_Global_Root_G3.pem 149s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 149s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 149s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 149s Adding debian:DigiCert_Trusted_Root_G4.pem 149s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 149s Adding debian:Entrust_Root_Certification_Authority.pem 149s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 149s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 149s Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem 149s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 149s Adding debian:GLOBALTRUST_2020.pem 149s Adding debian:GTS_Root_R1.pem 149s Adding debian:GTS_Root_R2.pem 149s Adding debian:GTS_Root_R3.pem 149s Adding debian:GTS_Root_R4.pem 149s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 149s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 149s Adding debian:GlobalSign_Root_CA.pem 149s Adding debian:GlobalSign_Root_CA_-_R3.pem 149s Adding debian:GlobalSign_Root_CA_-_R6.pem 149s Adding debian:GlobalSign_Root_E46.pem 149s Adding debian:GlobalSign_Root_R46.pem 149s Adding debian:Go_Daddy_Class_2_CA.pem 149s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 149s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 149s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 149s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 149s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 149s Adding debian:HiPKI_Root_CA_-_G1.pem 149s Adding debian:Hongkong_Post_Root_CA_3.pem 149s Adding debian:ISRG_Root_X1.pem 149s Adding debian:ISRG_Root_X2.pem 149s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 149s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 149s Adding debian:Izenpe.com.pem 149s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 149s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 149s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 149s Adding debian:NAVER_Global_Root_Certification_Authority.pem 149s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 149s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 149s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 149s Adding debian:QuoVadis_Root_CA_1_G3.pem 149s Adding debian:QuoVadis_Root_CA_2.pem 149s Adding debian:QuoVadis_Root_CA_2_G3.pem 149s Adding debian:QuoVadis_Root_CA_3.pem 149s Adding debian:QuoVadis_Root_CA_3_G3.pem 149s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 149s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 149s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 149s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 149s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 149s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 149s Adding debian:SZAFIR_ROOT_CA2.pem 149s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 149s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 149s Adding debian:SecureSign_Root_CA12.pem 149s Adding debian:SecureSign_Root_CA14.pem 149s Adding debian:SecureSign_Root_CA15.pem 149s Adding debian:SecureTrust_CA.pem 149s Adding debian:Secure_Global_CA.pem 149s Adding debian:Security_Communication_ECC_RootCA1.pem 149s Adding debian:Security_Communication_RootCA2.pem 149s Adding debian:Starfield_Class_2_CA.pem 149s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 149s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 149s Adding debian:SwissSign_Gold_CA_-_G2.pem 149s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 149s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 149s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 149s Adding debian:TWCA_CYBER_Root_CA.pem 149s Adding debian:TWCA_Global_Root_CA.pem 149s Adding debian:TWCA_Root_Certification_Authority.pem 149s Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem 149s Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem 149s Adding debian:TeliaSonera_Root_CA_v1.pem 149s Adding debian:Telia_Root_CA_v2.pem 149s Adding debian:TrustAsia_Global_Root_CA_G3.pem 149s Adding debian:TrustAsia_Global_Root_CA_G4.pem 149s Adding debian:Trustwave_Global_Certification_Authority.pem 149s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 149s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 149s Adding debian:TunTrust_Root_CA.pem 149s Adding debian:UCA_Extended_Validation_Root.pem 149s Adding debian:UCA_Global_G2_Root.pem 149s Adding debian:USERTrust_ECC_Certification_Authority.pem 149s Adding debian:USERTrust_RSA_Certification_Authority.pem 149s Adding debian:XRamp_Global_CA_Root.pem 149s Adding debian:certSIGN_ROOT_CA.pem 149s Adding debian:certSIGN_Root_CA_G2.pem 149s Adding debian:e-Szigno_Root_CA_2017.pem 149s Adding debian:ePKI_Root_Certification_Authority.pem 149s Adding debian:emSign_ECC_Root_CA_-_C3.pem 149s Adding debian:emSign_ECC_Root_CA_-_G3.pem 149s Adding debian:emSign_Root_CA_-_C1.pem 149s Adding debian:emSign_Root_CA_-_G1.pem 149s Adding debian:vTrus_ECC_Root_CA.pem 149s Adding debian:vTrus_Root_CA.pem 149s done. 149s Setting up junit4 (4.13.2-5) ... 