0s autopkgtest [21:32:30]: starting date and time: 2024-03-21 21:32:30+0000 0s autopkgtest [21:32:30]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [21:32:30]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.xs0pr_wp/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:openjdk-17,src:alsa-lib,src:at-spi2-core,src:cups,src:glib2.0,src:gnutls28,src:gtk+2.0,src:gtk+3.0,src:libpng1.6,src:nettle,src:wp2latex --apt-upgrade picard-tools --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=openjdk-17/17.0.11~7ea-1 alsa-lib/1.2.11-1build1 at-spi2-core/2.51.90-3 cups/2.4.7-1.2ubuntu1 glib2.0/2.79.3-3ubuntu5 gnutls28/3.8.3-1.1ubuntu2 gtk+2.0/2.24.33-3.1ubuntu3 gtk+3.0/3.24.41-1.1ubuntu3 libpng1.6/1.6.43-3 nettle/3.9.1-2.2 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-arm64-15.secgroup --name adt-noble-arm64-picard-tools-20240321-213230-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/ 73s autopkgtest [21:33:43]: testbed dpkg architecture: arm64 73s autopkgtest [21:33:43]: testbed apt version: 2.7.12 73s autopkgtest [21:33:43]: @@@@@@@@@@@@@@@@@@@@ test bed setup 74s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 74s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 74s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3795 kB] 74s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [53.9 kB] 74s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB] 74s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [677 kB] 74s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 74s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 74s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 74s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4179 kB] 74s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 74s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [67.4 kB] 74s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 77s Fetched 9434 kB in 2s (5435 kB/s) 77s Reading package lists... 79s Reading package lists... 80s Building dependency tree... 80s Reading state information... 80s Calculating upgrade... 80s The following packages will be REMOVED: 80s libglib2.0-0 80s The following NEW packages will be installed: 80s libglib2.0-0t64 xdg-user-dirs 80s The following packages will be upgraded: 80s gir1.2-glib-2.0 libglib2.0-data 81s 2 upgraded, 2 newly installed, 1 to remove and 0 not upgraded. 81s Need to get 1774 kB of archives. 81s After this operation, 138 kB of additional disk space will be used. 81s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB] 81s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB] 81s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 81s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB] 82s Fetched 1774 kB in 1s (2744 kB/s) 82s (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 ... 74820 files and directories currently installed.) 82s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_arm64.deb ... 82s Unpacking gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 82s dpkg: libglib2.0-0:arm64: dependency problems, but removing anyway as you requested: 82s udisks2 depends on libglib2.0-0 (>= 2.77.0). 82s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 82s python3-gi depends on libglib2.0-0 (>= 2.77.0). 82s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 82s netplan.io depends on libglib2.0-0 (>= 2.70.0). 82s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 82s libxmlb2:arm64 depends on libglib2.0-0 (>= 2.54.0). 82s libvolume-key1:arm64 depends on libglib2.0-0 (>= 2.18.0). 82s libudisks2-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 82s libqrtr-glib0:arm64 depends on libglib2.0-0 (>= 2.56). 82s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 82s libqmi-glib5:arm64 depends on libglib2.0-0 (>= 2.54.0). 82s libpolkit-gobject-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 82s libpolkit-agent-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 82s libnetplan0:arm64 depends on libglib2.0-0 (>= 2.75.3). 82s libmm-glib0:arm64 depends on libglib2.0-0 (>= 2.62.0). 82s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 82s libmbim-glib4:arm64 depends on libglib2.0-0 (>= 2.56). 82s libjson-glib-1.0-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 82s libjcat1:arm64 depends on libglib2.0-0 (>= 2.75.3). 82s libgusb2:arm64 depends on libglib2.0-0 (>= 2.75.3). 82s libgudev-1.0-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 82s libgirepository-1.0-1:arm64 depends on libglib2.0-0 (>= 2.79.0). 82s libfwupd2:arm64 depends on libglib2.0-0 (>= 2.79.0). 82s libblockdev3:arm64 depends on libglib2.0-0 (>= 2.42.2). 82s libblockdev-utils3:arm64 depends on libglib2.0-0 (>= 2.75.3). 82s libblockdev-swap3:arm64 depends on libglib2.0-0 (>= 2.42.2). 82s libblockdev-part3:arm64 depends on libglib2.0-0 (>= 2.42.2). 82s libblockdev-nvme3:arm64 depends on libglib2.0-0 (>= 2.42.2). 82s libblockdev-mdraid3:arm64 depends on libglib2.0-0 (>= 2.42.2). 82s libblockdev-loop3:arm64 depends on libglib2.0-0 (>= 2.42.2). 82s libblockdev-fs3:arm64 depends on libglib2.0-0 (>= 2.42.2). 82s libblockdev-crypto3:arm64 depends on libglib2.0-0 (>= 2.42.2). 82s fwupd depends on libglib2.0-0 (>= 2.79.0). 82s bolt depends on libglib2.0-0 (>= 2.56.0). 82s 82s (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 ... 74820 files and directories currently installed.) 82s Removing libglib2.0-0:arm64 (2.79.2-1~ubuntu1) ... 82s Selecting previously unselected package libglib2.0-0t64:arm64. 82s (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 ... 74795 files and directories currently installed.) 82s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_arm64.deb ... 82s 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... 82s removed '/var/lib/dpkg/info/libglib2.0-0:arm64.postrm' 82s Unpacking libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 82s Preparing to unpack .../libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 82s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 82s Selecting previously unselected package xdg-user-dirs. 82s Preparing to unpack .../xdg-user-dirs_0.18-1_arm64.deb ... 82s Unpacking xdg-user-dirs (0.18-1) ... 82s Setting up xdg-user-dirs (0.18-1) ... 82s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 82s No schema files found: doing nothing. 82s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 82s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ... 82s Processing triggers for man-db (2.12.0-3) ... 