0s autopkgtest [17:18:03]: starting date and time: 2024-03-16 17:18:03+0000 0s autopkgtest [17:18:03]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [17:18:03]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.z54s45y5/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:r-base,src:curl,src:glib2.0,src:libpng1.6,src:libpsl,src:libtirpc,src:libxt,src:openssl,src:orthanc-python,src:readline,src:wp2latex --apt-upgrade paleomix --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=r-base/4.3.3-2build1 curl/8.5.0-2ubuntu7 glib2.0/2.79.3-3ubuntu5 libpng1.6/1.6.43-3 libpsl/0.21.2-1.1 libtirpc/1.3.4+ds-1.1 libxt/1:1.2.1-1.2 openssl/3.0.13-0ubuntu1 orthanc-python/4.1+ds-2build3 readline/8.2-3.1 wp2latex/4.4~ds-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-20.secgroup --name adt-noble-arm64-paleomix-20240316-171803-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 115s autopkgtest [17:19:58]: testbed dpkg architecture: arm64 116s autopkgtest [17:19:59]: testbed apt version: 2.7.12 116s autopkgtest [17:19:59]: @@@@@@@@@@@@@@@@@@@@ test bed setup 117s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 117s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 117s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 117s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 117s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3673 kB] 118s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 118s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 118s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 118s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 118s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3994 kB] 118s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 118s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.6 kB] 118s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 121s Fetched 9063 kB in 2s (3929 kB/s) 121s Reading package lists... 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 128s Calculating upgrade... 128s The following packages will be REMOVED: 128s libglib2.0-0 libssl3 128s The following NEW packages will be installed: 128s libglib2.0-0t64 libssl3t64 xdg-user-dirs 128s The following packages have been kept back: 128s curl 128s The following packages will be upgraded: 128s gir1.2-glib-2.0 libglib2.0-data libtirpc-common openssl readline-common 128s ubuntu-minimal ubuntu-standard 128s 7 upgraded, 3 newly installed, 2 to remove and 1 not upgraded. 128s Need to get 4613 kB of archives. 128s After this operation, 211 kB of additional disk space will be used. 128s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB] 128s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB] 129s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 129s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 129s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 129s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-common all 1.3.4+ds-1.1 [8018 B] 129s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-3.1 [56.4 kB] 129s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB] 129s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB] 129s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB] 129s Fetched 4613 kB in 1s (5412 kB/s) 130s (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 ... 74758 files and directories currently installed.) 130s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_arm64.deb ... 130s Unpacking gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 131s dpkg: libglib2.0-0:arm64: dependency problems, but removing anyway as you requested: 131s udisks2 depends on libglib2.0-0 (>= 2.77.0). 131s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 131s python3-gi depends on libglib2.0-0 (>= 2.77.0). 131s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 131s netplan.io depends on libglib2.0-0 (>= 2.70.0). 131s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 131s libxmlb2:arm64 depends on libglib2.0-0 (>= 2.54.0). 131s libvolume-key1:arm64 depends on libglib2.0-0 (>= 2.18.0). 131s libudisks2-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 131s libqrtr-glib0:arm64 depends on libglib2.0-0 (>= 2.56). 131s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 131s libqmi-glib5:arm64 depends on libglib2.0-0 (>= 2.54.0). 131s libpolkit-gobject-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 131s libpolkit-agent-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 131s libnetplan0:arm64 depends on libglib2.0-0 (>= 2.75.3). 131s libmm-glib0:arm64 depends on libglib2.0-0 (>= 2.62.0). 131s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 131s libmbim-glib4:arm64 depends on libglib2.0-0 (>= 2.56). 131s libjson-glib-1.0-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 131s libjcat1:arm64 depends on libglib2.0-0 (>= 2.75.3). 131s libgusb2:arm64 depends on libglib2.0-0 (>= 2.75.3). 131s libgudev-1.0-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 131s libgirepository-1.0-1:arm64 depends on libglib2.0-0 (>= 2.79.0). 131s libfwupd2:arm64 depends on libglib2.0-0 (>= 2.79.0). 131s libblockdev3:arm64 depends on libglib2.0-0 (>= 2.42.2). 131s libblockdev-utils3:arm64 depends on libglib2.0-0 (>= 2.75.3). 131s libblockdev-swap3:arm64 depends on libglib2.0-0 (>= 2.42.2). 131s libblockdev-part3:arm64 depends on libglib2.0-0 (>= 2.42.2). 131s libblockdev-nvme3:arm64 depends on libglib2.0-0 (>= 2.42.2). 131s libblockdev-mdraid3:arm64 depends on libglib2.0-0 (>= 2.42.2). 131s libblockdev-loop3:arm64 depends on libglib2.0-0 (>= 2.42.2). 131s libblockdev-fs3:arm64 depends on libglib2.0-0 (>= 2.42.2). 131s libblockdev-crypto3:arm64 depends on libglib2.0-0 (>= 2.42.2). 131s fwupd depends on libglib2.0-0 (>= 2.79.0). 131s bolt depends on libglib2.0-0 (>= 2.56.0). 131s 131s (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 ... 74758 files and directories currently installed.) 131s Removing libglib2.0-0:arm64 (2.79.2-1~ubuntu1) ... 131s Selecting previously unselected package libglib2.0-0t64:arm64. 131s (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 ... 74733 files and directories currently installed.) 131s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_arm64.deb ... 131s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:arm64.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled... 131s removed '/var/lib/dpkg/info/libglib2.0-0:arm64.postrm' 131s Unpacking libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 131s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 131s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 132s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 132s wget depends on libssl3 (>= 3.0.0). 132s u-boot-tools depends on libssl3 (>= 3.0.0). 132s tnftp depends on libssl3 (>= 3.0.0). 132s tcpdump depends on libssl3 (>= 3.0.0). 132s systemd-resolved depends on libssl3 (>= 3.0.0). 132s systemd depends on libssl3 (>= 3.0.0). 132s sudo depends on libssl3 (>= 3.0.0). 132s sbsigntool depends on libssl3 (>= 3.0.0). 132s rsync depends on libssl3 (>= 3.0.0). 132s python3-cryptography depends on libssl3 (>= 3.0.0). 132s openssh-server depends on libssl3 (>= 3.0.10). 132s openssh-client depends on libssl3 (>= 3.0.10). 132s mtd-utils depends on libssl3 (>= 3.0.0). 132s mokutil depends on libssl3 (>= 3.0.0). 132s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 132s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 132s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 132s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 132s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 132s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 132s libnvme1 depends on libssl3 (>= 3.0.0). 132s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 132s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 132s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 132s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 132s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 132s kmod depends on libssl3 (>= 3.0.0). 132s dhcpcd-base depends on libssl3 (>= 3.0.0). 132s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 132s 132s (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 ... 74758 files and directories currently installed.) 132s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 132s Selecting previously unselected package libssl3t64:arm64. 132s (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 ... 74747 files and directories currently installed.) 132s Preparing to unpack .../0-libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 132s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 132s Preparing to unpack .../1-libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 132s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 132s Preparing to unpack .../2-libtirpc-common_1.3.4+ds-1.1_all.deb ... 132s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ... 133s Preparing to unpack .../3-readline-common_8.2-3.1_all.deb ... 133s Unpacking readline-common (8.2-3.1) over (8.2-3) ... 133s Preparing to unpack .../4-ubuntu-minimal_1.536_arm64.deb ... 133s Unpacking ubuntu-minimal (1.536) over (1.535) ... 133s Selecting previously unselected package xdg-user-dirs. 133s Preparing to unpack .../5-xdg-user-dirs_0.18-1_arm64.deb ... 133s Unpacking xdg-user-dirs (0.18-1) ... 134s Preparing to unpack .../6-ubuntu-standard_1.536_arm64.deb ... 134s Unpacking ubuntu-standard (1.536) over (1.535) ... 134s Setting up ubuntu-minimal (1.536) ... 134s Setting up xdg-user-dirs (0.18-1) ... 134s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 134s Setting up libtirpc-common (1.3.4+ds-1.1) ... 134s Setting up ubuntu-standard (1.536) ... 134s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 134s No schema files found: doing nothing. 134s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 134s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ... 134s Setting up openssl (3.0.13-0ubuntu1) ... 134s Setting up readline-common (8.2-3.1) ... 134s Processing triggers for man-db (2.12.0-3) ... 135s Processing triggers for install-info (7.1-3) ... 136s Processing triggers for libc-bin (2.39-0ubuntu2) ... 137s Reading package lists... 137s Building dependency tree... 137s Reading state information... 137s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 138s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 139s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 139s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 139s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 141s Reading package lists... 141s Reading package lists... 142s Building dependency tree... 142s Reading state information... 142s Calculating upgrade... 143s The following packages have been kept back: 143s curl 143s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 143s Reading package lists... 143s Building dependency tree... 143s Reading state information... 144s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 149s autopkgtest [17:20:32]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 149s autopkgtest [17:20:32]: @@@@@@@@@@@@@@@@@@@@ apt-source paleomix 152s Get:1 http://ftpmaster.internal/ubuntu noble/universe paleomix 1.3.8-1 (dsc) [2466 B] 152s Get:2 http://ftpmaster.internal/ubuntu noble/universe paleomix 1.3.8-1 (tar) [1137 kB] 152s Get:3 http://ftpmaster.internal/ubuntu noble/universe paleomix 1.3.8-1 (diff) [11.0 kB] 152s gpgv: Signature made Sun Jun 11 21:51:17 2023 UTC 152s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 152s gpgv: issuer "emollier@debian.org" 152s gpgv: Can't check signature: No public key 152s dpkg-source: warning: cannot verify inline signature for ./paleomix_1.3.8-1.dsc: no acceptable signature found 152s autopkgtest [17:20:35]: testing package paleomix version 1.3.8-1 153s autopkgtest [17:20:36]: build not needed 153s autopkgtest [17:20:36]: test run-unit-test: preparing testbed 155s Reading package lists... 155s Building dependency tree... 155s Reading state information... 155s Starting pkgProblemResolver with broken count: 0 155s Starting 2 pkgProblemResolver with broken count: 0 155s Done 156s The following additional packages will be installed: 156s adapterremoval adwaita-icon-theme at-spi2-common bcftools bedtools bowtie2 156s bwa ca-certificates-java curl default-jre default-jre-headless examl 156s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 156s gtk-update-icon-cache hicolor-icon-theme humanity-icon-theme java-common 156s libamd-comgr2 libamdhip64-5 libapache-pom-java libasound2 libasound2-data 156s libatk1.0-0 libatomic1 libavahi-client3 libavahi-common-data 156s libavahi-common3 libbarclay-java libblas3 libcairo2 libcommons-codec-java 156s libcommons-compress-java libcommons-io-java libcommons-jexl2-java 156s libcommons-lang3-java libcommons-logging-java libcommons-math3-java 156s libcommons-parent-java libcups2 libcurl4t64 libdatrie1 libdeflate0 156s libdrm-amdgpu1 libdrm-nouveau2 libdrm-radeon1 libevent-pthreads-2.1-7 156s libfabric1 libfontconfig1 libfreemarker-java libgatk-native-bindings-java 156s libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgif7 libgkl-java 156s libgl1 libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libgomp1 156s libgoogle-gson-java libgraphite2-3 libgsl-dev libgsl27 libgslcblas0 156s libgtk2.0-0 libgtk2.0-common libharfbuzz0b libhsa-runtime64-1 libhsakmt1 156s libhts3 libhtscodecs2 libhtsjdk-java libhttpclient-java libhttpcore-java 156s libhwloc-plugins libhwloc15 libice6 libjbig0 libjoptsimple-java 156s libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 liblightcouch-java 156s libllvm17 liblog4j2-java libmbedcrypto7 libmbedtls14 libmbedx509-1 156s libmjson-java libmongodb-java libmunge2 libncbi-ngs3 libncbi-vdb3 156s libngs-java libngs-jni libopenblas-dev libopenblas-pthread-dev libopenblas0 156s libopenblas0-pthread libopenmpi3 libpango-1.0-0 libpangocairo-1.0-0 156s libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcsclite1 156s libpicard-java libpixman-1-0 libpmix2 libpng16-16t64 libpsl5t64 156s librdmacm1t64 libreadline8t64 librhino-java libsharpyuv0 libslf4j-java 156s libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libtcl8.6 libthai-data 156s libthai0 libtiff6 libtirpc3t64 libtk8.6 libucx0 libvulkan1 libwebp7 156s libx11-xcb1 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 156s libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 156s libxcomposite1 libxcursor1 