149s Setting up default-jre-headless (2:1.21-76) ... 149s Setting up openjdk-21-jre:arm64 (21.0.9~8ea-1) ... 149s Setting up libjson-java (3.1.0+dfsg-2) ... 149s Setting up libhtsjdk-java (4.1.3+dfsg-2) ... 149s Setting up libgkl-java (0.8.11+dfsg-2build1) ... 149s Setting up default-jre (2:1.21-76) ... 149s Setting up libpicard-java (3.3.0+dfsg-2) ... 149s Setting up picard-tools (3.3.0+dfsg-2) ... 149s Setting up paleomix (1.3.8-2) ... 150s Processing triggers for libc-bin (2.42-0ubuntu3) ... 151s autopkgtest [20:27:58]: test run-unit-test: [----------------------- 154s ============================= test session starts ============================== 154s platform linux -- Python 3.13.7, pytest-8.4.2, pluggy-1.6.0 154s rootdir: /tmp/autopkgtest.JLNaCG/autopkgtest_tmp 154s plugins: typeguard-4.4.2 154s collected 1387 items 154s 154s tests/atomiccmd_test/builder_test.py ................................... [ 2%] 155s ...................................................... [ 6%] 155s tests/atomiccmd_test/command_test.py ................................... [ 8%] 155s ........................................................................ [ 14%] 155s ................ [ 15%] 156s tests/atomiccmd_test/pprint_test.py .................................... [ 17%] 156s .. [ 18%] 156s tests/atomiccmd_test/sets_test.py ...................................... [ 20%] 156s ............ [ 21%] 157s tests/common_tests/bedtools_test.py ............................... [ 23%] 157s tests/common_tests/formats_tests/fasta_test.py ......................... [ 25%] 157s ............. [ 26%] 157s tests/common_tests/formats_tests/fastq_test.py ......................... [ 28%] 157s ........... [ 29%] 157s tests/common_tests/formats_tests/msa_test.py ........................... [ 31%] 157s ................... [ 32%] 157s tests/common_tests/formats_tests/newick_test.py ........................ [ 34%] 157s ........................................................................ [ 39%] 157s ...... [ 39%] 157s tests/common_tests/formats_tests/phylip_test.py ........ [ 40%] 157s tests/common_tests/makefile_test.py .................................... [ 43%] 157s ........................................................................ [ 48%] 157s ........................................................................ [ 53%] 157s ........................................................................ [ 58%] 157s ........................................................................ [ 63%] 157s ............................... [ 66%] 158s tests/common_tests/sampling_test.py ........................ [ 67%] 158s tests/common_tests/sequences_test.py ................................... [ 70%] 158s ............... [ 71%] 158s tests/common_tests/text_test.py ....................................... [ 74%] 158s tests/common_tests/utilities_test.py ................................... [ 76%] 158s ........................................................................ [ 81%] 158s .. [ 82%] 158s tests/common_tests/versions_test.py .................................... [ 84%] 158s ............................................................ [ 88%] 158s tests/node_test.py ..................................................... [ 92%] 159s ....................................... [ 95%] 159s tests/nodegraph_test.py ......... [ 96%] 174s tests/tools_test/factory_test.py XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX [ 99%] 177s XXXXXXXXXXXXX [100%] 177s 177s =============================== warnings summary =============================== 177s tests/tools_test/factory_test.py:64 177s /tmp/autopkgtest.JLNaCG/autopkgtest_tmp/tests/tools_test/factory_test.py:64: PytestUnknownMarkWarning: Unknown pytest.mark.slow - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html 177s @pytest.mark.slow 177s 177s tests/tools_test/factory_test.py:74 177s /tmp/autopkgtest.JLNaCG/autopkgtest_tmp/tests/tools_test/factory_test.py:74: PytestUnknownMarkWarning: Unknown pytest.mark.slow - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html 177s @pytest.mark.slow 177s 177s tests/tools_test/factory_test.py:88 177s /tmp/autopkgtest.JLNaCG/autopkgtest_tmp/tests/tools_test/factory_test.py:88: PytestUnknownMarkWarning: Unknown pytest.mark.slow - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html 177s @pytest.mark.slow 177s 177s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 177s ================ 1335 passed, 52 xpassed, 3 warnings in 24.51s ================= 178s autopkgtest [20:28:25]: test run-unit-test: -----------------------] 178s run-unit-test PASS 178s autopkgtest [20:28:25]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 179s autopkgtest [20:28:26]: @@@@@@@@@@@@@@@@@@@@ summary 179s run-unit-test PASS