83s Processing triggers for libc-bin (2.39-0ubuntu2) ... 83s Reading package lists... 84s Building dependency tree... 84s Reading state information... 84s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 85s sh: Attempting to set up Debian/Ubuntu apt sources automatically 85s sh: Distribution appears to be Ubuntu 85s Reading package lists... 86s Building dependency tree... 86s Reading state information... 86s eatmydata is already the newest version (131-1). 86s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 86s Reading package lists... 86s Building dependency tree... 86s Reading state information... 87s dbus is already the newest version (1.14.10-4ubuntu1). 87s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 87s Reading package lists... 87s Building dependency tree... 87s Reading state information... 88s rng-tools-debian is already the newest version (2.4). 88s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 88s Reading package lists... 88s Building dependency tree... 88s Reading state information... 88s The following packages will be REMOVED: 88s cloud-init* python3-configobj* python3-debconf* 89s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 89s After this operation, 3252 kB disk space will be freed. 89s (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 ... 74834 files and directories currently installed.) 89s Removing cloud-init (24.1.1-0ubuntu1) ... 89s Removing python3-configobj (5.0.8-3) ... 89s Removing python3-debconf (1.5.86) ... 89s Processing triggers for man-db (2.12.0-3) ... 90s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74445 files and directories currently installed.) 90s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 90s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 90s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 91s invoke-rc.d: policy-rc.d denied execution of try-restart. 91s Reading package lists... 91s Building dependency tree... 91s Reading state information... 91s linux-generic is already the newest version (6.8.0-11.11+1). 91s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 92s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 92s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 92s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 93s Reading package lists... 94s Reading package lists... 94s Building dependency tree... 94s Reading state information... 94s Calculating upgrade... 94s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 94s Reading package lists... 96s Building dependency tree... 96s Reading state information...autopkgtest [21:34:05]: rebooting testbed after setup commands that affected boot 96s 96s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 122s autopkgtest [21:34:32]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 125s autopkgtest [21:34:35]: @@@@@@@@@@@@@@@@@@@@ apt-source picard-tools 130s Get:1 http://ftpmaster.internal/ubuntu noble/universe picard-tools 3.1.1+dfsg-1 (dsc) [2737 B] 130s Get:2 http://ftpmaster.internal/ubuntu noble/universe picard-tools 3.1.1+dfsg-1 (tar) [20.4 MB] 130s Get:3 http://ftpmaster.internal/ubuntu noble/universe picard-tools 3.1.1+dfsg-1 (diff) [22.8 kB] 130s gpgv: Signature made Sat Dec 16 21:39:31 2023 UTC 130s gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 130s gpgv: Can't check signature: No public key 130s dpkg-source: warning: cannot verify inline signature for ./picard-tools_3.1.1+dfsg-1.dsc: no acceptable signature found 132s autopkgtest [21:34:42]: testing package picard-tools version 3.1.1+dfsg-1 133s autopkgtest [21:34:43]: build not needed 139s autopkgtest [21:34:49]: test run-unit-test: preparing testbed 148s Reading package lists... 148s Building dependency tree... 148s Reading state information... 149s Starting pkgProblemResolver with broken count: 0 149s Starting 2 pkgProblemResolver with broken count: 0 149s Done 149s The following additional packages will be installed: 149s adwaita-icon-theme at-spi2-common ca-certificates-java default-jre 149s default-jre-headless fontconfig fontconfig-config fonts-dejavu-core 149s fonts-dejavu-mono gtk-update-icon-cache hicolor-icon-theme 149s humanity-icon-theme java-common libapache-pom-java libasound2 149s libasound2-data libatk1.0-0 libavahi-client3 libavahi-common-data 149s libavahi-common3 libbarclay-java libcairo2 libcommons-codec-java 149s libcommons-compress-java libcommons-io-java libcommons-jexl2-java 149s libcommons-lang3-java libcommons-logging-java libcommons-math3-java 149s libcommons-parent-java libcups2 libdatrie1 libdeflate0 libdrm-amdgpu1 149s libdrm-nouveau2 libdrm-radeon1 libfontconfig1 libfreemarker-java 149s libgatk-native-bindings-java libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common 149s libgif7 libgkl-java libgl1 libgl1-mesa-dri libglapi-mesa libglvnd0 149s libglx-mesa0 libglx0 libgoogle-gson-java libgraphite2-3 libgtk2.0-0 149s libgtk2.0-common libharfbuzz0b libhtsjdk-java libhttpclient-java 149s libhttpcore-java libjbig0 libjoptsimple-java libjpeg-turbo8 libjpeg8 149s liblcms2-2 liblerc4 liblightcouch-java libllvm17 liblog4j2-java 149s libmbedcrypto7 libmbedtls14 libmbedx509-1 libmjson-java libmongodb-java 149s libncbi-ngs3 libncbi-vdb3 libngs-java libngs-jni libpango-1.0-0 149s libpangocairo-1.0-0 libpangoft2-1.0-0 libpcsclite1 libpicard-java 149s libpixman-1-0 librhino-java libsharpyuv0 libslf4j-java libsnappy-java 149s libsnappy-jni libsnappy1v5 libthai-data libthai0 libtiff6 libvulkan1 149s libwebp7 libx11-xcb1 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 149s libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 149s libxcomposite1 libxcursor1 libxdamage1 libxfixes3 libxi6 libxinerama1 149s libxrandr2 libxrender1 libxshmfence1 libxtst6 libxxf86vm1 ncbi-vdb-data 149s openjdk-21-jre openjdk-21-jre-headless picard-tools ubuntu-mono x11-common 149s Suggested packages: 149s libasound2-plugins alsa-utils libasm-java libxz-java libcommons-io-java-doc 149s libavalon-framework-java libexcalibur-logkit-java liblog4j1.2-java 149s cups-common jython libdom4j-java libjaxen-java libjdom1-java libxalan2-java 149s libgoogle-gson-java-doc gvfs libjoptsimple-java-doc liblcms2-utils 149s libactivation-java libcommons-csv-java libconversant-disruptor-java 149s libdisruptor-java libgeronimo-jms-1.1-spec-java 149s libjackson2-dataformat-xml-java libjackson2-dataformat-yaml libjansi-java 149s libjctools-java libjeromq-java libmail-java libwoodstox-java libngs-java-doc 149s pcscd