libxdamage1 libxfixes3 libxft2 libxi6 156s libxinerama1 libxnvctrl0 libxrandr2 libxrender1 libxshmfence1 libxss1 156s libxt6t64 libxtst6 libxxf86vm1 littler mafft mapdamage ncbi-vdb-data 156s ocl-icd-libopencl1 openjdk-21-jre openjdk-21-jre-headless openmpi-bin 156s openmpi-common paleomix phylip picard-tools python3-coloredlogs 156s python3-configargparse python3-humanfriendly python3-iniconfig 156s python3-packaging python3-pluggy python3-pysam python3-pytest 156s python3-ruamel.yaml python3-ruamel.yaml.clib python3-setproctitle 156s r-base-core r-cran-cli r-cran-codetools r-cran-colorspace r-cran-fansi 156s r-cran-farver r-cran-foreach r-cran-gam r-cran-ggplot2 r-cran-glue 156s r-cran-gtable r-cran-inline r-cran-isoband r-cran-iterators r-cran-labeling 156s r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass 156s r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar 156s r-cran-pkgconfig r-cran-pkgkitten r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp 156s r-cran-rcppgsl r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8 156s r-cran-vctrs r-cran-viridislite r-cran-withr radiant raxml samtools seqtk 156s ubuntu-mono unzip x11-common xdg-utils zip 156s Suggested packages: 156s python3-numpy python3-matplotlib texlive-latex-recommended bowtie2-examples 156s libasound2-plugins alsa-utils libasm-java libxz-java libcommons-io-java-doc 156s libavalon-framework-java libexcalibur-logkit-java liblog4j1.2-java 156s cups-common jython libdom4j-java libjaxen-java libjdom1-java libxalan2-java 156s libgoogle-gson-java-doc gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info 156s | gsl-ref-html gvfs libjoptsimple-java-doc liblcms2-utils libactivation-java 156s libcommons-csv-java libconversant-disruptor-java libdisruptor-java 156s libgeronimo-jms-1.1-spec-java libjackson2-dataformat-xml-java 156s libjackson2-dataformat-yaml libjansi-java libjctools-java libjeromq-java 156s libmail-java libwoodstox-java libngs-java-doc pcscd rhino tcl8.6 tk8.6 156s opencl-icd libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic 156s fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic 156s gfortran | fortran-compiler phylip-doc elpa-ess r-doc-info | r-doc-pdf 156s r-mathlib r-base-html r-cran-kernsmooth r-cran-kernlab r-cran-mvtnorm 156s r-cran-vcd r-cran-shiny r-cran-shinyjs r-cran-dplyr r-cran-png r-cran-jpeg 156s r-cran-knitr r-cran-rmarkdown r-cran-viridis r-cran-covr r-cran-magick 156s r-cran-sf r-cran-getopt r-cran-bit64 r-cran-dbi r-cran-formattable 156s r-cran-nanotime r-cran-palmerpenguins r-cran-stringi r-cran-survival 156s r-cran-units r-cran-vdiffr r-cran-testthat r-cran-bench r-cran-blob 156s r-cran-brio r-cran-callr r-cran-crayon r-cran-evaluate r-cran-here 156s r-cran-hms r-cran-htmltools r-cran-pkgbuild r-cran-pkgload r-cran-purrr 156s r-cran-tidyr cwltool 156s Recommended packages: 156s librsvg2-common alsa-ucm-conf alsa-topology-conf libgdk-pixbuf2.0-bin 156s libgkl-jni libgl1-amber-dri libgail-common libgtk2.0-bin mesa-vulkan-drivers 156s | vulkan-icd blast2 libwww-perl lynx ruby libatk-wrapper-java-jni 156s fonts-dejavu-extra r-recommended r-base-dev r-doc-html r-cran-callr 156s r-cran-covr r-cran-crayon r-cran-digest r-cran-htmltools r-cran-htmlwidgets 156s r-cran-knitr r-cran-mockery r-cran-processx r-cran-ps r-cran-rmarkdown 156s r-cran-rprojroot r-cran-rstudioapi r-cran-testthat r-cran-whoami 156s r-cran-unitizer r-cran-interp r-cran-dplyr r-cran-hexbin r-cran-hmisc 156s r-cran-mapproj r-cran-maps r-cran-multcomp r-cran-profvis r-cran-quantreg 156s r-cran-ragg r-cran-rpart r-cran-sf r-cran-svglite r-cran-vdiffr r-cran-xml2 156s r-cran-dbi r-cran-rsqlite r-cran-waldo r-cran-lintr r-cran-tidyverse 156s r-cran-lubridate r-cran-fs r-cran-usethis r-cran-bit64 r-cran-dichromat 156s r-cran-hms r-cran-stringi r-cran-data.table r-cran-mockr r-cran-formattable 156s r-cran-generics r-cran-pkgdown r-cran-zeallot libfile-mimeinfo-perl 156s libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils 156s The following packages will be REMOVED: 156s libcurl4 libpng16-16 libpsl5 libreadline8 libtirpc3 156s The following NEW packages will be installed: 156s adapterremoval adwaita-icon-theme at-spi2-common autopkgtest-satdep bcftools 156s bedtools bowtie2 bwa ca-certificates-java default-jre default-jre-headless 156s examl fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 156s gtk-update-icon-cache hicolor-icon-theme humanity-icon-theme java-common 156s libamd-comgr2 libamdhip64-5 libapache-pom-java libasound2 libasound2-data 156s libatk1.0-0 libatomic1 libavahi-client3 libavahi-common-data 156s libavahi-common3 libbarclay-java libblas3 libcairo2 libcommons-codec-java 156s libcommons-compress-java libcommons-io-java libcommons-jexl2-java 156s libcommons-lang3-java libcommons-logging-java libcommons-math3-java 156s libcommons-parent-java libcups2 libcurl4t64 libdatrie1 libdeflate0 156s libdrm-amdgpu1 libdrm-nouveau2 libdrm-radeon1 libevent-pthreads-2.1-7 156s libfabric1 libfontconfig1 libfreemarker-java libgatk-native-bindings-java 156s libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgif7 libgkl-java 156s libgl1 libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libgomp1 156s libgoogle-gson-java libgraphite2-3 libgsl-dev libgsl27 libgslcblas0 156s libgtk2.0-0 libgtk2.0-common libharfbuzz0b libhsa-runtime64-1 libhsakmt1 156s libhts3 libhtscodecs2 libhtsjdk-java libhttpclient-java libhttpcore-java 156s libhwloc-plugins libhwloc15 libice6 libjbig0 libjoptsimple-java 156s libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 liblightcouch-java 156s libllvm17 liblog4j2-java libmbedcrypto7 libmbedtls14 libmbedx509-1 156s libmjson-java libmongodb-java libmunge2 libncbi-ngs3 libncbi-vdb3 156s libngs-java libngs-jni libopenblas-dev libopenblas-pthread-dev libopenblas0 156s libopenblas0-pthread libopenmpi3 libpango-1.0-0 libpangocairo-1.0-0 156s libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcsclite1 156s libpicard-java libpixman-1-0 libpmix2 libpng16-16t64 libpsl5t64 156s librdmacm1t64 libreadline8t64 librhino-java libsharpyuv0 libslf4j-java 156s libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libtcl8.6 libthai-data 156s libthai0 libtiff6 libtirpc3t64 libtk8.6 libucx0 libvulkan1 libwebp7 156s libx11-xcb1 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 156s libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 156s libxcomposite1 libxcursor1 libxdamage1 libxfixes3 libxft2 libxi6 156s libxinerama1 libxnvctrl0 libxrandr2 libxrender1 libxshmfence1 libxss1 156s libxt6t64 libxtst6 libxxf86vm1 littler mafft mapdamage ncbi-vdb-data 156s ocl-icd-libopencl1 openjdk-21-jre openjdk-21-jre-headless openmpi-bin 156s openmpi-common paleomix phylip picard-tools python3-coloredlogs 156s python3-configargparse python3-humanfriendly python3-iniconfig 156s python3-packaging python3-pluggy python3-pysam python3-pytest 156s python3-ruamel.yaml python3-ruamel.yaml.clib python3-setproctitle 156s r-base-core r-cran-cli r-cran-codetools r-cran-colorspace r-cran-fansi 156s r-cran-farver r-cran-foreach r-cran-gam r-cran-ggplot2 r-cran-glue 156s r-cran-gtable r-cran-inline r-cran-isoband r-cran-iterators r-cran-labeling 156s r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass 156s r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar 156s r-cran-pkgconfig r-cran-pkgkitten r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp 156s r-cran-rcppgsl r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8 156s r-cran-vctrs r-cran-viridislite r-cran-withr radiant raxml samtools seqtk 156s ubuntu-mono unzip x11-common xdg-utils zip 156s The following packages will be upgraded: 156s curl 156s 1 upgraded, 233 newly installed, 5 to remove and 0 not upgraded. 156s Need to get 226 MB/226 MB of archives. 156s After this operation, 813 MB of additional disk space will be used. 156s Get:1 /tmp/autopkgtest.HW16oD/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [716 B] 156s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpsl5t64 arm64 0.21.2-1.1 [57.4 kB] 156s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 curl arm64 8.5.0-2ubuntu7 [222 kB] 157s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl4t64 arm64 8.5.0-2ubuntu7 [332 kB] 157s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng16-16t64 arm64 1.6.43-3 [185 kB] 157s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline8t64 arm64 8.2-3.1 [153 kB] 157s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.1 [83.5 kB] 157s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 adapterremoval arm64 2.3.3-2 [151 kB] 157s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-3 [7624 B] 157s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 157s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 157s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 157s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 157s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 157s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 157s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 157s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 157s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.10+dfsg-3 [144 kB] 157s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 gtk-update-icon-cache arm64 3.24.40-2ubuntu1 [50.5 kB] 157s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 hicolor-icon-theme all 0.17-2 [9976 B] 157s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 humanity-icon-theme all 0.6.16 [1282 kB] 158s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-mono all 24.04-0ubuntu1 [151 kB] 158s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 adwaita-icon-theme all 46~rc-1 [723 kB] 158s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 at-spi2-common all 2.50.0-1 [7864 B] 158s Get:25 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 158s Get:26 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 158s Get:27 http://ftpmaster.internal/ubuntu noble/universe arm64 bcftools arm64 1.19-1 [763 kB] 158s Get:28 http://ftpmaster.internal/ubuntu noble/universe arm64 bedtools arm64 2.31.1+dfsg-2 [636 kB] 158s Get:29 http://ftpmaster.internal/ubuntu noble/universe arm64 bwa arm64 0.7.17-7 [192 kB] 158s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 ca-certificates-java all 20240118 [11.6 kB] 158s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 java-common all 0.75+exp1 [6798 B] 158s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-common-data arm64 0.8-13ubuntu2 [29.5 kB] 158s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-common3 arm64 0.8-13ubuntu2 [23.2 kB] 158s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-client3 arm64 0.8-13ubuntu2 [27.3 kB] 158s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libcups2 arm64 2.4.6-0ubuntu3 [270 kB] 158s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] 158s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 158s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 158s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 158s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 158s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libasound2-data all 1.2.10-3build1 [20.7 kB] 158s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libasound2 arm64 1.2.10-3build1 [386 kB] 158s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 158s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 158s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libpcsclite1 arm64 2.0.0-1 [21.2 kB] 158s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 openjdk-21-jre-headless arm64 21.0.2+13-2 [45.8 MB] 161s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 default-jre-headless arm64 2:1.21-75+exp1 [3096 B] 161s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libgtk2.0-common all 2.24.33-2ubuntu2 [125 kB] 161s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libatk1.0-0 arm64 2.50.0-1 [53.8 kB] 161s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 161s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 161s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 161s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 161s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 161s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 161s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 161s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 161s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 161s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 161s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 161s Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 161s Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 libxcomposite1 arm64 1:0.4.5-1build2 [7080 B] 161s Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 libxfixes3 arm64 1:6.0.0-2 [11.0 kB] 161s Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 libxcursor1 arm64 1:1.2.1-1 [21.3 kB] 161s Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 libxdamage1 arm64 1:1.1.6-1 [6032 B] 161s Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 libxi6 arm64 2:1.8.1-1 [31.9 kB] 161s Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 libxinerama1 arm64 2:1.1.4-3 [7056 B] 161s Get:68 http://ftpmaster.internal/ubuntu noble/main arm64 libxrandr2 arm64 2:1.5.2-2 [19.6 kB] 161s Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 libgtk2.0-0 arm64 2.24.33-2ubuntu2 [1981 kB] 161s Get:70 http://ftpmaster.internal/ubuntu noble/main arm64 libglvnd0 arm64 1.7.0-1 [60.0 kB] 161s Get:71 http://ftpmaster.internal/ubuntu noble/main arm64 libglapi-mesa arm64 24.0.1-1ubuntu1 [57.8 kB] 161s Get:72 http://ftpmaster.internal/ubuntu noble/main arm64 libx11-xcb1 arm64 2:1.8.7-1 [7836 B] 161s Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-dri2-0 arm64 1.15-1 [7244 B] 161s Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-dri3-0 arm64 1.15-1 [7108 B] 161s Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-glx0 arm64 1.15-1 [25.2 kB] 161s Get:76 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-present0 arm64 1.15-1 [5732 B] 161s Get:77 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-randr0 arm64 1.15-1 [18.2 kB] 161s Get:78 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-sync1 arm64 1.15-1 [9412 B] 161s Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-xfixes0 arm64 1.15-1 [10.3 kB] 161s Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 libxshmfence1 arm64 