rhino libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic 149s fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic 149s Recommended packages: 149s librsvg2-common alsa-ucm-conf alsa-topology-conf libgdk-pixbuf2.0-bin 149s libgkl-jni libgl1-amber-dri libgail-common libgtk2.0-bin r-base-core 149s mesa-vulkan-drivers | vulkan-icd libatk-wrapper-java-jni fonts-dejavu-extra 149s The following NEW packages will be installed: 149s adwaita-icon-theme at-spi2-common autopkgtest-satdep ca-certificates-java 149s default-jre default-jre-headless fontconfig fontconfig-config 149s fonts-dejavu-core fonts-dejavu-mono gtk-update-icon-cache hicolor-icon-theme 149s humanity-icon-theme java-common libapache-pom-java libasound2 149s libasound2-data libatk1.0-0 libavahi-client3 libavahi-common-data 149s libavahi-common3 libbarclay-java libcairo2 libcommons-codec-java 149s libcommons-compress-java libcommons-io-java libcommons-jexl2-java 149s libcommons-lang3-java libcommons-logging-java libcommons-math3-java 149s libcommons-parent-java libcups2 libdatrie1 libdeflate0 libdrm-amdgpu1 149s libdrm-nouveau2 libdrm-radeon1 libfontconfig1 libfreemarker-java 149s libgatk-native-bindings-java libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common 149s libgif7 libgkl-java libgl1 libgl1-mesa-dri libglapi-mesa libglvnd0 149s libglx-mesa0 libglx0 libgoogle-gson-java libgraphite2-3 libgtk2.0-0 149s libgtk2.0-common libharfbuzz0b libhtsjdk-java libhttpclient-java 149s libhttpcore-java libjbig0 libjoptsimple-java libjpeg-turbo8 libjpeg8 149s liblcms2-2 liblerc4 liblightcouch-java libllvm17 liblog4j2-java 149s libmbedcrypto7 libmbedtls14 libmbedx509-1 libmjson-java libmongodb-java 149s libncbi-ngs3 libncbi-vdb3 libngs-java libngs-jni libpango-1.0-0 149s libpangocairo-1.0-0 libpangoft2-1.0-0 libpcsclite1 libpicard-java 149s libpixman-1-0 librhino-java libsharpyuv0 libslf4j-java libsnappy-java 149s libsnappy-jni libsnappy1v5 libthai-data libthai0 libtiff6 libvulkan1 149s libwebp7 libx11-xcb1 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 149s libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 149s libxcomposite1 libxcursor1 libxdamage1 libxfixes3 libxi6 libxinerama1 150s libxrandr2 libxrender1 libxshmfence1 libxtst6 libxxf86vm1 ncbi-vdb-data 150s openjdk-21-jre openjdk-21-jre-headless picard-tools ubuntu-mono x11-common 150s 0 upgraded, 120 newly installed, 0 to remove and 0 not upgraded. 150s Need to get 110 MB/110 MB of archives. 150s After this operation, 453 MB of additional disk space will be used. 150s Get:1 /tmp/autopkgtest.u2Kjdy/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [708 B] 150s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-3 [7624 B] 150s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 150s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 150s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 150s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 150s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 150s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 150s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 150s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 150s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.10+dfsg-3 [144 kB] 150s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 gtk-update-icon-cache arm64 3.24.40-2ubuntu1 [50.5 kB] 150s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 hicolor-icon-theme all 0.17-2 [9976 B] 150s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 humanity-icon-theme all 0.6.16 [1282 kB] 150s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-mono all 24.04-0ubuntu1 [151 kB] 150s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 adwaita-icon-theme all 46~rc-1 [723 kB] 150s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 at-spi2-common all 2.50.0-1 [7864 B] 150s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 ca-certificates-java all 20240118 [11.6 kB] 150s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 java-common all 0.75+exp1 [6798 B] 150s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-common-data arm64 0.8-13ubuntu2 [29.5 kB] 150s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-common3 arm64 0.8-13ubuntu2 [23.2 kB] 150s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-client3 arm64 0.8-13ubuntu2 [27.3 kB] 150s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libcups2 arm64 2.4.6-0ubuntu3 [270 kB] 150s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] 150s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 150s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 150s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 150s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 150s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libasound2-data all 1.2.10-3build1 [20.7 kB] 150s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libasound2 arm64 1.2.10-3build1 [386 kB] 150s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 150s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 150s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libpcsclite1 arm64 2.0.0-1 [21.2 kB] 150s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 openjdk-21-jre-headless arm64 21.0.2+13-2 [45.8 MB] 152s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 default-jre-headless arm64 2:1.21-75+exp1 [3096 B] 152s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libgtk2.0-common all 2.24.33-2ubuntu2 [125 kB] 152s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libatk1.0-0 arm64 2.50.0-1 [53.8 kB] 152s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 152s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 152s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 152s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 152s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 152s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 152s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 152s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 152s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 152s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 152s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 152s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 152s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libxcomposite1 arm64 1:0.4.5-1build2 [7080 B] 152s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libxfixes3 arm64 1:6.0.0-2 [11.0 kB] 152s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 libxcursor1 arm64 1:1.2.1-1 [21.3 kB] 152s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 libxdamage1 arm64 1:1.1.6-1 [6032 B] 152s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libxi6 arm64 2:1.8.1-1 [31.9 kB] 152s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 libxinerama1 arm64 2:1.1.4-3 [7056 B] 152s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 libxrandr2 arm64 2:1.5.2-2 [19.6 kB] 152s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 libgtk2.0-0 arm64 2.24.33-2ubuntu2 [1981 kB] 152s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libglvnd0 arm64 1.7.0-1 [60.0 kB] 152s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libglapi-mesa arm64 24.0.1-1ubuntu1 [57.8 kB] 152s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 libx11-xcb1 arm64 2:1.8.7-1 [7836 B] 152s Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-dri2-0 arm64 1.15-1 [7244 B] 152s Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-dri3-0 arm64 1.15-1 [7108 B] 152s Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-glx0 arm64 1.15-1 [25.2 kB] 152s Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-present0 arm64 1.15-1 [5732 B] 152s Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-randr0 arm64 1.15-1 [18.2 kB] 152s Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-sync1 arm64 1.15-1 [9412 B] 152s Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-xfixes0 arm64 1.15-1 [10.3 kB] 152s Get:68 http://ftpmaster.internal/ubuntu noble/main arm64 libxshmfence1 arm64 1.3-1build4 [5444 B] 152s Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 libxxf86vm1 arm64 1:1.1.4-1build3 [10.3 kB] 152s Get:70 http://ftpmaster.internal/ubuntu noble/main arm64 libvulkan1 arm64 1.3.275.0-1 [150 kB] 152s Get:71 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-amdgpu1 arm64 2.4.120-2 [20.4 kB] 152s Get:72 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-nouveau2 arm64 2.4.120-2 [17.8 kB] 152s Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-radeon1 arm64 2.4.120-2 [20.9 kB] 152s Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 libllvm17 arm64 1:17.0.6-5build1 [25.0 MB] 153s Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 libgl1-mesa-dri arm64 24.0.1-1ubuntu1 [8226 kB] 153s Get:76 http://ftpmaster.internal/ubuntu noble/main arm64 libglx-mesa0 arm64 24.0.1-1ubuntu1 [166 kB] 153s Get:77 http://ftpmaster.internal/ubuntu noble/main arm64 libglx0 arm64 1.7.0-1 [32.4 kB] 153s Get:78 http://ftpmaster.internal/ubuntu noble/main arm64 libgl1 arm64 1.7.0-1 [107 kB] 153s Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 libgif7 arm64 5.2.1-2.5 [34.2 kB] 153s Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 153s Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 libxtst6 arm64 2:1.2.3-1.1 [13.7 kB] 153s Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 openjdk-21-jre arm64 21.0.2+13-2 [226 kB] 153s Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 default-jre arm64 2:1.21-75+exp1 [922 B] 153s Get:84 http://ftpmaster.internal/ubuntu noble/universe arm64 libapache-pom-java all 29-2 [5284 B] 153s Get:85 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-parent-java all 56-1 [10.7 kB] 153s Get:86 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-lang3-java all 3.14.0-1 [586 kB] 153s Get:87 http://ftpmaster.internal/ubuntu noble/universe arm64 libfreemarker-java all 2.3.32-2 [1542 kB] 153s Get:88 http://ftpmaster.internal/ubuntu noble/universe arm64 libgoogle-gson-java all 2.10.1-1 [252 kB] 153s Get:89 http://ftpmaster.internal/ubuntu noble/universe arm64 libjoptsimple-java all 5.0.4-4 [73.1 kB] 153s Get:90 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-codec-java all 1.16.0-1 [306 kB] 153s Get:91 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 153s Get:92 http://ftpmaster.internal/ubuntu noble/universe arm64 libhttpcore-java all 4.4.16-1 [612 kB] 153s Get:93 http://ftpmaster.internal/ubuntu noble/universe arm64 libhttpclient-java all 4.5.14-1 [1241 kB] 153s Get:94 http://ftpmaster.internal/ubuntu noble/universe arm64 liblightcouch-java all 0.2.0-1 [74.2 kB] 153s Get:95 http://ftpmaster.internal/ubuntu noble/universe arm64 libmongodb-java all 3.6.3-2 [1899 kB] 153s Get:96 http://ftpmaster.internal/ubuntu noble/universe arm64 libslf4j-java all 1.7.32-1 [141 kB] 153s Get:97 http://ftpmaster.internal/ubuntu noble/universe arm64 liblog4j2-java all 2.19.0-2 [2294 kB] 153s Get:98 http://ftpmaster.internal/ubuntu noble/universe arm64 libbarclay-java all 5.0.0+dfsg-1 [108 kB] 153s Get:99 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-compress-java all 1.25.0-1 [612 kB] 153s Get:100 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-io-java all 2.11.0-2 [297 kB] 153s Get:101 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-jexl2-java all 2.1.1-6 [250 kB] 153s Get:102 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-math3-java all 3.6.1-3 [2016 kB] 153s Get:103 http://ftpmaster.internal/ubuntu noble/universe arm64 libgatk-native-bindings-java all 1.0.0+dfsg-2 [8014 B] 153s Get:104 http://ftpmaster.internal/ubuntu noble/universe arm64 libmjson-java all 1.4.0-3 [60.4 kB] 154s Get:105 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedcrypto7 arm64 2.28.7-1ubuntu1 [206 kB] 154s Get:106 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedx509-1 arm64 2.28.7-1ubuntu1 [46.8 kB] 154s Get:107 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedtls14 arm64 2.28.7-1ubuntu1 [82.0 kB] 154s Get:108 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-vdb-data all 3.0.2+dfsg-2 [65.8 kB] 154s Get:109 http://ftpmaster.internal/ubuntu noble/universe arm64 libncbi-vdb3 arm64 3.0.2+dfsg-2 [1130 kB] 154s Get:110 http://ftpmaster.internal/ubuntu noble/universe arm64 libncbi-ngs3 arm64 3.0.3+dfsg-6ubuntu1 [146 kB] 154s Get:111 http://ftpmaster.internal/ubuntu noble/universe arm64 libngs-jni arm64 3.0.3+dfsg-6ubuntu1 [4832 B] 154s Get:112 http://ftpmaster.internal/ubuntu noble/universe arm64 libngs-java arm64 3.0.3+dfsg-6ubuntu1 [91.8 kB] 154s Get:113 http://ftpmaster.internal/ubuntu noble/universe arm64 librhino-java all 1.7.14-2.1 [1330 kB] 154s Get:114 http://ftpmaster.internal/ubuntu noble/main arm64 libsnappy1v5 arm64 1.1.10-1 [28.2 kB] 154s Get:115 http://ftpmaster.internal/ubuntu noble/universe arm64 libsnappy-jni arm64 1.1.10.5-1 [6542 B] 154s Get:116 http://ftpmaster.internal/ubuntu noble/universe arm64 libsnappy-java all 1.1.10.5-1 [83.6 kB] 154s Get:117 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtsjdk-java all 4.1.0+dfsg-1 [1821 kB] 154s Get:118 http://ftpmaster.internal/ubuntu noble/universe arm64 libgkl-java all 0.8.11+dfsg-2 [24.8 kB] 154s Get:119 http://ftpmaster.internal/ubuntu noble/universe arm64 libpicard-java all 3.1.1+dfsg-1 [1731 kB] 154s Get:120 http://ftpmaster.internal/ubuntu noble/universe arm64 picard-tools all 3.1.1+dfsg-1 [308 kB] 155s Fetched 110 MB in 5s (22.5 MB/s) 155s Selecting previously unselected package libgdk-pixbuf2.0-common. 