1.3-1build4 [5444 B] 161s Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 libxxf86vm1 arm64 1:1.1.4-1build3 [10.3 kB] 161s Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 libvulkan1 arm64 1.3.275.0-1 [150 kB] 161s Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-amdgpu1 arm64 2.4.120-2 [20.4 kB] 161s Get:84 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-nouveau2 arm64 2.4.120-2 [17.8 kB] 161s Get:85 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-radeon1 arm64 2.4.120-2 [20.9 kB] 161s Get:86 http://ftpmaster.internal/ubuntu noble/main arm64 libllvm17 arm64 1:17.0.6-5build1 [25.0 MB] 162s Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 libgl1-mesa-dri arm64 24.0.1-1ubuntu1 [8226 kB] 162s Get:88 http://ftpmaster.internal/ubuntu noble/main arm64 libglx-mesa0 arm64 24.0.1-1ubuntu1 [166 kB] 162s Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 libglx0 arm64 1.7.0-1 [32.4 kB] 162s Get:90 http://ftpmaster.internal/ubuntu noble/main arm64 libgl1 arm64 1.7.0-1 [107 kB] 162s Get:91 http://ftpmaster.internal/ubuntu noble/main arm64 libgif7 arm64 5.2.1-2.5 [34.2 kB] 162s Get:92 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 162s Get:93 http://ftpmaster.internal/ubuntu noble/main arm64 libxtst6 arm64 2:1.2.3-1.1 [13.7 kB] 162s Get:94 http://ftpmaster.internal/ubuntu noble/main arm64 openjdk-21-jre arm64 21.0.2+13-2 [226 kB] 162s Get:95 http://ftpmaster.internal/ubuntu noble/main arm64 default-jre arm64 2:1.21-75+exp1 [922 B] 162s Get:96 http://ftpmaster.internal/ubuntu noble/main arm64 libevent-pthreads-2.1-7 arm64 2.1.12-stable-9 [7738 B] 162s Get:97 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] 162s Get:98 http://ftpmaster.internal/ubuntu noble/main arm64 librdmacm1t64 arm64 50.0-2 [70.6 kB] 162s Get:99 http://ftpmaster.internal/ubuntu noble/universe arm64 libfabric1 arm64 1.17.0-3 [537 kB] 162s Get:100 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc15 arm64 2.10.0-1 [158 kB] 162s Get:101 http://ftpmaster.internal/ubuntu noble/universe arm64 libmunge2 arm64 0.5.15-3ubuntu1 [14.8 kB] 162s Get:102 http://ftpmaster.internal/ubuntu noble/main arm64 libpciaccess0 arm64 0.17-3 [18.6 kB] 162s Get:103 http://ftpmaster.internal/ubuntu noble/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu1 [11.1 kB] 162s Get:104 http://ftpmaster.internal/ubuntu noble/universe arm64 ocl-icd-libopencl1 arm64 2.3.2-1 [37.3 kB] 162s Get:105 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc-plugins arm64 2.10.0-1 [15.7 kB] 162s Get:106 http://ftpmaster.internal/ubuntu noble/universe arm64 libpmix2 arm64 5.0.1-4 [659 kB] 163s Get:107 http://ftpmaster.internal/ubuntu noble/universe arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3 [14.1 MB] 163s Get:108 http://ftpmaster.internal/ubuntu noble/universe arm64 libhsakmt1 arm64 5.7.0-1 [63.6 kB] 163s Get:109 http://ftpmaster.internal/ubuntu noble/universe arm64 libhsa-runtime64-1 arm64 5.7.1-1 [286 kB] 163s Get:110 http://ftpmaster.internal/ubuntu noble/universe arm64 libamdhip64-5 arm64 5.2.3-12 [5134 kB] 163s Get:111 http://ftpmaster.internal/ubuntu noble/universe arm64 libucx0 arm64 1.16.0+ds-4 [1076 kB] 163s Get:112 http://ftpmaster.internal/ubuntu noble/universe arm64 libopenmpi3 arm64 4.1.6-5ubuntu1 [3081 kB] 163s Get:113 http://ftpmaster.internal/ubuntu noble/universe arm64 openmpi-common all 4.1.6-5ubuntu1 [178 kB] 163s Get:114 http://ftpmaster.internal/ubuntu noble/universe arm64 openmpi-bin arm64 4.1.6-5ubuntu1 [123 kB] 163s Get:115 http://ftpmaster.internal/ubuntu noble/universe arm64 examl arm64 3.0.22-4 [830 kB] 163s Get:116 http://ftpmaster.internal/ubuntu noble/universe arm64 libapache-pom-java all 29-2 [5284 B] 163s Get:117 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-parent-java all 56-1 [10.7 kB] 163s Get:118 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-lang3-java all 3.14.0-1 [586 kB] 163s Get:119 http://ftpmaster.internal/ubuntu noble/universe arm64 libfreemarker-java all 2.3.32-2 [1542 kB] 163s Get:120 http://ftpmaster.internal/ubuntu noble/universe arm64 libgoogle-gson-java all 2.10.1-1 [252 kB] 163s Get:121 http://ftpmaster.internal/ubuntu noble/universe arm64 libjoptsimple-java all 5.0.4-4 [73.1 kB] 163s Get:122 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-codec-java all 1.16.0-1 [306 kB] 163s Get:123 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-logging-java all 1.3.0-1 [68.1 kB] 163s Get:124 http://ftpmaster.internal/ubuntu noble/universe arm64 libhttpcore-java all 4.4.16-1 [612 kB] 164s Get:125 http://ftpmaster.internal/ubuntu noble/universe arm64 libhttpclient-java all 4.5.14-1 [1241 kB] 164s Get:126 http://ftpmaster.internal/ubuntu noble/universe arm64 liblightcouch-java all 0.2.0-1 [74.2 kB] 164s Get:127 http://ftpmaster.internal/ubuntu noble/universe arm64 libmongodb-java all 3.6.3-2 [1899 kB] 164s Get:128 http://ftpmaster.internal/ubuntu noble/universe arm64 libslf4j-java all 1.7.32-1 [141 kB] 164s Get:129 http://ftpmaster.internal/ubuntu noble/universe arm64 liblog4j2-java all 2.19.0-2 [2294 kB] 164s Get:130 http://ftpmaster.internal/ubuntu noble/universe arm64 libbarclay-java all 5.0.0+dfsg-1 [108 kB] 164s Get:131 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 164s Get:132 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-compress-java all 1.25.0-1 [612 kB] 164s Get:133 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-io-java all 2.11.0-2 [297 kB] 164s Get:134 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-jexl2-java all 2.1.1-6 [250 kB] 164s Get:135 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-math3-java all 3.6.1-3 [2016 kB] 164s Get:136 http://ftpmaster.internal/ubuntu noble/universe arm64 libgatk-native-bindings-java all 1.0.0+dfsg-2 [8014 B] 164s Get:137 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 164s Get:138 http://ftpmaster.internal/ubuntu noble/universe arm64 libmjson-java all 1.4.0-3 [60.4 kB] 164s Get:139 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedcrypto7 arm64 2.28.7-1ubuntu1 [206 kB] 164s Get:140 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedx509-1 arm64 2.28.7-1ubuntu1 [46.8 kB] 164s Get:141 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedtls14 arm64 2.28.7-1ubuntu1 [82.0 kB] 164s Get:142 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-vdb-data all 3.0.2+dfsg-2 [65.8 kB] 164s Get:143 http://ftpmaster.internal/ubuntu noble/universe arm64 libncbi-vdb3 arm64 3.0.2+dfsg-2 [1130 kB] 164s Get:144 http://ftpmaster.internal/ubuntu noble/universe arm64 libncbi-ngs3 arm64 3.0.3+dfsg-6ubuntu1 [146 kB] 164s Get:145 http://ftpmaster.internal/ubuntu noble/universe arm64 libngs-jni arm64 3.0.3+dfsg-6ubuntu1 [4832 B] 164s Get:146 http://ftpmaster.internal/ubuntu noble/universe arm64 libngs-java arm64 3.0.3+dfsg-6ubuntu1 [91.8 kB] 164s Get:147 http://ftpmaster.internal/ubuntu noble/universe arm64 librhino-java all 1.7.14-2.1 [1330 kB] 164s Get:148 http://ftpmaster.internal/ubuntu noble/main arm64 libsnappy1v5 arm64 1.1.10-1 [28.2 kB] 164s Get:149 http://ftpmaster.internal/ubuntu noble/universe arm64 libsnappy-jni arm64 1.1.10.5-1 [6542 B] 164s Get:150 http://ftpmaster.internal/ubuntu noble/universe arm64 libsnappy-java all 1.1.10.5-1 [83.6 kB] 164s Get:151 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtsjdk-java all 4.1.0+dfsg-1 [1821 kB] 164s Get:152 http://ftpmaster.internal/ubuntu noble/universe arm64 libgkl-java all 0.8.11+dfsg-2 [24.8 kB] 164s Get:153 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 164s Get:154 http://ftpmaster.internal/ubuntu noble/universe arm64 libgslcblas0 arm64 2.7.1+dfsg-6ubuntu1 [72.5 kB] 164s Get:155 http://ftpmaster.internal/ubuntu noble/universe arm64 libgsl27 arm64 2.7.1+dfsg-6ubuntu1 [912 kB] 164s Get:156 http://ftpmaster.internal/ubuntu noble/universe arm64 libgsl-dev arm64 2.7.1+dfsg-6ubuntu1 [1185 kB] 164s Get:157 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] 164s Get:158 http://ftpmaster.internal/ubuntu noble/universe arm64 libopenblas0-pthread arm64 0.3.26+ds-1 [5464 kB] 164s Get:159 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 164s Get:160 http://ftpmaster.internal/ubuntu noble/universe arm64 libopenblas0 arm64 0.3.26+ds-1 [6170 B] 164s Get:161 http://ftpmaster.internal/ubuntu noble/universe arm64 libopenblas-pthread-dev arm64 0.3.26+ds-1 [3790 kB] 164s Get:162 http://ftpmaster.internal/ubuntu noble/universe arm64 libopenblas-dev arm64 0.3.26+ds-1 [19.6 kB] 164s Get:163 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB] 164s Get:164 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B] 164s Get:165 http://ftpmaster.internal/ubuntu noble/universe arm64 libpicard-java all 3.1.1+dfsg-1 [1731 kB] 164s Get:166 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] 164s Get:167 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 164s Get:168 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 164s Get:169 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 164s Get:170 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB] 164s Get:171 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libxt6t64 arm64 1:1.2.1-1.2 [168 kB] 164s Get:172 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB] 164s Get:173 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB] 164s Get:174 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 164s Get:175 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-base-core arm64 4.3.3-2build1 [26.8 MB] 165s Get:176 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-littler arm64 0.3.19-1 [93.4 kB] 165s Get:177 http://ftpmaster.internal/ubuntu noble/universe arm64 littler all 0.3.19-1 [2472 B] 165s Get:178 http://ftpmaster.internal/ubuntu noble/universe arm64 mafft arm64 7.505-1 [756 kB] 165s Get:179 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-codetools all 0.2-19-1 [90.5 kB] 165s Get:180 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-iterators all 1.0.14-1 [336 kB] 165s Get:181 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-foreach all 1.5.2-1 [124 kB] 165s Get:182 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-gam arm64 1.22-3-1 [407 kB] 165s Get:183 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cli arm64 3.6.2-1 [1377 kB] 165s Get:184 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-glue arm64 1.7.0-1 [154 kB] 165s Get:185 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rlang arm64 1.1.3-1 [1663 kB] 165s Get:186 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 165s Get:187 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-gtable all 0.3.4+dfsg-1 [191 kB] 165s Get:188 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-isoband arm64 0.2.7-1 [1481 kB] 165s Get:189 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mass arm64 7.3-60.0.1-1 [1119 kB] 165s Get:190 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lattice arm64 0.22-5-1 [1342 kB] 165s Get:191 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nlme arm64 3.1.164-1 [2259 kB] 165s Get:192 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-matrix arm64 1.6-5-1 [3776 kB] 165s Get:193 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB] 166s Get:194 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-farver arm64 2.1.1-1 [1336 kB] 166s Get:195 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-labeling all 0.4.3-1 [62.1 kB] 166s Get:196 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-colorspace arm64 2.1-0+dfsg-1 [1540 kB] 166s Get:197 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-munsell all 0.5.0-2build1 [208 kB] 166s Get:198 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-r6 all 2.5.1-1 [99.0 kB] 166s Get:199 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 166s Get:200 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-viridislite all 0.4.2-2 [1088 kB] 166s Get:201 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-scales all 1.3.0-1 [603 kB] 166s Get:202 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fansi arm64 1.0.5-1 [616 kB] 166s Get:203 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 166s Get:204 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-utf8 arm64 1.2.4-1 [140 kB] 166s Get:205 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB] 166s Get:206 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pillar all 1.9.0+dfsg-1 [464 kB] 166s Get:207 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 166s Get:208 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tibble arm64 3.2.1+dfsg-2 [415 kB] 166s Get:209 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-withr all 2.5.0-1 [225 kB] 166s Get:210 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ggplot2 all 3.4.4+dfsg-1 [3411 kB] 166s Get:211 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-inline all 0.3.19-2 [129 kB] 166s Get:212 http://ftpmaster.internal/ubuntu noble/universe arm64 seqtk arm64 1.4-2 [34.5 kB] 166s Get:213 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pysam arm64 0.22.0+ds-1 [4399 kB] 167s Get:214 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgkitten all 0.2.3-1 [25.1 kB] 167s Get:215 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcpp arm64 1.0.12-1 [1971 kB] 167s Get:216 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcppgsl arm64 0.3.13-1 [198 kB] 167s Get:217 http://ftpmaster.internal/ubuntu noble/universe arm64 mapdamage all 2.2.1+dfsg-3 [43.1 kB] 167s Get:218 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-humanfriendly all 10.0-3 [70.4 kB] 167s Get:219 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-coloredlogs all 15.0.1-1 [38.2 kB] 167s Get:220 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-configargparse all 1.7-1 [31.7 kB] 167s Get:221 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-ruamel.yaml.clib arm64 0.2.8-1 [187 kB] 167s Get:222 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-ruamel.yaml all 0.17.21-1 [86.6 kB] 167s Get:223 http://ftpmaster.internal/ubuntu noble/main arm64 python3-setproctitle arm64 1.3.3-1build1 [20.0 kB] 167s Get:224 http://ftpmaster.internal/ubuntu noble/universe arm64 bowtie2 arm64 2.5.2-1 [1261 kB] 167s Get:225 http://ftpmaster.internal/ubuntu noble/universe arm64 phylip arm64 1:3.697+dfsg-3 [844 kB] 167s Get:226 http://ftpmaster.internal/ubuntu noble/universe arm64 picard-tools all 3.1.1+dfsg-1 [308 kB] 167s Get:227 http://ftpmaster.internal/ubuntu noble/universe arm64 radiant all 2.8.1+dfsg-2 [184 kB] 167s Get:228 http://ftpmaster.internal/ubuntu noble/universe arm64 raxml arm64 8.2.13+dfsg-1 [999 kB] 167s Get:229 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools arm64 1.19.2-1 [584 kB] 167s Get:230 http://ftpmaster.internal/ubuntu noble/universe arm64 paleomix arm64 1.3.8-1 [971 kB] 167s Get:231 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 167s Get:232 http://ftpmaster.internal/ubuntu noble/main arm64 python3-packaging all 23.2-1 [40.6 kB] 167s Get:233 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pluggy all 1.4.0-1 [20.4 kB] 167s Get:234 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pytest all 7.4.4-1 [305 kB] 169s Preconfiguring packages ... 169s Fetched 226 MB in 11s (20.7 MB/s) 169s dpkg: libpsl5:arm64: dependency problems, but removing anyway as you requested: 169s wget depends on libpsl5 (>= 0.16.0). 169s libcurl4:arm64 depends on libpsl5 (>= 0.16.0). 169s libcurl3-gnutls:arm64 depends on libpsl5 (>= 0.16.0). 169s 169s (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 ... 74774 files and directories currently installed.) 169s Removing libpsl5:arm64 (0.21.2-1build1) ... 169s Selecting previously unselected package libpsl5t64:arm64. 169s (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 ... 74769 files and directories currently installed.) 169s Preparing to unpack .../libpsl5t64_0.21.2-1.1_arm64.deb ... 169s Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... 169s Preparing to unpack .../curl_8.5.0-2ubuntu7_arm64.deb ... 169s Unpacking curl (8.5.0-2ubuntu7) over (8.5.0-2ubuntu2) ... 169s (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 ... 74775 files and directories currently installed.) 169s Removing libcurl4:arm64 (8.5.0-2ubuntu2) ... 169s Selecting previously unselected package libcurl4t64:arm64. 169s (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 ... 74770 files and directories currently installed.) 169s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu7_arm64.deb ... 169s Unpacking libcurl4t64:arm64 (8.5.0-2ubuntu7) ... 169s dpkg: libpng16-16:arm64: dependency problems, but removing anyway as you requested: 169s libplymouth5:arm64 depends on libpng16-16 (>= 1.6.2). 169s libfreetype6:arm64 depends on libpng16-16 (>= 1.6.2-1). 169s 169s (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 ... 74776 files and directories currently installed.) 169s Removing libpng16-16:arm64 (1.6.43-1) ... 169s Selecting previously unselected package libpng16-16t64:arm64. 169s (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 ... 74766 files and directories currently installed.) 169s Preparing to unpack .../libpng16-16t64_1.6.43-3_arm64.deb ... 169s Unpacking libpng16-16t64:arm64 (1.6.43-3) ... 170s dpkg: libreadline8:arm64: dependency problems, but removing anyway as you requested: 170s parted depends on libreadline8 (>= 6.0). 170s libpython3.12-stdlib:arm64 depends on libreadline8 (>= 7.0~beta). 170s gpgsm depends on libreadline8 (>= 6.0). 170s gpgconf depends on libreadline8 (>= 6.0). 170s gpg depends on libreadline8 (>= 6.0). 170s gawk depends on libreadline8 (>= 6.0). 170s fdisk depends on libreadline8 (>= 6.0). 170s 170s (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 ... 74777 files and directories currently installed.) 170s Removing libreadline8:arm64 (8.2-3) ... 170s Selecting previously unselected package libreadline8t64:arm64. 170s (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 ... 74765 files and directories currently installed.) 170s Preparing to unpack .../libreadline8t64_8.2-3.1_arm64.deb ... 170s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' 170s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' 170s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' 170s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' 170s Unpacking libreadline8t64:arm64 (8.2-3.1) ... 170s dpkg: libtirpc3:arm64: dependency problems, but removing anyway as you requested: 170s lsof depends on libtirpc3 (>= 1.0.2). 170s libpython3.12-stdlib:arm64 depends on libtirpc3 (>= 1.0.2). 170s libnss-nisplus:arm64 depends on libtirpc3 (>= 1.0.2). 170s libnsl2:arm64 depends on libtirpc3 (>= 1.0.2). 170s iproute2 depends on libtirpc3 (>= 1.0.2). 170s 170s (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 ... 74785 files and directories currently installed.) 170s Removing libtirpc3:arm64 (1.3.4+ds-1build1) ... 170s Selecting previously unselected package libtirpc3t64:arm64. 170s (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 ... 74779 files and directories currently installed.) 170s Preparing to unpack .../000-libtirpc3t64_1.3.4+ds-1.1_arm64.deb ... 170s Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' 170s Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' 170s Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.1) ... 170s Selecting previously unselected package adapterremoval. 170s Preparing to unpack .../001-adapterremoval_2.3.3-2_arm64.deb ... 170s Unpacking adapterremoval (2.3.3-2) ... 170s Selecting previously unselected package libgdk-pixbuf2.0-common. 171s Preparing to unpack .../002-libgdk-pixbuf2.0-common_2.42.10+dfsg-3_all.deb ... 171s Unpacking libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ... 171s Selecting previously unselected package libjpeg-turbo8:arm64. 171s Preparing to unpack .../003-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 171s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 171s Selecting previously unselected package libjpeg8:arm64. 171s Preparing to unpack .../004-libjpeg8_8c-2ubuntu11_arm64.deb ... 171s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 171s Selecting previously unselected package libdeflate0:arm64. 171s Preparing to unpack .../005-libdeflate0_1.19-1_arm64.deb ... 171s Unpacking libdeflate0:arm64 (1.19-1) ... 171s Selecting previously unselected package libjbig0:arm64. 171s Preparing to unpack .../006-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 171s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 171s Selecting previously unselected package liblerc4:arm64. 171s Preparing to unpack .../007-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 171s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 171s Selecting previously unselected package libsharpyuv0:arm64. 171s Preparing to unpack .../008-libsharpyuv0_1.3.2-0.4_arm64.deb ... 171s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 171s Selecting previously unselected package libwebp7:arm64. 171s Preparing to unpack .../009-libwebp7_1.3.2-0.4_arm64.deb ... 171s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 171s Selecting previously unselected package libtiff6:arm64. 171s Preparing to unpack .../010-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 171s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 171s Selecting previously unselected package libgdk-pixbuf-2.0-0:arm64. 171s Preparing to unpack .../011-libgdk-pixbuf-2.0-0_2.42.10+dfsg-3_arm64.deb ... 171s Unpacking libgdk-pixbuf-2.0-0:arm64 (2.42.10+dfsg-3) ... 171s Selecting previously unselected package gtk-update-icon-cache. 171s Preparing to unpack .../012-gtk-update-icon-cache_3.24.40-2ubuntu1_arm64.deb ... 171s Unpacking gtk-update-icon-cache (3.24.40-2ubuntu1) ... 171s Selecting previously unselected package hicolor-icon-theme. 171s Preparing to unpack .../013-hicolor-icon-theme_0.17-2_all.deb ... 171s Unpacking hicolor-icon-theme (0.17-2) ... 171s Selecting previously unselected package humanity-icon-theme. 171s Preparing to unpack .../014-humanity-icon-theme_0.6.16_all.deb ... 171s Unpacking humanity-icon-theme (0.6.16) ... 172s Selecting previously unselected package ubuntu-mono. 172s Preparing to unpack .../015-ubuntu-mono_24.04-0ubuntu1_all.deb ... 172s Unpacking ubuntu-mono (24.04-0ubuntu1) ... 172s Selecting previously unselected package adwaita-icon-theme. 172s Preparing to unpack .../016-adwaita-icon-theme_46~rc-1_all.deb ... 172s Unpacking adwaita-icon-theme (46~rc-1) ... 172s Selecting previously unselected package at-spi2-common. 172s Preparing to unpack .../017-at-spi2-common_2.50.0-1_all.deb ... 172s Unpacking at-spi2-common (2.50.0-1) ... 172s Selecting previously unselected package libhtscodecs2:arm64. 172s Preparing to unpack .../018-libhtscodecs2_1.6.0-1_arm64.deb ... 172s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 172s Selecting previously unselected package libhts3:arm64. 172s Preparing to unpack .../019-libhts3_1.18+ds-1_arm64.deb ... 172s Unpacking libhts3:arm64 (1.18+ds-1) ... 172s Selecting previously unselected package bcftools. 172s Preparing to unpack .../020-bcftools_1.19-1_arm64.deb ... 172s Unpacking bcftools (1.19-1) ... 172s Selecting previously unselected package bedtools. 172s Preparing to unpack .../021-bedtools_2.31.1+dfsg-2_arm64.deb ... 172s Unpacking bedtools (2.31.1+dfsg-2) ... 172s Selecting previously unselected package bwa. 172s Preparing to unpack .../022-bwa_0.7.17-7_arm64.deb ... 172s Unpacking bwa (0.7.17-7) ... 172s Selecting previously unselected package ca-certificates-java. 172s Preparing to unpack .../023-ca-certificates-java_20240118_all.deb ... 172s Unpacking ca-certificates-java (20240118) ... 173s Selecting previously unselected package java-common. 173s Preparing to unpack .../024-java-common_0.75+exp1_all.deb ... 173s Unpacking java-common (0.75+exp1) ... 173s Selecting previously unselected package libavahi-common-data:arm64. 173s Preparing to unpack .../025-libavahi-common-data_0.8-13ubuntu2_arm64.deb ... 173s Unpacking libavahi-common-data:arm64 (0.8-13ubuntu2) ... 173s Selecting previously unselected package libavahi-common3:arm64. 173s Preparing to unpack .../026-libavahi-common3_0.8-13ubuntu2_arm64.deb ... 173s Unpacking libavahi-common3:arm64 (0.8-13ubuntu2) ... 173s Selecting previously unselected package libavahi-client3:arm64. 173s Preparing to unpack .../027-libavahi-client3_0.8-13ubuntu2_arm64.deb ... 173s Unpacking libavahi-client3:arm64 (0.8-13ubuntu2) ... 173s Selecting previously unselected package libcups2:arm64. 173s Preparing to unpack .../028-libcups2_2.4.6-0ubuntu3_arm64.deb ... 173s Unpacking libcups2:arm64 (2.4.6-0ubuntu3) ... 173s Selecting previously unselected package liblcms2-2:arm64. 173s Preparing to unpack .../029-liblcms2-2_2.14-2_arm64.deb ... 173s Unpacking liblcms2-2:arm64 (2.14-2) ... 173s Selecting previously unselected package fonts-dejavu-mono. 173s Preparing to unpack .../030-fonts-dejavu-mono_2.37-8_all.deb ... 173s Unpacking fonts-dejavu-mono (2.37-8) ... 173s Selecting previously unselected package fonts-dejavu-core. 173s Preparing to unpack .../031-fonts-dejavu-core_2.37-8_all.deb ... 173s Unpacking fonts-dejavu-core (2.37-8) ... 173s Selecting previously unselected package fontconfig-config. 173s Preparing to unpack .../032-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 173s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 173s Selecting previously unselected package libfontconfig1:arm64. 173s Preparing to unpack .../033-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 173s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 173s Selecting previously unselected package libasound2-data. 174s Preparing to unpack .../034-libasound2-data_1.2.10-3build1_all.deb ... 174s Unpacking libasound2-data (1.2.10-3build1) ... 174s Selecting previously unselected package libasound2:arm64. 174s Preparing to unpack .../035-libasound2_1.2.10-3build1_arm64.deb ... 174s Unpacking libasound2:arm64 (1.2.10-3build1) ... 174s Selecting previously unselected package libgraphite2-3:arm64. 174s Preparing to unpack .../036-libgraphite2-3_1.3.14-2_arm64.deb ... 174s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 174s Selecting previously unselected package libharfbuzz0b:arm64. 174s Preparing to unpack .../037-libharfbuzz0b_8.3.0-2_arm64.deb ... 174s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 174s Selecting previously unselected package libpcsclite1:arm64. 174s Preparing to unpack .../038-libpcsclite1_2.0.0-1_arm64.deb ... 174s Unpacking libpcsclite1:arm64 (2.0.0-1) ... 174s Selecting previously unselected package openjdk-21-jre-headless:arm64. 174s Preparing to unpack .../039-openjdk-21-jre-headless_21.0.2+13-2_arm64.deb ... 174s Unpacking openjdk-21-jre-headless:arm64 (21.0.2+13-2) ... 175s Selecting previously unselected package default-jre-headless. 178s Preparing to unpack .../040-default-jre-headless_2%3a1.21-75+exp1_arm64.deb ... 178s Unpacking default-jre-headless (2:1.21-75+exp1) ... 179s Selecting previously unselected package libgtk2.0-common. 181s Preparing to unpack .../041-libgtk2.0-common_2.24.33-2ubuntu2_all.deb ... 181s Unpacking libgtk2.0-common (2.24.33-2ubuntu2) ... 182s Selecting previously unselected package libatk1.0-0:arm64. 183s Preparing to unpack .../042-libatk1.0-0_2.50.0-1_arm64.deb ... 183s Unpacking libatk1.0-0:arm64 (2.50.0-1) ... 183s Selecting previously unselected package libpixman-1-0:arm64. 183s Preparing to unpack .../043-libpixman-1-0_0.42.2-1_arm64.deb ... 183s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 183s Selecting previously unselected package libxcb-render0:arm64. 183s Preparing to unpack .../044-libxcb-render0_1.15-1_arm64.deb ... 183s Unpacking libxcb-render0:arm64 (1.15-1) ... 183s Selecting previously unselected package libxcb-shm0:arm64. 183s Preparing to unpack .../045-libxcb-shm0_1.15-1_arm64.deb ... 183s Unpacking libxcb-shm0:arm64 (1.15-1) ... 183s Selecting previously unselected package libxrender1:arm64. 183s Preparing to unpack .../046-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 183s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 183s Selecting previously unselected package libcairo2:arm64. 183s Preparing to unpack .../047-libcairo2_1.18.0-1_arm64.deb ... 183s Unpacking libcairo2:arm64 (1.18.0-1) ... 183s Selecting previously unselected package fontconfig. 183s Preparing to unpack .../048-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 183s Unpacking fontconfig (2.15.0-1ubuntu1) ... 183s Selecting previously unselected package libthai-data. 183s Preparing to unpack .../049-libthai-data_0.1.29-2_all.deb ... 183s Unpacking libthai-data (0.1.29-2) ... 183s Selecting previously unselected package libdatrie1:arm64. 184s Preparing to unpack .../050-libdatrie1_0.2.13-3_arm64.deb ... 184s Unpacking libdatrie1:arm64 (0.2.13-3) ... 184s Selecting previously unselected package libthai0:arm64. 184s Preparing to unpack .../051-libthai0_0.1.29-2_arm64.deb ... 