156s (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 ... 74390 files and directories currently installed.) 156s Preparing to unpack .../000-libgdk-pixbuf2.0-common_2.42.10+dfsg-3_all.deb ... 156s Unpacking libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ... 156s Selecting previously unselected package libjpeg-turbo8:arm64. 156s Preparing to unpack .../001-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 156s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 156s Selecting previously unselected package libjpeg8:arm64. 156s Preparing to unpack .../002-libjpeg8_8c-2ubuntu11_arm64.deb ... 156s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 156s Selecting previously unselected package libdeflate0:arm64. 156s Preparing to unpack .../003-libdeflate0_1.19-1_arm64.deb ... 156s Unpacking libdeflate0:arm64 (1.19-1) ... 156s Selecting previously unselected package libjbig0:arm64. 156s Preparing to unpack .../004-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 156s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 156s Selecting previously unselected package liblerc4:arm64. 156s Preparing to unpack .../005-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 156s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 156s Selecting previously unselected package libsharpyuv0:arm64. 156s Preparing to unpack .../006-libsharpyuv0_1.3.2-0.4_arm64.deb ... 156s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 156s Selecting previously unselected package libwebp7:arm64. 156s Preparing to unpack .../007-libwebp7_1.3.2-0.4_arm64.deb ... 156s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 156s Selecting previously unselected package libtiff6:arm64. 156s Preparing to unpack .../008-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 156s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 156s Selecting previously unselected package libgdk-pixbuf-2.0-0:arm64. 156s Preparing to unpack .../009-libgdk-pixbuf-2.0-0_2.42.10+dfsg-3_arm64.deb ... 156s Unpacking libgdk-pixbuf-2.0-0:arm64 (2.42.10+dfsg-3) ... 156s Selecting previously unselected package gtk-update-icon-cache. 156s Preparing to unpack .../010-gtk-update-icon-cache_3.24.40-2ubuntu1_arm64.deb ... 156s Unpacking gtk-update-icon-cache (3.24.40-2ubuntu1) ... 156s Selecting previously unselected package hicolor-icon-theme. 156s Preparing to unpack .../011-hicolor-icon-theme_0.17-2_all.deb ... 156s Unpacking hicolor-icon-theme (0.17-2) ... 156s Selecting previously unselected package humanity-icon-theme. 156s Preparing to unpack .../012-humanity-icon-theme_0.6.16_all.deb ... 156s Unpacking humanity-icon-theme (0.6.16) ... 157s Selecting previously unselected package ubuntu-mono. 157s Preparing to unpack .../013-ubuntu-mono_24.04-0ubuntu1_all.deb ... 157s Unpacking ubuntu-mono (24.04-0ubuntu1) ... 157s Selecting previously unselected package adwaita-icon-theme. 157s Preparing to unpack .../014-adwaita-icon-theme_46~rc-1_all.deb ... 157s Unpacking adwaita-icon-theme (46~rc-1) ... 157s Selecting previously unselected package at-spi2-common. 157s Preparing to unpack .../015-at-spi2-common_2.50.0-1_all.deb ... 157s Unpacking at-spi2-common (2.50.0-1) ... 157s Selecting previously unselected package ca-certificates-java. 157s Preparing to unpack .../016-ca-certificates-java_20240118_all.deb ... 157s Unpacking ca-certificates-java (20240118) ... 157s Selecting previously unselected package java-common. 157s Preparing to unpack .../017-java-common_0.75+exp1_all.deb ... 157s Unpacking java-common (0.75+exp1) ... 157s Selecting previously unselected package libavahi-common-data:arm64. 158s Preparing to unpack .../018-libavahi-common-data_0.8-13ubuntu2_arm64.deb ... 158s Unpacking libavahi-common-data:arm64 (0.8-13ubuntu2) ... 158s Selecting previously unselected package libavahi-common3:arm64. 158s Preparing to unpack .../019-libavahi-common3_0.8-13ubuntu2_arm64.deb ... 158s Unpacking libavahi-common3:arm64 (0.8-13ubuntu2) ... 158s Selecting previously unselected package libavahi-client3:arm64. 158s Preparing to unpack .../020-libavahi-client3_0.8-13ubuntu2_arm64.deb ... 158s Unpacking libavahi-client3:arm64 (0.8-13ubuntu2) ... 158s Selecting previously unselected package libcups2:arm64. 158s Preparing to unpack .../021-libcups2_2.4.6-0ubuntu3_arm64.deb ... 158s Unpacking libcups2:arm64 (2.4.6-0ubuntu3) ... 158s Selecting previously unselected package liblcms2-2:arm64. 158s Preparing to unpack .../022-liblcms2-2_2.14-2_arm64.deb ... 158s Unpacking liblcms2-2:arm64 (2.14-2) ... 158s Selecting previously unselected package fonts-dejavu-mono. 158s Preparing to unpack .../023-fonts-dejavu-mono_2.37-8_all.deb ... 158s Unpacking fonts-dejavu-mono (2.37-8) ... 158s Selecting previously unselected package fonts-dejavu-core. 158s Preparing to unpack .../024-fonts-dejavu-core_2.37-8_all.deb ... 158s Unpacking fonts-dejavu-core (2.37-8) ... 158s Selecting previously unselected package fontconfig-config. 158s Preparing to unpack .../025-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 158s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 158s Selecting previously unselected package libfontconfig1:arm64. 158s Preparing to unpack .../026-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 158s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 158s Selecting previously unselected package libasound2-data. 158s Preparing to unpack .../027-libasound2-data_1.2.10-3build1_all.deb ... 158s Unpacking libasound2-data (1.2.10-3build1) ... 158s Selecting previously unselected package libasound2:arm64. 158s Preparing to unpack .../028-libasound2_1.2.10-3build1_arm64.deb ... 158s Unpacking libasound2:arm64 (1.2.10-3build1) ... 158s Selecting previously unselected package libgraphite2-3:arm64. 158s Preparing to unpack .../029-libgraphite2-3_1.3.14-2_arm64.deb ... 158s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 158s Selecting previously unselected package libharfbuzz0b:arm64. 