184s Unpacking libthai0:arm64 (0.1.29-2) ... 184s Selecting previously unselected package libpango-1.0-0:arm64. 184s Preparing to unpack .../052-libpango-1.0-0_1.51.0+ds-4_arm64.deb ... 184s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ... 184s Selecting previously unselected package libpangoft2-1.0-0:arm64. 184s Preparing to unpack .../053-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 184s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 184s Selecting previously unselected package libpangocairo-1.0-0:arm64. 184s Preparing to unpack .../054-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ... 184s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 184s Selecting previously unselected package libxcomposite1:arm64. 184s Preparing to unpack .../055-libxcomposite1_1%3a0.4.5-1build2_arm64.deb ... 184s Unpacking libxcomposite1:arm64 (1:0.4.5-1build2) ... 184s Selecting previously unselected package libxfixes3:arm64. 184s Preparing to unpack .../056-libxfixes3_1%3a6.0.0-2_arm64.deb ... 184s Unpacking libxfixes3:arm64 (1:6.0.0-2) ... 184s Selecting previously unselected package libxcursor1:arm64. 184s Preparing to unpack .../057-libxcursor1_1%3a1.2.1-1_arm64.deb ... 184s Unpacking libxcursor1:arm64 (1:1.2.1-1) ... 184s Selecting previously unselected package libxdamage1:arm64. 184s Preparing to unpack .../058-libxdamage1_1%3a1.1.6-1_arm64.deb ... 184s Unpacking libxdamage1:arm64 (1:1.1.6-1) ... 184s Selecting previously unselected package libxi6:arm64. 184s Preparing to unpack .../059-libxi6_2%3a1.8.1-1_arm64.deb ... 184s Unpacking libxi6:arm64 (2:1.8.1-1) ... 184s Selecting previously unselected package libxinerama1:arm64. 184s Preparing to unpack .../060-libxinerama1_2%3a1.1.4-3_arm64.deb ... 184s Unpacking libxinerama1:arm64 (2:1.1.4-3) ... 184s Selecting previously unselected package libxrandr2:arm64. 184s Preparing to unpack .../061-libxrandr2_2%3a1.5.2-2_arm64.deb ... 184s Unpacking libxrandr2:arm64 (2:1.5.2-2) ... 184s Selecting previously unselected package libgtk2.0-0:arm64. 184s Preparing to unpack .../062-libgtk2.0-0_2.24.33-2ubuntu2_arm64.deb ... 184s Unpacking libgtk2.0-0:arm64 (2.24.33-2ubuntu2) ... 184s Selecting previously unselected package libglvnd0:arm64. 184s Preparing to unpack .../063-libglvnd0_1.7.0-1_arm64.deb ... 184s Unpacking libglvnd0:arm64 (1.7.0-1) ... 184s Selecting previously unselected package libglapi-mesa:arm64. 184s Preparing to unpack .../064-libglapi-mesa_24.0.1-1ubuntu1_arm64.deb ... 184s Unpacking libglapi-mesa:arm64 (24.0.1-1ubuntu1) ... 184s Selecting previously unselected package libx11-xcb1:arm64. 184s Preparing to unpack .../065-libx11-xcb1_2%3a1.8.7-1_arm64.deb ... 184s Unpacking libx11-xcb1:arm64 (2:1.8.7-1) ... 184s Selecting previously unselected package libxcb-dri2-0:arm64. 184s Preparing to unpack .../066-libxcb-dri2-0_1.15-1_arm64.deb ... 184s Unpacking libxcb-dri2-0:arm64 (1.15-1) ... 184s Selecting previously unselected package libxcb-dri3-0:arm64. 184s Preparing to unpack .../067-libxcb-dri3-0_1.15-1_arm64.deb ... 184s Unpacking libxcb-dri3-0:arm64 (1.15-1) ... 184s Selecting previously unselected package libxcb-glx0:arm64. 184s Preparing to unpack .../068-libxcb-glx0_1.15-1_arm64.deb ... 184s Unpacking libxcb-glx0:arm64 (1.15-1) ... 184s Selecting previously unselected package libxcb-present0:arm64. 184s Preparing to unpack .../069-libxcb-present0_1.15-1_arm64.deb ... 184s Unpacking libxcb-present0:arm64 (1.15-1) ... 184s Selecting previously unselected package libxcb-randr0:arm64. 184s Preparing to unpack .../070-libxcb-randr0_1.15-1_arm64.deb ... 184s Unpacking libxcb-randr0:arm64 (1.15-1) ... 184s Selecting previously unselected package libxcb-sync1:arm64. 184s Preparing to unpack .../071-libxcb-sync1_1.15-1_arm64.deb ... 184s Unpacking libxcb-sync1:arm64 (1.15-1) ... 184s Selecting previously unselected package libxcb-xfixes0:arm64. 184s Preparing to unpack .../072-libxcb-xfixes0_1.15-1_arm64.deb ... 184s Unpacking libxcb-xfixes0:arm64 (1.15-1) ... 184s Selecting previously unselected package libxshmfence1:arm64. 184s Preparing to unpack .../073-libxshmfence1_1.3-1build4_arm64.deb ... 184s Unpacking libxshmfence1:arm64 (1.3-1build4) ... 185s Selecting previously unselected package libxxf86vm1:arm64. 185s Preparing to unpack .../074-libxxf86vm1_1%3a1.1.4-1build3_arm64.deb ... 185s Unpacking libxxf86vm1:arm64 (1:1.1.4-1build3) ... 185s Selecting previously unselected package libvulkan1:arm64. 185s Preparing to unpack .../075-libvulkan1_1.3.275.0-1_arm64.deb ... 185s Unpacking libvulkan1:arm64 (1.3.275.0-1) ... 185s Selecting previously unselected package libdrm-amdgpu1:arm64. 185s Preparing to unpack .../076-libdrm-amdgpu1_2.4.120-2_arm64.deb ... 185s Unpacking libdrm-amdgpu1:arm64 (2.4.120-2) ... 185s Selecting previously unselected package libdrm-nouveau2:arm64. 185s Preparing to unpack .../077-libdrm-nouveau2_2.4.120-2_arm64.deb ... 185s Unpacking libdrm-nouveau2:arm64 (2.4.120-2) ... 185s Selecting previously unselected package libdrm-radeon1:arm64. 185s Preparing to unpack .../078-libdrm-radeon1_2.4.120-2_arm64.deb ... 185s Unpacking libdrm-radeon1:arm64 (2.4.120-2) ... 185s Selecting previously unselected package libllvm17:arm64. 185s Preparing to unpack .../079-libllvm17_1%3a17.0.6-5build1_arm64.deb ... 185s Unpacking libllvm17:arm64 (1:17.0.6-5build1) ... 185s Selecting previously unselected package libgl1-mesa-dri:arm64. 185s Preparing to unpack .../080-libgl1-mesa-dri_24.0.1-1ubuntu1_arm64.deb ... 185s Unpacking libgl1-mesa-dri:arm64 (24.0.1-1ubuntu1) ... 186s Selecting previously unselected package libglx-mesa0:arm64. 186s Preparing to unpack .../081-libglx-mesa0_24.0.1-1ubuntu1_arm64.deb ... 186s Unpacking libglx-mesa0:arm64 (24.0.1-1ubuntu1) ... 186s Selecting previously unselected package libglx0:arm64. 186s Preparing to unpack .../082-libglx0_1.7.0-1_arm64.deb ... 186s Unpacking libglx0:arm64 (1.7.0-1) ... 186s Selecting previously unselected package libgl1:arm64. 186s Preparing to unpack .../083-libgl1_1.7.0-1_arm64.deb ... 186s Unpacking libgl1:arm64 (1.7.0-1) ... 186s Selecting previously unselected package libgif7:arm64. 186s Preparing to unpack .../084-libgif7_5.2.1-2.5_arm64.deb ... 186s Unpacking libgif7:arm64 (5.2.1-2.5) ... 186s Selecting previously unselected package x11-common. 186s Preparing to unpack .../085-x11-common_1%3a7.7+23ubuntu2_all.deb ... 186s Unpacking x11-common (1:7.7+23ubuntu2) ... 186s Selecting previously unselected package libxtst6:arm64. 186s Preparing to unpack .../086-libxtst6_2%3a1.2.3-1.1_arm64.deb ... 186s Unpacking libxtst6:arm64 (2:1.2.3-1.1) ... 186s Selecting previously unselected package openjdk-21-jre:arm64. 186s Preparing to unpack .../087-openjdk-21-jre_21.0.2+13-2_arm64.deb ... 186s Unpacking openjdk-21-jre:arm64 (21.0.2+13-2) ... 186s Selecting previously unselected package default-jre. 186s Preparing to unpack .../088-default-jre_2%3a1.21-75+exp1_arm64.deb ... 186s Unpacking default-jre (2:1.21-75+exp1) ... 186s Selecting previously unselected package libevent-pthreads-2.1-7:arm64. 186s Preparing to unpack .../089-libevent-pthreads-2.1-7_2.1.12-stable-9_arm64.deb ... 186s Unpacking libevent-pthreads-2.1-7:arm64 (2.1.12-stable-9) ... 186s Selecting previously unselected package libatomic1:arm64. 186s Preparing to unpack .../090-libatomic1_14-20240303-1ubuntu1_arm64.deb ... 186s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ... 186s Selecting previously unselected package librdmacm1t64:arm64. 186s Preparing to unpack .../091-librdmacm1t64_50.0-2_arm64.deb ... 186s Unpacking librdmacm1t64:arm64 (50.0-2) ... 186s Selecting previously unselected package libfabric1:arm64. 186s Preparing to unpack .../092-libfabric1_1.17.0-3_arm64.deb ... 186s Unpacking libfabric1:arm64 (1.17.0-3) ... 186s Selecting previously unselected package libhwloc15:arm64. 186s Preparing to unpack .../093-libhwloc15_2.10.0-1_arm64.deb ... 186s Unpacking libhwloc15:arm64 (2.10.0-1) ... 187s Selecting previously unselected package libmunge2:arm64. 187s Preparing to unpack .../094-libmunge2_0.5.15-3ubuntu1_arm64.deb ... 187s Unpacking libmunge2:arm64 (0.5.15-3ubuntu1) ... 187s Selecting previously unselected package libpciaccess0:arm64. 187s Preparing to unpack .../095-libpciaccess0_0.17-3_arm64.deb ... 187s Unpacking libpciaccess0:arm64 (0.17-3) ... 187s Selecting previously unselected package libxnvctrl0:arm64. 187s Preparing to unpack .../096-libxnvctrl0_510.47.03-0ubuntu1_arm64.deb ... 187s Unpacking libxnvctrl0:arm64 (510.47.03-0ubuntu1) ... 187s Selecting previously unselected package ocl-icd-libopencl1:arm64. 187s Preparing to unpack .../097-ocl-icd-libopencl1_2.3.2-1_arm64.deb ... 187s Unpacking ocl-icd-libopencl1:arm64 (2.3.2-1) ... 187s Selecting previously unselected package libhwloc-plugins:arm64. 187s Preparing to unpack .../098-libhwloc-plugins_2.10.0-1_arm64.deb ... 187s Unpacking libhwloc-plugins:arm64 (2.10.0-1) ... 187s Selecting previously unselected package libpmix2:arm64. 187s Preparing to unpack .../099-libpmix2_5.0.1-4_arm64.deb ... 187s Unpacking libpmix2:arm64 (5.0.1-4) ... 187s Selecting previously unselected package libamd-comgr2:arm64. 187s Preparing to unpack .../100-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3_arm64.deb ... 187s Unpacking libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3) ... 187s Selecting previously unselected package libhsakmt1:arm64. 187s Preparing to unpack .../101-libhsakmt1_5.7.0-1_arm64.deb ... 187s Unpacking libhsakmt1:arm64 (5.7.0-1) ... 187s Selecting previously unselected package libhsa-runtime64-1. 187s Preparing to unpack .../102-libhsa-runtime64-1_5.7.1-1_arm64.deb ... 187s Unpacking libhsa-runtime64-1 (5.7.1-1) ... 188s Selecting previously unselected package libamdhip64-5. 188s Preparing to unpack .../103-libamdhip64-5_5.2.3-12_arm64.deb ... 188s Unpacking libamdhip64-5 (5.2.3-12) ... 188s Selecting previously unselected package libucx0:arm64. 188s Preparing to unpack .../104-libucx0_1.16.0+ds-4_arm64.deb ... 188s Unpacking libucx0:arm64 (1.16.0+ds-4) ... 188s Selecting previously unselected package libopenmpi3:arm64. 188s Preparing to unpack .../105-libopenmpi3_4.1.6-5ubuntu1_arm64.deb ... 188s Unpacking libopenmpi3:arm64 (4.1.6-5ubuntu1) ... 188s Selecting previously unselected package openmpi-common. 188s Preparing to unpack .../106-openmpi-common_4.1.6-5ubuntu1_all.deb ... 188s Unpacking openmpi-common (4.1.6-5ubuntu1) ... 188s Selecting previously unselected package openmpi-bin. 188s Preparing to unpack .../107-openmpi-bin_4.1.6-5ubuntu1_arm64.deb ... 188s Unpacking openmpi-bin (4.1.6-5ubuntu1) ... 188s Selecting previously unselected package examl. 188s Preparing to unpack .../108-examl_3.0.22-4_arm64.deb ... 188s Unpacking examl (3.0.22-4) ... 188s Selecting previously unselected package libapache-pom-java. 188s Preparing to unpack .../109-libapache-pom-java_29-2_all.deb ... 188s Unpacking libapache-pom-java (29-2) ... 188s Selecting previously unselected package libcommons-parent-java. 188s Preparing to unpack .../110-libcommons-parent-java_56-1_all.deb ... 188s Unpacking libcommons-parent-java (56-1) ... 188s Selecting previously unselected package libcommons-lang3-java. 188s Preparing to unpack .../111-libcommons-lang3-java_3.14.0-1_all.deb ... 188s Unpacking libcommons-lang3-java (3.14.0-1) ... 188s Selecting previously unselected package libfreemarker-java. 188s Preparing to unpack .../112-libfreemarker-java_2.3.32-2_all.deb ... 188s Unpacking libfreemarker-java (2.3.32-2) ... 188s Selecting previously unselected package libgoogle-gson-java. 188s Preparing to unpack .../113-libgoogle-gson-java_2.10.1-1_all.deb ... 188s Unpacking libgoogle-gson-java (2.10.1-1) ... 188s Selecting previously unselected package libjoptsimple-java. 188s Preparing to unpack .../114-libjoptsimple-java_5.0.4-4_all.deb ... 188s Unpacking libjoptsimple-java (5.0.4-4) ... 188s Selecting previously unselected package libcommons-codec-java. 189s Preparing to unpack .../115-libcommons-codec-java_1.16.0-1_all.deb ... 189s Unpacking libcommons-codec-java (1.16.0-1) ... 189s Selecting previously unselected package libcommons-logging-java. 189s Preparing to unpack .../116-libcommons-logging-java_1.3.0-1_all.deb ... 189s Unpacking libcommons-logging-java (1.3.0-1) ... 189s Selecting previously unselected package libhttpcore-java. 189s Preparing to unpack .../117-libhttpcore-java_4.4.16-1_all.deb ... 189s Unpacking libhttpcore-java (4.4.16-1) ... 189s Selecting previously unselected package libhttpclient-java. 189s Preparing to unpack .../118-libhttpclient-java_4.5.14-1_all.deb ... 189s Unpacking libhttpclient-java (4.5.14-1) ... 189s Selecting previously unselected package liblightcouch-java. 189s Preparing to unpack .../119-liblightcouch-java_0.2.0-1_all.deb ... 189s Unpacking liblightcouch-java (0.2.0-1) ... 189s Selecting previously unselected package libmongodb-java. 189s Preparing to unpack .../120-libmongodb-java_3.6.3-2_all.deb ... 189s Unpacking libmongodb-java (3.6.3-2) ... 189s Selecting previously unselected package libslf4j-java. 189s Preparing to unpack .../121-libslf4j-java_1.7.32-1_all.deb ... 189s Unpacking libslf4j-java (1.7.32-1) ... 189s Selecting previously unselected package liblog4j2-java. 189s Preparing to unpack .../122-liblog4j2-java_2.19.0-2_all.deb ... 189s Unpacking liblog4j2-java (2.19.0-2) ... 189s Selecting previously unselected package libbarclay-java. 189s Preparing to unpack .../123-libbarclay-java_5.0.0+dfsg-1_all.deb ... 189s Unpacking libbarclay-java (5.0.0+dfsg-1) ... 189s Selecting previously unselected package libblas3:arm64. 189s Preparing to unpack .../124-libblas3_3.12.0-3_arm64.deb ... 189s Unpacking libblas3:arm64 (3.12.0-3) ... 189s Selecting previously unselected package libcommons-compress-java. 189s Preparing to unpack .../125-libcommons-compress-java_1.25.0-1_all.deb ... 189s Unpacking libcommons-compress-java (1.25.0-1) ... 189s Selecting previously unselected package libcommons-io-java. 189s Preparing to unpack .../126-libcommons-io-java_2.11.0-2_all.deb ... 189s Unpacking libcommons-io-java (2.11.0-2) ... 189s Selecting previously unselected package libcommons-jexl2-java. 189s Preparing to unpack .../127-libcommons-jexl2-java_2.1.1-6_all.deb ... 189s Unpacking libcommons-jexl2-java (2.1.1-6) ... 189s Selecting previously unselected package libcommons-math3-java. 189s Preparing to unpack .../128-libcommons-math3-java_3.6.1-3_all.deb ... 