158s Preparing to unpack .../030-libharfbuzz0b_8.3.0-2_arm64.deb ... 158s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 158s Selecting previously unselected package libpcsclite1:arm64. 158s Preparing to unpack .../031-libpcsclite1_2.0.0-1_arm64.deb ... 158s Unpacking libpcsclite1:arm64 (2.0.0-1) ... 158s Selecting previously unselected package openjdk-21-jre-headless:arm64. 158s Preparing to unpack .../032-openjdk-21-jre-headless_21.0.2+13-2_arm64.deb ... 158s Unpacking openjdk-21-jre-headless:arm64 (21.0.2+13-2) ... 159s Selecting previously unselected package default-jre-headless. 159s Preparing to unpack .../033-default-jre-headless_2%3a1.21-75+exp1_arm64.deb ... 159s Unpacking default-jre-headless (2:1.21-75+exp1) ... 159s Selecting previously unselected package libgtk2.0-common. 159s Preparing to unpack .../034-libgtk2.0-common_2.24.33-2ubuntu2_all.deb ... 159s Unpacking libgtk2.0-common (2.24.33-2ubuntu2) ... 159s Selecting previously unselected package libatk1.0-0:arm64. 159s Preparing to unpack .../035-libatk1.0-0_2.50.0-1_arm64.deb ... 159s Unpacking libatk1.0-0:arm64 (2.50.0-1) ... 159s Selecting previously unselected package libpixman-1-0:arm64. 160s Preparing to unpack .../036-libpixman-1-0_0.42.2-1_arm64.deb ... 160s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 160s Selecting previously unselected package libxcb-render0:arm64. 160s Preparing to unpack .../037-libxcb-render0_1.15-1_arm64.deb ... 160s Unpacking libxcb-render0:arm64 (1.15-1) ... 160s Selecting previously unselected package libxcb-shm0:arm64. 160s Preparing to unpack .../038-libxcb-shm0_1.15-1_arm64.deb ... 160s Unpacking libxcb-shm0:arm64 (1.15-1) ... 160s Selecting previously unselected package libxrender1:arm64. 160s Preparing to unpack .../039-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 160s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 160s Selecting previously unselected package libcairo2:arm64. 160s Preparing to unpack .../040-libcairo2_1.18.0-1_arm64.deb ... 160s Unpacking libcairo2:arm64 (1.18.0-1) ... 160s Selecting previously unselected package fontconfig. 160s Preparing to unpack .../041-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 160s Unpacking fontconfig (2.15.0-1ubuntu1) ... 160s Selecting previously unselected package libthai-data. 160s Preparing to unpack .../042-libthai-data_0.1.29-2_all.deb ... 160s Unpacking libthai-data (0.1.29-2) ... 160s Selecting previously unselected package libdatrie1:arm64. 160s Preparing to unpack .../043-libdatrie1_0.2.13-3_arm64.deb ... 160s Unpacking libdatrie1:arm64 (0.2.13-3) ... 160s Selecting previously unselected package libthai0:arm64. 160s Preparing to unpack .../044-libthai0_0.1.29-2_arm64.deb ... 160s Unpacking libthai0:arm64 (0.1.29-2) ... 160s Selecting previously unselected package libpango-1.0-0:arm64. 160s Preparing to unpack .../045-libpango-1.0-0_1.51.0+ds-4_arm64.deb ... 160s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ... 160s Selecting previously unselected package libpangoft2-1.0-0:arm64. 160s Preparing to unpack .../046-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 160s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 160s Selecting previously unselected package libpangocairo-1.0-0:arm64. 160s Preparing to unpack .../047-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ... 160s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 160s Selecting previously unselected package libxcomposite1:arm64. 160s Preparing to unpack .../048-libxcomposite1_1%3a0.4.5-1build2_arm64.deb ... 160s Unpacking libxcomposite1:arm64 (1:0.4.5-1build2) ... 160s Selecting previously unselected package libxfixes3:arm64. 160s Preparing to unpack .../049-libxfixes3_1%3a6.0.0-2_arm64.deb ... 160s Unpacking libxfixes3:arm64 (1:6.0.0-2) ... 160s Selecting previously unselected package libxcursor1:arm64. 160s Preparing to unpack .../050-libxcursor1_1%3a1.2.1-1_arm64.deb ... 160s Unpacking libxcursor1:arm64 (1:1.2.1-1) ... 160s Selecting previously unselected package libxdamage1:arm64. 160s Preparing to unpack .../051-libxdamage1_1%3a1.1.6-1_arm64.deb ... 160s Unpacking libxdamage1:arm64 (1:1.1.6-1) ... 160s Selecting previously unselected package libxi6:arm64. 160s Preparing to unpack .../052-libxi6_2%3a1.8.1-1_arm64.deb ... 160s Unpacking libxi6:arm64 (2:1.8.1-1) ... 160s Selecting previously unselected package libxinerama1:arm64. 160s Preparing to unpack .../053-libxinerama1_2%3a1.1.4-3_arm64.deb ... 160s Unpacking libxinerama1:arm64 (2:1.1.4-3) ... 160s Selecting previously unselected package libxrandr2:arm64. 160s Preparing to unpack .../054-libxrandr2_2%3a1.5.2-2_arm64.deb ... 160s Unpacking libxrandr2:arm64 (2:1.5.2-2) ... 160s Selecting previously unselected package libgtk2.0-0:arm64. 160s Preparing to unpack .../055-libgtk2.0-0_2.24.33-2ubuntu2_arm64.deb ... 160s Unpacking libgtk2.0-0:arm64 (2.24.33-2ubuntu2) ... 160s Selecting previously unselected package libglvnd0:arm64. 160s Preparing to unpack .../056-libglvnd0_1.7.0-1_arm64.deb ... 160s Unpacking libglvnd0:arm64 (1.7.0-1) ... 160s Selecting previously unselected package libglapi-mesa:arm64. 160s Preparing to unpack .../057-libglapi-mesa_24.0.1-1ubuntu1_arm64.deb ... 160s Unpacking libglapi-mesa:arm64 (24.0.1-1ubuntu1) ... 160s Selecting previously unselected package libx11-xcb1:arm64. 160s Preparing to unpack .../058-libx11-xcb1_2%3a1.8.7-1_arm64.deb ... 160s Unpacking libx11-xcb1:arm64 (2:1.8.7-1) ... 161s Selecting previously unselected package libxcb-dri2-0:arm64. 161s Preparing to unpack .../059-libxcb-dri2-0_1.15-1_arm64.deb ... 161s Unpacking libxcb-dri2-0:arm64 (1.15-1) ... 161s Selecting previously unselected package libxcb-dri3-0:arm64. 161s Preparing to unpack .../060-libxcb-dri3-0_1.15-1_arm64.deb ... 161s Unpacking libxcb-dri3-0:arm64 (1.15-1) ... 161s Selecting previously unselected package libxcb-glx0:arm64. 161s Preparing to unpack .../061-libxcb-glx0_1.15-1_arm64.deb ... 161s Unpacking libxcb-glx0:arm64 (1.15-1) ... 161s Selecting previously unselected package libxcb-present0:arm64. 161s Preparing to unpack .../062-libxcb-present0_1.15-1_arm64.deb ... 161s Unpacking libxcb-present0:arm64 (1.15-1) ... 161s Selecting previously unselected package libxcb-randr0:arm64. 161s Preparing to unpack .../063-libxcb-randr0_1.15-1_arm64.deb ... 161s Unpacking libxcb-randr0:arm64 (1.15-1) ... 161s Selecting previously unselected package libxcb-sync1:arm64. 