189s Unpacking libcommons-math3-java (3.6.1-3) ... 190s Selecting previously unselected package libgatk-native-bindings-java. 190s Preparing to unpack .../129-libgatk-native-bindings-java_1.0.0+dfsg-2_all.deb ... 190s Unpacking libgatk-native-bindings-java (1.0.0+dfsg-2) ... 190s Selecting previously unselected package libgfortran5:arm64. 190s Preparing to unpack .../130-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 190s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 190s Selecting previously unselected package libmjson-java. 190s Preparing to unpack .../131-libmjson-java_1.4.0-3_all.deb ... 190s Unpacking libmjson-java (1.4.0-3) ... 190s Selecting previously unselected package libmbedcrypto7:arm64. 190s Preparing to unpack .../132-libmbedcrypto7_2.28.7-1ubuntu1_arm64.deb ... 190s Unpacking libmbedcrypto7:arm64 (2.28.7-1ubuntu1) ... 190s Selecting previously unselected package libmbedx509-1:arm64. 190s Preparing to unpack .../133-libmbedx509-1_2.28.7-1ubuntu1_arm64.deb ... 190s Unpacking libmbedx509-1:arm64 (2.28.7-1ubuntu1) ... 190s Selecting previously unselected package libmbedtls14:arm64. 190s Preparing to unpack .../134-libmbedtls14_2.28.7-1ubuntu1_arm64.deb ... 190s Unpacking libmbedtls14:arm64 (2.28.7-1ubuntu1) ... 190s Selecting previously unselected package ncbi-vdb-data. 190s Preparing to unpack .../135-ncbi-vdb-data_3.0.2+dfsg-2_all.deb ... 190s Unpacking ncbi-vdb-data (3.0.2+dfsg-2) ... 190s Selecting previously unselected package libncbi-vdb3:arm64. 190s Preparing to unpack .../136-libncbi-vdb3_3.0.2+dfsg-2_arm64.deb ... 190s Unpacking libncbi-vdb3:arm64 (3.0.2+dfsg-2) ... 190s Selecting previously unselected package libncbi-ngs3:arm64. 190s Preparing to unpack .../137-libncbi-ngs3_3.0.3+dfsg-6ubuntu1_arm64.deb ... 190s Unpacking libncbi-ngs3:arm64 (3.0.3+dfsg-6ubuntu1) ... 190s Selecting previously unselected package libngs-jni:arm64. 190s Preparing to unpack .../138-libngs-jni_3.0.3+dfsg-6ubuntu1_arm64.deb ... 190s Unpacking libngs-jni:arm64 (3.0.3+dfsg-6ubuntu1) ... 190s Selecting previously unselected package libngs-java:arm64. 190s Preparing to unpack .../139-libngs-java_3.0.3+dfsg-6ubuntu1_arm64.deb ... 190s Unpacking libngs-java:arm64 (3.0.3+dfsg-6ubuntu1) ... 190s Selecting previously unselected package librhino-java. 190s Preparing to unpack .../140-librhino-java_1.7.14-2.1_all.deb ... 190s Unpacking librhino-java (1.7.14-2.1) ... 190s Selecting previously unselected package libsnappy1v5:arm64. 190s Preparing to unpack .../141-libsnappy1v5_1.1.10-1_arm64.deb ... 190s Unpacking libsnappy1v5:arm64 (1.1.10-1) ... 190s Selecting previously unselected package libsnappy-jni. 190s Preparing to unpack .../142-libsnappy-jni_1.1.10.5-1_arm64.deb ... 190s Unpacking libsnappy-jni (1.1.10.5-1) ... 190s Selecting previously unselected package libsnappy-java. 190s Preparing to unpack .../143-libsnappy-java_1.1.10.5-1_all.deb ... 190s Unpacking libsnappy-java (1.1.10.5-1) ... 190s Selecting previously unselected package libhtsjdk-java. 190s Preparing to unpack .../144-libhtsjdk-java_4.1.0+dfsg-1_all.deb ... 190s Unpacking libhtsjdk-java (4.1.0+dfsg-1) ... 190s Selecting previously unselected package libgkl-java. 191s Preparing to unpack .../145-libgkl-java_0.8.11+dfsg-2_all.deb ... 191s Unpacking libgkl-java (0.8.11+dfsg-2) ... 191s Selecting previously unselected package libgomp1:arm64. 191s Preparing to unpack .../146-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 191s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 191s Selecting previously unselected package libgslcblas0:arm64. 191s Preparing to unpack .../147-libgslcblas0_2.7.1+dfsg-6ubuntu1_arm64.deb ... 191s Unpacking libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu1) ... 191s Selecting previously unselected package libgsl27:arm64. 191s Preparing to unpack .../148-libgsl27_2.7.1+dfsg-6ubuntu1_arm64.deb ... 191s Unpacking libgsl27:arm64 (2.7.1+dfsg-6ubuntu1) ... 191s Selecting previously unselected package libgsl-dev. 191s Preparing to unpack .../149-libgsl-dev_2.7.1+dfsg-6ubuntu1_arm64.deb ... 191s Unpacking libgsl-dev (2.7.1+dfsg-6ubuntu1) ... 191s Selecting previously unselected package libice6:arm64. 191s Preparing to unpack .../150-libice6_2%3a1.0.10-1build2_arm64.deb ... 191s Unpacking libice6:arm64 (2:1.0.10-1build2) ... 191s Selecting previously unselected package libopenblas0-pthread:arm64. 191s Preparing to unpack .../151-libopenblas0-pthread_0.3.26+ds-1_arm64.deb ... 191s Unpacking libopenblas0-pthread:arm64 (0.3.26+ds-1) ... 191s Selecting previously unselected package liblapack3:arm64. 191s Preparing to unpack .../152-liblapack3_3.12.0-3_arm64.deb ... 191s Unpacking liblapack3:arm64 (3.12.0-3) ... 191s Selecting previously unselected package libopenblas0:arm64. 191s Preparing to unpack .../153-libopenblas0_0.3.26+ds-1_arm64.deb ... 191s Unpacking libopenblas0:arm64 (0.3.26+ds-1) ... 191s Selecting previously unselected package libopenblas-pthread-dev:arm64. 191s Preparing to unpack .../154-libopenblas-pthread-dev_0.3.26+ds-1_arm64.deb ... 191s Unpacking libopenblas-pthread-dev:arm64 (0.3.26+ds-1) ... 192s Selecting previously unselected package libopenblas-dev:arm64. 192s Preparing to unpack .../155-libopenblas-dev_0.3.26+ds-1_arm64.deb ... 192s Unpacking libopenblas-dev:arm64 (0.3.26+ds-1) ... 192s Selecting previously unselected package libpaper1:arm64. 192s Preparing to unpack .../156-libpaper1_1.1.29_arm64.deb ... 192s Unpacking libpaper1:arm64 (1.1.29) ... 192s Selecting previously unselected package libpaper-utils. 192s Preparing to unpack .../157-libpaper-utils_1.1.29_arm64.deb ... 192s Unpacking libpaper-utils (1.1.29) ... 192s Selecting previously unselected package libpicard-java. 192s Preparing to unpack .../158-libpicard-java_3.1.1+dfsg-1_all.deb ... 192s Unpacking libpicard-java (3.1.1+dfsg-1) ... 192s Selecting previously unselected package libsm6:arm64. 192s Preparing to unpack .../159-libsm6_2%3a1.2.3-1build2_arm64.deb ... 192s Unpacking libsm6:arm64 (2:1.2.3-1build2) ... 192s Selecting previously unselected package libtcl8.6:arm64. 192s Preparing to unpack .../160-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... 192s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... 192s Selecting previously unselected package libxft2:arm64. 192s Preparing to unpack .../161-libxft2_2.3.6-1_arm64.deb ... 192s Unpacking libxft2:arm64 (2.3.6-1) ... 192s Selecting previously unselected package libxss1:arm64. 192s Preparing to unpack .../162-libxss1_1%3a1.2.3-1build2_arm64.deb ... 192s Unpacking libxss1:arm64 (1:1.2.3-1build2) ... 192s Selecting previously unselected package libtk8.6:arm64. 192s Preparing to unpack .../163-libtk8.6_8.6.13-2_arm64.deb ... 192s Unpacking libtk8.6:arm64 (8.6.13-2) ... 192s Selecting previously unselected package libxt6t64:arm64. 192s Preparing to unpack .../164-libxt6t64_1%3a1.2.1-1.2_arm64.deb ... 192s Unpacking libxt6t64:arm64 (1:1.2.1-1.2) ... 192s Selecting previously unselected package zip. 192s Preparing to unpack .../165-zip_3.0-13_arm64.deb ... 192s Unpacking zip (3.0-13) ... 192s Selecting previously unselected package unzip. 192s Preparing to unpack .../166-unzip_6.0-28ubuntu3_arm64.deb ... 192s Unpacking unzip (6.0-28ubuntu3) ... 192s Selecting previously unselected package xdg-utils. 192s Preparing to unpack .../167-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 192s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 192s Selecting previously unselected package r-base-core. 192s Preparing to unpack .../168-r-base-core_4.3.3-2build1_arm64.deb ... 192s Unpacking r-base-core (4.3.3-2build1) ... 192s Selecting previously unselected package r-cran-littler. 192s Preparing to unpack .../169-r-cran-littler_0.3.19-1_arm64.deb ... 192s Unpacking r-cran-littler (0.3.19-1) ... 192s Selecting previously unselected package littler. 192s Preparing to unpack .../170-littler_0.3.19-1_all.deb ... 192s Unpacking littler (0.3.19-1) ... 192s Selecting previously unselected package mafft. 192s Preparing to unpack .../171-mafft_7.505-1_arm64.deb ... 192s Unpacking mafft (7.505-1) ... 193s Selecting previously unselected package r-cran-codetools. 193s Preparing to unpack .../172-r-cran-codetools_0.2-19-1_all.deb ... 193s Unpacking r-cran-codetools (0.2-19-1) ... 193s Selecting previously unselected package r-cran-iterators. 193s Preparing to unpack .../173-r-cran-iterators_1.0.14-1_all.deb ... 193s Unpacking r-cran-iterators (1.0.14-1) ... 193s Selecting previously unselected package r-cran-foreach. 193s Preparing to unpack .../174-r-cran-foreach_1.5.2-1_all.deb ... 193s Unpacking r-cran-foreach (1.5.2-1) ... 193s Selecting previously unselected package r-cran-gam. 193s Preparing to unpack .../175-r-cran-gam_1.22-3-1_arm64.deb ... 193s Unpacking r-cran-gam (1.22-3-1) ... 193s Selecting previously unselected package r-cran-cli. 193s Preparing to unpack .../176-r-cran-cli_3.6.2-1_arm64.deb ... 193s Unpacking r-cran-cli (3.6.2-1) ... 193s Selecting previously unselected package r-cran-glue. 193s Preparing to unpack .../177-r-cran-glue_1.7.0-1_arm64.deb ... 193s Unpacking r-cran-glue (1.7.0-1) ... 193s Selecting previously unselected package r-cran-rlang. 193s Preparing to unpack .../178-r-cran-rlang_1.1.3-1_arm64.deb ... 193s Unpacking r-cran-rlang (1.1.3-1) ... 193s Selecting previously unselected package r-cran-lifecycle. 193s Preparing to unpack .../179-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 193s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 193s Selecting previously unselected package r-cran-gtable. 193s Preparing to unpack .../180-r-cran-gtable_0.3.4+dfsg-1_all.deb ... 193s Unpacking r-cran-gtable (0.3.4+dfsg-1) ... 193s Selecting previously unselected package r-cran-isoband. 193s Preparing to unpack .../181-r-cran-isoband_0.2.7-1_arm64.deb ... 193s Unpacking r-cran-isoband (0.2.7-1) ... 193s Selecting previously unselected package r-cran-mass. 193s Preparing to unpack .../182-r-cran-mass_7.3-60.0.1-1_arm64.deb ... 193s Unpacking r-cran-mass (7.3-60.0.1-1) ... 193s Selecting previously unselected package r-cran-lattice. 193s Preparing to unpack .../183-r-cran-lattice_0.22-5-1_arm64.deb ... 193s Unpacking r-cran-lattice (0.22-5-1) ... 193s Selecting previously unselected package r-cran-nlme. 193s Preparing to unpack .../184-r-cran-nlme_3.1.164-1_arm64.deb ... 193s Unpacking r-cran-nlme (3.1.164-1) ... 193s Selecting previously unselected package r-cran-matrix. 193s Preparing to unpack .../185-r-cran-matrix_1.6-5-1_arm64.deb ... 193s Unpacking r-cran-matrix (1.6-5-1) ... 193s Selecting previously unselected package r-cran-mgcv. 193s Preparing to unpack .../186-r-cran-mgcv_1.9-1-1_arm64.deb ... 193s Unpacking r-cran-mgcv (1.9-1-1) ... 193s Selecting previously unselected package r-cran-farver. 193s Preparing to unpack .../187-r-cran-farver_2.1.1-1_arm64.deb ... 193s Unpacking r-cran-farver (2.1.1-1) ... 193s Selecting previously unselected package r-cran-labeling. 193s Preparing to unpack .../188-r-cran-labeling_0.4.3-1_all.deb ... 193s Unpacking r-cran-labeling (0.4.3-1) ... 193s Selecting previously unselected package r-cran-colorspace. 194s Preparing to unpack .../189-r-cran-colorspace_2.1-0+dfsg-1_arm64.deb ... 194s Unpacking r-cran-colorspace (2.1-0+dfsg-1) ... 194s Selecting previously unselected package r-cran-munsell. 194s Preparing to unpack .../190-r-cran-munsell_0.5.0-2build1_all.deb ... 194s Unpacking r-cran-munsell (0.5.0-2build1) ... 194s Selecting previously unselected package r-cran-r6. 194s Preparing to unpack .../191-r-cran-r6_2.5.1-1_all.deb ... 194s Unpacking r-cran-r6 (2.5.1-1) ... 194s Selecting previously unselected package r-cran-rcolorbrewer. 194s Preparing to unpack .../192-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ... 194s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ... 194s Selecting previously unselected package r-cran-viridislite. 194s Preparing to unpack .../193-r-cran-viridislite_0.4.2-2_all.deb ... 194s Unpacking r-cran-viridislite (0.4.2-2) ... 194s Selecting previously unselected package r-cran-scales. 194s Preparing to unpack .../194-r-cran-scales_1.3.0-1_all.deb ... 194s Unpacking r-cran-scales (1.3.0-1) ... 194s Selecting previously unselected package r-cran-fansi. 194s Preparing to unpack .../195-r-cran-fansi_1.0.5-1_arm64.deb ... 194s Unpacking r-cran-fansi (1.0.5-1) ... 194s Selecting previously unselected package r-cran-magrittr. 194s Preparing to unpack .../196-r-cran-magrittr_2.0.3-1_arm64.deb ... 194s Unpacking r-cran-magrittr (2.0.3-1) ... 194s Selecting previously unselected package r-cran-utf8. 194s Preparing to unpack .../197-r-cran-utf8_1.2.4-1_arm64.deb ... 194s Unpacking r-cran-utf8 (1.2.4-1) ... 194s Selecting previously unselected package r-cran-vctrs. 194s Preparing to unpack .../198-r-cran-vctrs_0.6.5-1_arm64.deb ... 194s Unpacking r-cran-vctrs (0.6.5-1) ... 194s Selecting previously unselected package r-cran-pillar. 194s Preparing to unpack .../199-r-cran-pillar_1.9.0+dfsg-1_all.deb ... 194s Unpacking r-cran-pillar (1.9.0+dfsg-1) ... 195s Selecting previously unselected package r-cran-pkgconfig. 195s Preparing to unpack .../200-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 195s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 195s Selecting previously unselected package r-cran-tibble. 195s Preparing to unpack .../201-r-cran-tibble_3.2.1+dfsg-2_arm64.deb ... 195s Unpacking r-cran-tibble (3.2.1+dfsg-2) ... 195s Selecting previously unselected package r-cran-withr. 195s Preparing to unpack .../202-r-cran-withr_2.5.0-1_all.deb ... 195s Unpacking r-cran-withr (2.5.0-1) ... 195s Selecting previously unselected package r-cran-ggplot2. 195s Preparing to unpack .../203-r-cran-ggplot2_3.4.4+dfsg-1_all.deb ... 195s Unpacking r-cran-ggplot2 (3.4.4+dfsg-1) ... 195s Selecting previously unselected package r-cran-inline. 195s Preparing to unpack .../204-r-cran-inline_0.3.19-2_all.deb ... 195s Unpacking r-cran-inline (0.3.19-2) ... 195s Selecting previously unselected package seqtk. 195s Preparing to unpack .../205-seqtk_1.4-2_arm64.deb ... 195s Unpacking seqtk (1.4-2) ... 195s Selecting previously unselected package python3-pysam. 195s Preparing to unpack .../206-python3-pysam_0.22.0+ds-1_arm64.deb ... 195s Unpacking python3-pysam (0.22.0+ds-1) ... 195s Selecting previously unselected package r-cran-pkgkitten. 