161s Preparing to unpack .../064-libxcb-sync1_1.15-1_arm64.deb ... 161s Unpacking libxcb-sync1:arm64 (1.15-1) ... 161s Selecting previously unselected package libxcb-xfixes0:arm64. 161s Preparing to unpack .../065-libxcb-xfixes0_1.15-1_arm64.deb ... 161s Unpacking libxcb-xfixes0:arm64 (1.15-1) ... 161s Selecting previously unselected package libxshmfence1:arm64. 161s Preparing to unpack .../066-libxshmfence1_1.3-1build4_arm64.deb ... 161s Unpacking libxshmfence1:arm64 (1.3-1build4) ... 161s Selecting previously unselected package libxxf86vm1:arm64. 161s Preparing to unpack .../067-libxxf86vm1_1%3a1.1.4-1build3_arm64.deb ... 161s Unpacking libxxf86vm1:arm64 (1:1.1.4-1build3) ... 161s Selecting previously unselected package libvulkan1:arm64. 161s Preparing to unpack .../068-libvulkan1_1.3.275.0-1_arm64.deb ... 161s Unpacking libvulkan1:arm64 (1.3.275.0-1) ... 161s Selecting previously unselected package libdrm-amdgpu1:arm64. 161s Preparing to unpack .../069-libdrm-amdgpu1_2.4.120-2_arm64.deb ... 161s Unpacking libdrm-amdgpu1:arm64 (2.4.120-2) ... 161s Selecting previously unselected package libdrm-nouveau2:arm64. 161s Preparing to unpack .../070-libdrm-nouveau2_2.4.120-2_arm64.deb ... 161s Unpacking libdrm-nouveau2:arm64 (2.4.120-2) ... 161s Selecting previously unselected package libdrm-radeon1:arm64. 161s Preparing to unpack .../071-libdrm-radeon1_2.4.120-2_arm64.deb ... 161s Unpacking libdrm-radeon1:arm64 (2.4.120-2) ... 161s Selecting previously unselected package libllvm17:arm64. 161s Preparing to unpack .../072-libllvm17_1%3a17.0.6-5build1_arm64.deb ... 161s Unpacking libllvm17:arm64 (1:17.0.6-5build1) ... 162s Selecting previously unselected package libgl1-mesa-dri:arm64. 162s Preparing to unpack .../073-libgl1-mesa-dri_24.0.1-1ubuntu1_arm64.deb ... 162s Unpacking libgl1-mesa-dri:arm64 (24.0.1-1ubuntu1) ... 162s Selecting previously unselected package libglx-mesa0:arm64. 162s Preparing to unpack .../074-libglx-mesa0_24.0.1-1ubuntu1_arm64.deb ... 162s Unpacking libglx-mesa0:arm64 (24.0.1-1ubuntu1) ... 162s Selecting previously unselected package libglx0:arm64. 162s Preparing to unpack .../075-libglx0_1.7.0-1_arm64.deb ... 162s Unpacking libglx0:arm64 (1.7.0-1) ... 162s Selecting previously unselected package libgl1:arm64. 162s Preparing to unpack .../076-libgl1_1.7.0-1_arm64.deb ... 162s Unpacking libgl1:arm64 (1.7.0-1) ... 162s Selecting previously unselected package libgif7:arm64. 162s Preparing to unpack .../077-libgif7_5.2.1-2.5_arm64.deb ... 162s Unpacking libgif7:arm64 (5.2.1-2.5) ... 162s Selecting previously unselected package x11-common. 162s Preparing to unpack .../078-x11-common_1%3a7.7+23ubuntu2_all.deb ... 162s Unpacking x11-common (1:7.7+23ubuntu2) ... 162s Selecting previously unselected package libxtst6:arm64. 162s Preparing to unpack .../079-libxtst6_2%3a1.2.3-1.1_arm64.deb ... 162s Unpacking libxtst6:arm64 (2:1.2.3-1.1) ... 162s Selecting previously unselected package openjdk-21-jre:arm64. 162s Preparing to unpack .../080-openjdk-21-jre_21.0.2+13-2_arm64.deb ... 162s Unpacking openjdk-21-jre:arm64 (21.0.2+13-2) ... 162s Selecting previously unselected package default-jre. 162s Preparing to unpack .../081-default-jre_2%3a1.21-75+exp1_arm64.deb ... 162s Unpacking default-jre (2:1.21-75+exp1) ... 162s Selecting previously unselected package libapache-pom-java. 162s Preparing to unpack .../082-libapache-pom-java_29-2_all.deb ... 162s Unpacking libapache-pom-java (29-2) ... 162s Selecting previously unselected package libcommons-parent-java. 162s Preparing to unpack .../083-libcommons-parent-java_56-1_all.deb ... 162s Unpacking libcommons-parent-java (56-1) ... 162s Selecting previously unselected package libcommons-lang3-java. 162s Preparing to unpack .../084-libcommons-lang3-java_3.14.0-1_all.deb ... 162s Unpacking libcommons-lang3-java (3.14.0-1) ... 162s Selecting previously unselected package libfreemarker-java. 162s Preparing to unpack .../085-libfreemarker-java_2.3.32-2_all.deb ... 162s Unpacking libfreemarker-java (2.3.32-2) ... 162s Selecting previously unselected package libgoogle-gson-java. 162s Preparing to unpack .../086-libgoogle-gson-java_2.10.1-1_all.deb ... 162s Unpacking libgoogle-gson-java (2.10.1-1) ... 163s Selecting previously unselected package libjoptsimple-java. 163s Preparing to unpack .../087-libjoptsimple-java_5.0.4-4_all.deb ... 163s Unpacking libjoptsimple-java (5.0.4-4) ... 163s Selecting previously unselected package libcommons-codec-java. 163s Preparing to unpack .../088-libcommons-codec-java_1.16.0-1_all.deb ... 163s Unpacking libcommons-codec-java (1.16.0-1) ... 163s Selecting previously unselected package libcommons-logging-java. 163s Preparing to unpack .../089-libcommons-logging-java_1.3.0-1ubuntu1_all.deb ... 163s Unpacking libcommons-logging-java (1.3.0-1ubuntu1) ... 163s Selecting previously unselected package libhttpcore-java. 163s Preparing to unpack .../090-libhttpcore-java_4.4.16-1_all.deb ... 163s Unpacking libhttpcore-java (4.4.16-1) ... 163s Selecting previously unselected package libhttpclient-java. 163s Preparing to unpack .../091-libhttpclient-java_4.5.14-1_all.deb ... 163s Unpacking libhttpclient-java (4.5.14-1) ... 163s Selecting previously unselected package liblightcouch-java. 163s Preparing to unpack .../092-liblightcouch-java_0.2.0-1_all.deb ... 163s Unpacking liblightcouch-java (0.2.0-1) ... 163s Selecting previously unselected package libmongodb-java. 163s Preparing to unpack .../093-libmongodb-java_3.6.3-2_all.deb ... 163s Unpacking libmongodb-java (3.6.3-2) ... 163s Selecting previously unselected package libslf4j-java. 163s Preparing to unpack .../094-libslf4j-java_1.7.32-1_all.deb ... 163s Unpacking libslf4j-java (1.7.32-1) ... 163s Selecting previously unselected package liblog4j2-java. 163s Preparing to unpack .../095-liblog4j2-java_2.19.0-2_all.deb ... 163s Unpacking liblog4j2-java (2.19.0-2) ... 163s Selecting previously unselected package libbarclay-java. 163s Preparing to unpack .../096-libbarclay-java_5.0.0+dfsg-1_all.deb ... 163s Unpacking libbarclay-java (5.0.0+dfsg-1) ... 163s Selecting previously unselected package libcommons-compress-java. 163s Preparing to unpack .../097-libcommons-compress-java_1.25.0-1_all.deb ... 163s Unpacking libcommons-compress-java (1.25.0-1) ... 163s Selecting previously unselected package libcommons-io-java. 163s Preparing to unpack .../098-libcommons-io-java_2.11.0-2_all.deb ... 163s Unpacking libcommons-io-java (2.11.0-2) ... 