195s Preparing to unpack .../207-r-cran-pkgkitten_0.2.3-1_all.deb ... 195s Unpacking r-cran-pkgkitten (0.2.3-1) ... 195s Selecting previously unselected package r-cran-rcpp. 195s Preparing to unpack .../208-r-cran-rcpp_1.0.12-1_arm64.deb ... 195s Unpacking r-cran-rcpp (1.0.12-1) ... 195s Selecting previously unselected package r-cran-rcppgsl. 195s Preparing to unpack .../209-r-cran-rcppgsl_0.3.13-1_arm64.deb ... 195s Unpacking r-cran-rcppgsl (0.3.13-1) ... 195s Selecting previously unselected package mapdamage. 195s Preparing to unpack .../210-mapdamage_2.2.1+dfsg-3_all.deb ... 195s Unpacking mapdamage (2.2.1+dfsg-3) ... 195s Selecting previously unselected package python3-humanfriendly. 196s Preparing to unpack .../211-python3-humanfriendly_10.0-3_all.deb ... 196s Unpacking python3-humanfriendly (10.0-3) ... 196s Selecting previously unselected package python3-coloredlogs. 196s Preparing to unpack .../212-python3-coloredlogs_15.0.1-1_all.deb ... 196s Unpacking python3-coloredlogs (15.0.1-1) ... 196s Selecting previously unselected package python3-configargparse. 196s Preparing to unpack .../213-python3-configargparse_1.7-1_all.deb ... 196s Unpacking python3-configargparse (1.7-1) ... 196s Selecting previously unselected package python3-ruamel.yaml.clib:arm64. 196s Preparing to unpack .../214-python3-ruamel.yaml.clib_0.2.8-1_arm64.deb ... 196s Unpacking python3-ruamel.yaml.clib:arm64 (0.2.8-1) ... 196s Selecting previously unselected package python3-ruamel.yaml. 196s Preparing to unpack .../215-python3-ruamel.yaml_0.17.21-1_all.deb ... 196s Unpacking python3-ruamel.yaml (0.17.21-1) ... 196s Selecting previously unselected package python3-setproctitle:arm64. 196s Preparing to unpack .../216-python3-setproctitle_1.3.3-1build1_arm64.deb ... 196s Unpacking python3-setproctitle:arm64 (1.3.3-1build1) ... 196s Selecting previously unselected package bowtie2. 196s Preparing to unpack .../217-bowtie2_2.5.2-1_arm64.deb ... 196s Unpacking bowtie2 (2.5.2-1) ... 196s Selecting previously unselected package phylip. 196s Preparing to unpack .../218-phylip_1%3a3.697+dfsg-3_arm64.deb ... 196s Unpacking phylip (1:3.697+dfsg-3) ... 196s Selecting previously unselected package picard-tools. 196s Preparing to unpack .../219-picard-tools_3.1.1+dfsg-1_all.deb ... 196s Unpacking picard-tools (3.1.1+dfsg-1) ... 196s Selecting previously unselected package radiant. 196s Preparing to unpack .../220-radiant_2.8.1+dfsg-2_all.deb ... 196s Unpacking radiant (2.8.1+dfsg-2) ... 196s Selecting previously unselected package raxml. 196s Preparing to unpack .../221-raxml_8.2.13+dfsg-1_arm64.deb ... 196s Unpacking raxml (8.2.13+dfsg-1) ... 196s Selecting previously unselected package samtools. 196s Preparing to unpack .../222-samtools_1.19.2-1_arm64.deb ... 196s Unpacking samtools (1.19.2-1) ... 196s Selecting previously unselected package paleomix. 196s Preparing to unpack .../223-paleomix_1.3.8-1_arm64.deb ... 196s Unpacking paleomix (1.3.8-1) ... 196s Selecting previously unselected package python3-iniconfig. 196s Preparing to unpack .../224-python3-iniconfig_1.1.1-2_all.deb ... 196s Unpacking python3-iniconfig (1.1.1-2) ... 196s Selecting previously unselected package python3-packaging. 196s Preparing to unpack .../225-python3-packaging_23.2-1_all.deb ... 196s Unpacking python3-packaging (23.2-1) ... 197s Selecting previously unselected package python3-pluggy. 197s Preparing to unpack .../226-python3-pluggy_1.4.0-1_all.deb ... 197s Unpacking python3-pluggy (1.4.0-1) ... 197s Selecting previously unselected package python3-pytest. 197s Preparing to unpack .../227-python3-pytest_7.4.4-1_all.deb ... 197s Unpacking python3-pytest (7.4.4-1) ... 197s Selecting previously unselected package autopkgtest-satdep. 197s Preparing to unpack .../228-1-autopkgtest-satdep.deb ... 197s Unpacking autopkgtest-satdep (0) ... 197s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 197s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 197s Setting up python3-configargparse (1.7-1) ... 197s Setting up libxcb-dri3-0:arm64 (1.15-1) ... 197s Setting up liblcms2-2:arm64 (2.14-2) ... 197s Setting up python3-iniconfig (1.1.1-2) ... 197s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 197s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 197s Setting up libpaper1:arm64 (1.1.29) ... 198s 198s Creating config file /etc/papersize with new version 198s Setting up libx11-xcb1:arm64 (2:1.8.7-1) ... 198s Setting up libpciaccess0:arm64 (0.17-3) ... 198s Setting up libslf4j-java (1.7.32-1) ... 198s Setting up adapterremoval (2.3.3-2) ... 198s Setting up libdrm-nouveau2:arm64 (2.4.120-2) ... 198s Setting up libxdamage1:arm64 (1:1.1.6-1) ... 198s Setting up libxcb-xfixes0:arm64 (1.15-1) ... 198s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 198s Setting up seqtk (1.4-2) ... 198s Setting up hicolor-icon-theme (0.17-2) ... 198s Setting up libxi6:arm64 (2:1.8.1-1) ... 198s Setting up libgatk-native-bindings-java (1.0.0+dfsg-2) ... 198s Setting up java-common (0.75+exp1) ... 198s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 198s Setting up libdatrie1:arm64 (0.2.13-3) ... 198s Setting up libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu1) ... 198s Setting up libtirpc3t64:arm64 (1.3.4+ds-1.1) ... 198s Setting up libxcb-render0:arm64 (1.15-1) ... 198s Setting up mafft (7.505-1) ... 198s Setting up libdrm-radeon1:arm64 (2.4.120-2) ... 198s Setting up bwa (0.7.17-7) ... 198s Setting up libglvnd0:arm64 (1.7.0-1) ... 198s Setting up libgoogle-gson-java (2.10.1-1) ... 198s Setting up radiant (2.8.1+dfsg-2) ... 198s Setting up libmjson-java (1.4.0-3) ... 198s Setting up libxcb-glx0:arm64 (1.15-1) ... 198s Setting up unzip (6.0-28ubuntu3) ... 198s Setting up libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ... 198s Setting up phylip (1:3.697+dfsg-3) ... 198s Setting up python3-ruamel.yaml.clib:arm64 (0.2.8-1) ... 198s Setting up x11-common (1:7.7+23ubuntu2) ... 199s Setting up libpsl5t64:arm64 (0.21.2-1.1) ... 199s Setting up libdeflate0:arm64 (1.19-1) ... 199s Setting up libgsl27:arm64 (2.7.1+dfsg-6ubuntu1) ... 199s Setting up libxcb-shm0:arm64 (1.15-1) ... 199s Setting up libpaper-utils (1.1.29) ... 199s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 199s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 199s Setting up libxxf86vm1:arm64 (1:1.1.4-1build3) ... 199s Setting up libsnappy1v5:arm64 (1.1.10-1) ... 199s Setting up bowtie2 (2.5.2-1) ... 199s Setting up libxnvctrl0:arm64 (510.47.03-0ubuntu1) ... 199s Setting up libxcb-present0:arm64 (1.15-1) ... 199s Setting up libasound2-data (1.2.10-3build1) ... 199s Setting up zip (3.0-13) ... 199s Setting up librhino-java (1.7.14-2.1) ... 199s Setting up libblas3:arm64 (3.12.0-3) ... 199s 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 199s Setting up python3-packaging (23.2-1) ... 199s Setting up libmunge2:arm64 (0.5.15-3ubuntu1) ... 199s Setting up python3-humanfriendly (10.0-3) ... 199s Setting up libmbedcrypto7:arm64 (2.28.7-1ubuntu1) ... 199s Setting up libxfixes3:arm64 (1:6.0.0-2) ... 199s Setting up libxcb-sync1:arm64 (1.15-1) ... 199s Setting up libapache-pom-java (29-2) ... 199s Setting up libavahi-common-data:arm64 (0.8-13ubuntu2) ... 199s Setting up libxinerama1:arm64 (2:1.1.4-3) ... 199s Setting up fonts-dejavu-mono (2.37-8) ... 199s Setting up libpng16-16t64:arm64 (1.6.43-3) ... 199s Setting up libhwloc15:arm64 (2.10.0-1) ... 199s Setting up libatomic1:arm64 (14-20240303-1ubuntu1) ... 199s Setting up python3-setproctitle:arm64 (1.3.3-1build1) ... 199s Setting up libxrandr2:arm64 (2:1.5.2-2) ... 199s Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ... 199s Setting up fonts-dejavu-core (2.37-8) ... 199s Setting up libpcsclite1:arm64 (2.0.0-1) ... 199s Setting up libmongodb-java (3.6.3-2) ... 199s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 199s Setting up libglapi-mesa:arm64 (24.0.1-1ubuntu1) ... 199s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 199s Setting up libvulkan1:arm64 (1.3.275.0-1) ... 199s Setting up python3-pluggy (1.4.0-1) ... 199s Setting up libwebp7:arm64 (1.3.2-0.4) ... 199s Setting up libreadline8t64:arm64 (8.2-3.1) ... 199s Setting up libxcb-dri2-0:arm64 (1.15-1) ... 199s Setting up python3-ruamel.yaml (0.17.21-1) ... 200s Setting up libgif7:arm64 (5.2.1-2.5) ... 200s Setting up libfreemarker-java (2.3.32-2) ... 200s Setting up ocl-icd-libopencl1:arm64 (2.3.2-1) ... 200s Setting up libxshmfence1:arm64 (1.3-1build4) ... 200s Setting up at-spi2-common (2.50.0-1) ... 200s Setting up libxcb-randr0:arm64 (1.15-1) ... 200s Setting up libasound2:arm64 (1.2.10-3build1) ... 200s Setting up openmpi-common (4.1.6-5ubuntu1) ... 200s Setting up librdmacm1t64:arm64 (50.0-2) ... 200s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 200s Setting up ncbi-vdb-data (3.0.2+dfsg-2) ... 200s Setting up libthai-data (0.1.29-2) ... 200s Setting up libcommons-math3-java (3.6.1-3) ... 200s Setting up libgtk2.0-common (2.24.33-2ubuntu2) ... 200s Setting up libatk1.0-0:arm64 (2.50.0-1) ... 200s Setting up libxss1:arm64 (1:1.2.3-1build2) ... 200s Setting up libhttpcore-java (4.4.16-1) ... 200s Setting up libjoptsimple-java (5.0.4-4) ... 200s Setting up ca-certificates-java (20240118) ... 200s No JRE found. Skipping Java certificates setup. 200s Setting up python3-coloredlogs (15.0.1-1) ... 200s Setting up libllvm17:arm64 (1:17.0.6-5build1) ... 200s Setting up libsnappy-jni (1.1.10.5-1) ... 200s Setting up libxcomposite1:arm64 (1:0.4.5-1build2) ... 200s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 200s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 200s Setting up bedtools (2.31.1+dfsg-2) ... 200s Setting up libevent-pthreads-2.1-7:arm64 (2.1.12-stable-9) ... 200s Setting up raxml (8.2.13+dfsg-1) ... 200s Setting up libdrm-amdgpu1:arm64 (2.4.120-2) ... 200s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 200s Setting up libfabric1:arm64 (1.17.0-3) ... 200s Setting up libice6:arm64 (2:1.0.10-1build2) ... 200s Setting up liblapack3:arm64 (3.12.0-3) ... 200s 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 200s Setting up libhts3:arm64 (1.18+ds-1) ... 200s Setting up libgsl-dev (2.7.1+dfsg-6ubuntu1) ... 200s Setting up libopenblas0-pthread:arm64 (0.3.26+ds-1) ... 200s 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 200s 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 200s 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 200s Setting up python3-pysam (0.22.0+ds-1) ... 200s Setting up libmbedx509-1:arm64 (2.28.7-1ubuntu1) ... 200s Setting up libmbedtls14:arm64 (2.28.7-1ubuntu1) ... 200s Setting up libcurl4t64:arm64 (8.5.0-2ubuntu7) ... 200s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 200s Setting up python3-pytest (7.4.4-1) ... 201s Setting up libxtst6:arm64 (2:1.2.3-1.1) ... 201s Setting up libxcursor1:arm64 (1:1.2.1-1) ... 201s Setting up libgl1-mesa-dri:arm64 (24.0.1-1ubuntu1) ... 201s Setting up bcftools (1.19-1) ... 201s Setting up libcommons-parent-java (56-1) ... 201s Setting up libavahi-common3:arm64 (0.8-13ubuntu2) ... 201s Setting up libncbi-vdb3:arm64 (3.0.2+dfsg-2) ... 201s Setting up libcommons-logging-java (1.3.0-1) ... 201s Setting up libhwloc-plugins:arm64 (2.10.0-1) ... 201s Setting up samtools (1.19.2-1) ... 201s Setting up libcommons-jexl2-java (2.1.1-6) ... 201s Setting up libthai0:arm64 (0.1.29-2) ... 201s Setting up libcommons-lang3-java (3.14.0-1) ... 201s Setting up libopenblas0:arm64 (0.3.26+ds-1) ... 201s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 201s Setting up libgdk-pixbuf-2.0-0:arm64 (2.42.10+dfsg-3) ... 201s Setting up libsnappy-java (1.1.10.5-1) ... 201s Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3) ... 201s Setting up curl (8.5.0-2ubuntu7) ... 201s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 201s Setting up libcommons-codec-java (1.16.0-1) ... 201s Setting up libsm6:arm64 (2:1.2.3-1build2) ... 201s Setting up libavahi-client3:arm64 (0.8-13ubuntu2) ... 201s Setting up libhsakmt1:arm64 (5.7.0-1) ... 201s Setting up libopenblas-pthread-dev:arm64 (0.3.26+ds-1) ... 201s 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 201s 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 201s 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 201s Setting up libncbi-ngs3:arm64 (3.0.3+dfsg-6ubuntu1) ... 201s Setting up gtk-update-icon-cache (3.24.40-2ubuntu1) ... 201s Setting up fontconfig (2.15.0-1ubuntu1) ... 203s Regenerating fonts cache... done. 203s Setting up libngs-jni:arm64 (3.0.3+dfsg-6ubuntu1) ... 203s Setting up libxft2:arm64 (2.3.6-1) ... 203s Setting up libglx-mesa0:arm64 (24.0.1-1ubuntu1) ... 203s Setting up libglx0:arm64 (1.7.0-1) ... 203s Setting up libcommons-compress-java (1.25.0-1) ... 203s Setting up libpmix2:arm64 (5.0.1-4) ... 203s Setting up libcommons-io-java (2.11.0-2) ... 203s Setting up libtk8.6:arm64 (8.6.13-2) ... 203s Setting up libpango-1.0-0:arm64 (1.51.0+ds-4) ... 203s Setting up libcairo2:arm64 (1.18.0-1) ... 203s Setting up libopenblas-dev:arm64 (0.3.26+ds-1) ... 203s Setting up libgl1:arm64 (1.7.0-1) ... 203s Setting up libxt6t64:arm64 (1:1.2.1-1.2) ... 203s Setting up libcups2:arm64 (2.4.6-0ubuntu3) ... 203s Setting up libhttpclient-java (4.5.14-1) ... 203s Setting up libhsa-runtime64-1 (5.7.1-1) ... 203s Setting up liblightcouch-java (0.2.0-1) ... 203s Setting up libngs-java:arm64 (3.0.3+dfsg-6ubuntu1) ... 203s Setting up libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 203s Setting up libhtsjdk-java (4.1.0+dfsg-1) ... 203s Setting up libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 203s Setting up openjdk-21-jre-headless:arm64 (21.0.2+13-2) ... 203s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode 203s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 203s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 203s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 203s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 203s Setting up liblog4j2-java (2.19.0-2) ... 203s Setting up libamdhip64-5 (5.2.3-12) ... 203s Setting up r-base-core (4.3.3-2build1) ... 203s 203s Creating config file /etc/R/Renviron with new version 204s Setting up r-cran-labeling (0.4.3-1) ... 204s Setting up r-cran-lattice (0.22-5-1) ... 204s Setting up r-cran-nlme (3.1.164-1) ... 204s Setting up r-cran-farver (2.1.1-1) ... 204s Setting up r-cran-viridislite (0.4.2-2) ... 204s Setting up r-cran-r6 (2.5.1-1) ... 204s Setting up r-cran-pkgkitten (0.2.3-1) ... 204s Setting up r-cran-magrittr (2.0.3-1) ... 204s Setting up libbarclay-java (5.0.0+dfsg-1) ... 204s Setting up r-cran-littler (0.3.19-1) ... 204s Setting up r-cran-rcpp (1.0.12-1) ... 204s Setting up r-cran-codetools (0.2-19-1) ... 204s Setting up r-cran-inline (0.3.19-2) ... 204s Setting up libucx0:arm64 (1.16.0+ds-4) ... 204s Setting up r-cran-rlang (1.1.3-1) ... 204s Setting up littler (0.3.19-1) ... 204s Setting up r-cran-withr (2.5.0-1) ... 204s Setting up libgkl-java (0.8.11+dfsg-2) ... 204s Setting up r-cran-iterators (1.0.14-1) ... 204s Setting up libopenmpi3:arm64 (4.1.6-5ubuntu1) ... 204s Setting up r-cran-foreach (1.5.2-1) ... 204s Setting up r-cran-fansi (1.0.5-1) ... 204s Setting up r-cran-mass (7.3-60.0.1-1) ... 204s Setting up r-cran-glue (1.7.0-1) ... 204s Setting up r-cran-gam (1.22-3-1) ... 204s Setting up r-cran-cli (3.6.2-1) ... 204s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... 204s Setting up r-cran-pkgconfig (2.0.3-2build1) ... 204s Setting up libpicard-java (3.1.1+dfsg-1) ... 204s Setting up r-cran-utf8 (1.2.4-1) ... 204s Setting up r-cran-colorspace (2.1-0+dfsg-1) ... 204s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ... 204s Setting up r-cran-isoband (0.2.7-1) ... 204s Setting up r-cran-gtable (0.3.4+dfsg-1) ... 204s Setting up r-cran-matrix (1.6-5-1) ... 204s Setting up r-cran-mgcv (1.9-1-1) ... 204s Setting up r-cran-rcppgsl (0.3.13-1) ... 204s Setting up r-cran-vctrs (0.6.5-1) ... 204s Setting up openmpi-bin (4.1.6-5ubuntu1) ... 204s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 204s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 204s Setting up r-cran-pillar (1.9.0+dfsg-1) ... 204s Setting up r-cran-munsell (0.5.0-2build1) ... 204s Setting up r-cran-tibble (3.2.1+dfsg-2) ... 204s Setting up examl (3.0.22-4) ... 204s Setting up r-cran-scales (1.3.0-1) ... 204s Setting up r-cran-ggplot2 (3.4.4+dfsg-1) ... 204s Setting up mapdamage (2.2.1+dfsg-3) ... 204s Setting up adwaita-icon-theme (46~rc-1) ... 204s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode 204s Setting up libgtk2.0-0:arm64 (2.24.33-2ubuntu2) ... 204s Setting up humanity-icon-theme (0.6.16) ... 204s Setting up ubuntu-mono (24.04-0ubuntu1) ... 204s Processing triggers for man-db (2.12.0-3) ... 205s Processing triggers for install-info (7.1-3) ... 205s Processing triggers for libc-bin (2.39-0ubuntu2) ... 205s Processing triggers for ca-certificates-java (20240118) ... 206s Adding debian:ACCVRAIZ1.pem 206s Adding debian:AC_RAIZ_FNMT-RCM.pem 206s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 206s Adding debian:ANF_Secure_Server_Root_CA.pem 206s Adding debian:Actalis_Authentication_Root_CA.pem 206s Adding debian:AffirmTrust_Commercial.pem 206s Adding debian:AffirmTrust_Networking.pem 206s Adding debian:AffirmTrust_Premium.pem 206s Adding debian:AffirmTrust_Premium_ECC.pem 206s Adding debian:Amazon_Root_CA_1.pem 206s Adding debian:Amazon_Root_CA_2.pem 206s Adding debian:Amazon_Root_CA_3.pem 206s Adding debian:Amazon_Root_CA_4.pem 206s Adding debian:Atos_TrustedRoot_2011.pem 206s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 206s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 206s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 206s Adding debian:BJCA_Global_Root_CA1.pem 206s Adding debian:BJCA_Global_Root_CA2.pem 206s Adding debian:Baltimore_CyberTrust_Root.pem 206s Adding debian:Buypass_Class_2_Root_CA.pem 206s Adding debian:Buypass_Class_3_Root_CA.pem 206s Adding debian:CA_Disig_Root_R2.pem 206s Adding debian:CFCA_EV_ROOT.pem 206s Adding debian:COMODO_Certification_Authority.pem 206s Adding debian:COMODO_ECC_Certification_Authority.pem 206s Adding debian:COMODO_RSA_Certification_Authority.pem 206s Adding debian:Certainly_Root_E1.pem 206s Adding debian:Certainly_Root_R1.pem 206s Adding debian:Certigna.pem 206s Adding debian:Certigna_Root_CA.pem 207s Adding debian:Certum_EC-384_CA.pem 207s Adding debian:Certum_Trusted_Network_CA.pem 207s Adding debian:Certum_Trusted_Network_CA_2.pem 207s Adding debian:Certum_Trusted_Root_CA.pem 207s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 207s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 207s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 207s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 207s Adding debian:Comodo_AAA_Services_root.pem 207s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 207s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 207s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 207s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 207s Adding debian:DigiCert_Assured_ID_Root_CA.pem 207s Adding debian:DigiCert_Assured_ID_Root_G2.pem 207s Adding debian:DigiCert_Assured_ID_Root_G3.pem 207s Adding debian:DigiCert_Global_Root_CA.pem 207s Adding debian:DigiCert_Global_Root_G2.pem 207s Adding debian:DigiCert_Global_Root_G3.pem 207s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 207s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 207s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 207s Adding debian:DigiCert_Trusted_Root_G4.pem 207s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 207s Adding debian:Entrust_Root_Certification_Authority.pem 207s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 207s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 207s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 207s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 207s Adding debian:GLOBALTRUST_2020.pem 207s Adding debian:GTS_Root_R1.pem 207s Adding debian:GTS_Root_R2.pem 207s Adding debian:GTS_Root_R3.pem 207s Adding debian:GTS_Root_R4.pem 207s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 207s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 207s Adding debian:GlobalSign_Root_CA.pem 207s Adding debian:GlobalSign_Root_CA_-_R3.pem 207s Adding debian:GlobalSign_Root_CA_-_R6.pem 207s Adding debian:GlobalSign_Root_E46.pem 207s Adding debian:GlobalSign_Root_R46.pem 207s Adding debian:Go_Daddy_Class_2_CA.pem 207s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 207s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 207s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 207s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 207s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 207s Adding debian:HiPKI_Root_CA_-_G1.pem 207s Adding debian:Hongkong_Post_Root_CA_3.pem 207s Adding debian:ISRG_Root_X1.pem 207s Adding debian:ISRG_Root_X2.pem 207s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 207s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 207s Adding debian:Izenpe.com.pem 207s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 207s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 207s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 207s Adding debian:NAVER_Global_Root_Certification_Authority.pem 207s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 207s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 207s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 207s Adding debian:QuoVadis_Root_CA_1_G3.pem 207s Adding debian:QuoVadis_Root_CA_2.pem 207s Adding debian:QuoVadis_Root_CA_2_G3.pem 207s Adding debian:QuoVadis_Root_CA_3.pem 207s Adding debian:QuoVadis_Root_CA_3_G3.pem 207s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 207s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 207s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 207s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 207s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 207s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 207s Adding debian:SZAFIR_ROOT_CA2.pem 207s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 207s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 207s Adding debian:SecureSign_RootCA11.pem 207s Adding debian:SecureTrust_CA.pem 207s Adding debian:Secure_Global_CA.pem 207s Adding debian:Security_Communication_ECC_RootCA1.pem 207s Adding debian:Security_Communication_RootCA2.pem 207s Adding debian:Security_Communication_RootCA3.pem 207s Adding debian:Security_Communication_Root_CA.pem 207s Adding debian:Starfield_Class_2_CA.pem 207s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 207s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 207s Adding debian:SwissSign_Gold_CA_-_G2.pem 207s Adding debian:SwissSign_Silver_CA_-_G2.pem 207s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 207s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 207s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 207s Adding debian:TWCA_Global_Root_CA.pem 207s Adding debian:TWCA_Root_Certification_Authority.pem 207s Adding debian:TeliaSonera_Root_CA_v1.pem 207s Adding debian:Telia_Root_CA_v2.pem 207s Adding debian:TrustAsia_Global_Root_CA_G3.pem 207s Adding debian:TrustAsia_Global_Root_CA_G4.pem 207s Adding debian:Trustwave_Global_Certification_Authority.pem 207s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 207s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 207s Adding debian:TunTrust_Root_CA.pem 207s Adding debian:UCA_Extended_Validation_Root.pem 207s Adding debian:UCA_Global_G2_Root.pem 207s Adding debian:USERTrust_ECC_Certification_Authority.pem 207s Adding debian:USERTrust_RSA_Certification_Authority.pem 207s Adding debian:XRamp_Global_CA_Root.pem 207s Adding debian:certSIGN_ROOT_CA.pem 207s Adding debian:certSIGN_Root_CA_G2.pem 207s Adding debian:e-Szigno_Root_CA_2017.pem 207s Adding debian:ePKI_Root_Certification_Authority.pem 207s Adding debian:emSign_ECC_Root_CA_-_C3.pem 207s Adding debian:emSign_ECC_Root_CA_-_G3.pem 207s Adding debian:emSign_Root_CA_-_C1.pem 207s Adding debian:emSign_Root_CA_-_G1.pem 207s Adding debian:vTrus_ECC_Root_CA.pem 207s Adding debian:vTrus_Root_CA.pem 207s done. 207s Setting up openjdk-21-jre:arm64 (21.0.2+13-2) ... 207s Setting up default-jre-headless (2:1.21-75+exp1) ... 207s Setting up default-jre (2:1.21-75+exp1) ... 207s Setting up picard-tools (3.1.1+dfsg-1) ... 207s Setting up paleomix (1.3.8-1) ... 207s Setting up autopkgtest-satdep (0) ... 223s (Reading database ... 97566 files and directories currently installed.) 223s Removing autopkgtest-satdep (0) ... 223s autopkgtest [17:21:46]: test run-unit-test: [----------------------- 226s ============================= test session starts ============================== 226s platform linux -- Python 3.12.2, pytest-7.4.4, pluggy-1.4.0 226s rootdir: /tmp/autopkgtest.HW16oD/autopkgtest_tmp 226s collected 1387 items 226s 226s tests/node_test.py ..................................................... [ 3%] 226s ....................................... [ 6%] 226s tests/nodegraph_test.py ......... [ 7%] 226s tests/atomiccmd_test/builder_test.py ................................... [ 9%] 226s ...................................................... [ 13%] 226s tests/atomiccmd_test/command_test.py ................................... [ 16%] 227s ........................................................................ [ 21%] 227s ................ [ 22%] 228s tests/atomiccmd_test/pprint_test.py .................................... [ 25%] 228s .. [ 25%] 228s tests/atomiccmd_test/sets_test.py ...................................... [ 28%] 228s ............ [ 28%] 228s tests/common_tests/bedtools_test.py ............................... [ 31%] 228s tests/common_tests/makefile_test.py .................................... [ 33%] 228s ........................................................................ [ 38%] 229s ........................................................................ [ 44%] 229s ........................................................................ [ 49%] 229s ........................................................................ [ 54%] 229s ............................... [ 56%] 229s tests/common_tests/sampling_test.py ........................ [ 58%] 229s tests/common_tests/sequences_test.py ................................... [ 60%] 229s ............... [ 62%] 229s tests/common_tests/text_test.py ....................................... [ 64%] 229s tests/common_tests/utilities_test.py ................................... [ 67%] 229s ........................................................................ [ 72%] 229s .. [ 72%] 229s tests/common_tests/versions_test.py .................................... [ 75%] 229s ............................................................ [ 79%] 229s tests/common_tests/formats_tests/fasta_test.py ......................... [ 81%] 229s ............. [ 82%] 229s tests/common_tests/formats_tests/fastq_test.py ......................... [ 84%] 229s ........... [ 85%] 229s tests/common_tests/formats_tests/msa_test.py ........................... [ 86%] 229s ................... [ 88%] 229s tests/common_tests/formats_tests/newick_test.py ........................ [ 90%] 229s ........................................................................ [ 95%] 229s ...... [ 95%] 229s tests/common_tests/formats_tests/phylip_test.py ........ [ 96%] 240s tests/tools_test/factory_test.py XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX [ 99%] 242s XXXXXXXXXXXXX [100%] 242s 242s =============================== warnings summary =============================== 242s ../../../usr/lib/python3/dist-packages/paleomix/atomiccmd/pprint.py:24 242s /usr/lib/python3/dist-packages/paleomix/atomiccmd/pprint.py:24: DeprecationWarning: 'pipes' is deprecated and slated for removal in Python 3.13 242s import pipes 242s 242s tests/tools_test/factory_test.py:64 242s /tmp/autopkgtest.HW16oD/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 242s @pytest.mark.slow 242s 242s tests/tools_test/factory_test.py:74 242s /tmp/autopkgtest.HW16oD/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 242s @pytest.mark.slow 242s 242s tests/tools_test/factory_test.py:88 242s /tmp/autopkgtest.HW16oD/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 242s @pytest.mark.slow 242s 242s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 242s ================ 1335 passed, 52 xpassed, 4 warnings in 17.39s ================= 243s autopkgtest [17:22:06]: test run-unit-test: -----------------------] 243s run-unit-test PASS 243s autopkgtest [17:22:06]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 244s autopkgtest [17:22:07]: @@@@@@@@@@@@@@@@@@@@ summary 244s run-unit-test PASS 255s Creating nova instance adt-noble-arm64-paleomix-20240316-171803-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)...