163s Selecting previously unselected package libcommons-jexl2-java. 163s Preparing to unpack .../099-libcommons-jexl2-java_2.1.1-6_all.deb ... 163s Unpacking libcommons-jexl2-java (2.1.1-6) ... 163s Selecting previously unselected package libcommons-math3-java. 163s Preparing to unpack .../100-libcommons-math3-java_3.6.1-3_all.deb ... 163s Unpacking libcommons-math3-java (3.6.1-3) ... 163s Selecting previously unselected package libgatk-native-bindings-java. 163s Preparing to unpack .../101-libgatk-native-bindings-java_1.0.0+dfsg-2_all.deb ... 163s Unpacking libgatk-native-bindings-java (1.0.0+dfsg-2) ... 163s Selecting previously unselected package libmjson-java. 163s Preparing to unpack .../102-libmjson-java_1.4.0-3_all.deb ... 163s Unpacking libmjson-java (1.4.0-3) ... 163s Selecting previously unselected package libmbedcrypto7:arm64. 163s Preparing to unpack .../103-libmbedcrypto7_2.28.7-1ubuntu1_arm64.deb ... 163s Unpacking libmbedcrypto7:arm64 (2.28.7-1ubuntu1) ... 163s Selecting previously unselected package libmbedx509-1:arm64. 163s Preparing to unpack .../104-libmbedx509-1_2.28.7-1ubuntu1_arm64.deb ... 163s Unpacking libmbedx509-1:arm64 (2.28.7-1ubuntu1) ... 163s Selecting previously unselected package libmbedtls14:arm64. 163s Preparing to unpack .../105-libmbedtls14_2.28.7-1ubuntu1_arm64.deb ... 163s Unpacking libmbedtls14:arm64 (2.28.7-1ubuntu1) ... 163s Selecting previously unselected package ncbi-vdb-data. 163s Preparing to unpack .../106-ncbi-vdb-data_3.0.2+dfsg-2_all.deb ... 163s Unpacking ncbi-vdb-data (3.0.2+dfsg-2) ... 163s Selecting previously unselected package libncbi-vdb3:arm64. 163s Preparing to unpack .../107-libncbi-vdb3_3.0.2+dfsg-2_arm64.deb ... 163s Unpacking libncbi-vdb3:arm64 (3.0.2+dfsg-2) ... 163s Selecting previously unselected package libncbi-ngs3:arm64. 163s Preparing to unpack .../108-libncbi-ngs3_3.0.3+dfsg-6ubuntu1_arm64.deb ... 163s Unpacking libncbi-ngs3:arm64 (3.0.3+dfsg-6ubuntu1) ... 163s Selecting previously unselected package libngs-jni:arm64. 164s Preparing to unpack .../109-libngs-jni_3.0.3+dfsg-6ubuntu1_arm64.deb ... 164s Unpacking libngs-jni:arm64 (3.0.3+dfsg-6ubuntu1) ... 164s Selecting previously unselected package libngs-java:arm64. 164s Preparing to unpack .../110-libngs-java_3.0.3+dfsg-6ubuntu1_arm64.deb ... 164s Unpacking libngs-java:arm64 (3.0.3+dfsg-6ubuntu1) ... 164s Selecting previously unselected package librhino-java. 164s Preparing to unpack .../111-librhino-java_1.7.14-2.1_all.deb ... 164s Unpacking librhino-java (1.7.14-2.1) ... 164s Selecting previously unselected package libsnappy1v5:arm64. 164s Preparing to unpack .../112-libsnappy1v5_1.1.10-1_arm64.deb ... 164s Unpacking libsnappy1v5:arm64 (1.1.10-1) ... 164s Selecting previously unselected package libsnappy-jni. 164s Preparing to unpack .../113-libsnappy-jni_1.1.10.5-1_arm64.deb ... 164s Unpacking libsnappy-jni (1.1.10.5-1) ... 164s Selecting previously unselected package libsnappy-java. 164s Preparing to unpack .../114-libsnappy-java_1.1.10.5-1_all.deb ... 164s Unpacking libsnappy-java (1.1.10.5-1) ... 164s Selecting previously unselected package libhtsjdk-java. 164s Preparing to unpack .../115-libhtsjdk-java_4.1.0+dfsg-1_all.deb ... 164s Unpacking libhtsjdk-java (4.1.0+dfsg-1) ... 164s Selecting previously unselected package libgkl-java. 164s Preparing to unpack .../116-libgkl-java_0.8.11+dfsg-2_all.deb ... 164s Unpacking libgkl-java (0.8.11+dfsg-2) ... 164s Selecting previously unselected package libpicard-java. 164s Preparing to unpack .../117-libpicard-java_3.1.1+dfsg-1_all.deb ... 164s Unpacking libpicard-java (3.1.1+dfsg-1) ... 164s Selecting previously unselected package picard-tools. 164s Preparing to unpack .../118-picard-tools_3.1.1+dfsg-1_all.deb ... 164s Unpacking picard-tools (3.1.1+dfsg-1) ... 164s Selecting previously unselected package autopkgtest-satdep. 164s Preparing to unpack .../119-1-autopkgtest-satdep.deb ... 164s Unpacking autopkgtest-satdep (0) ... 164s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 164s Setting up libxcb-dri3-0:arm64 (1.15-1) ... 164s Setting up liblcms2-2:arm64 (2.14-2) ... 164s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 164s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 164s Setting up libx11-xcb1:arm64 (2:1.8.7-1) ... 164s Setting up libslf4j-java (1.7.32-1) ... 164s Setting up libdrm-nouveau2:arm64 (2.4.120-2) ... 164s Setting up libxdamage1:arm64 (1:1.1.6-1) ... 164s Setting up libxcb-xfixes0:arm64 (1.15-1) ... 164s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 164s Setting up hicolor-icon-theme (0.17-2) ... 164s Setting up libxi6:arm64 (2:1.8.1-1) ... 164s Setting up libgatk-native-bindings-java (1.0.0+dfsg-2) ... 164s Setting up java-common (0.75+exp1) ... 164s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 164s Setting up libdatrie1:arm64 (0.2.13-3) ... 164s Setting up libxcb-render0:arm64 (1.15-1) ... 164s Setting up libdrm-radeon1:arm64 (2.4.120-2) ... 164s Setting up libglvnd0:arm64 (1.7.0-1) ... 164s Setting up libgoogle-gson-java (2.10.1-1) ... 164s Setting up libmjson-java (1.4.0-3) ... 164s Setting up libxcb-glx0:arm64 (1.15-1) ... 164s Setting up libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ... 164s Setting up x11-common (1:7.7+23ubuntu2) ... 164s Setting up libdeflate0:arm64 (1.19-1) ... 164s Setting up libxcb-shm0:arm64 (1.15-1) ... 164s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 164s Setting up libxxf86vm1:arm64 (1:1.1.4-1build3) ... 164s Setting up libsnappy1v5:arm64 (1.1.10-1) ... 164s Setting up libxcb-present0:arm64 (1.15-1) ... 164s Setting up libasound2-data (1.2.10-3build1) ... 164s Setting up librhino-java (1.7.14-2.1) ... 164s Setting up libmbedcrypto7:arm64 (2.28.7-1ubuntu1) ... 164s Setting up libxfixes3:arm64 (1:6.0.0-2) ... 164s Setting up libxcb-sync1:arm64 (1.15-1) ... 164s Setting up libapache-pom-java (29-2) ... 165s Setting up libavahi-common-data:arm64 (0.8-13ubuntu2) ... 165s Setting up libxinerama1:arm64 (2:1.1.4-3) ... 165s Setting up fonts-dejavu-mono (2.37-8) ... 165s Setting up libxrandr2:arm64 (2:1.5.2-2) ... 165s Setting up fonts-dejavu-core (2.37-8) ... 165s Setting up libpcsclite1:arm64 (2.0.0-1) ... 165s Setting up libmongodb-java (3.6.3-2) ... 165s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 165s Setting up libglapi-mesa:arm64 (24.0.1-1ubuntu1) ... 165s Setting up libvulkan1:arm64 (1.3.275.0-1) ... 165s Setting up libwebp7:arm64 (1.3.2-0.4) ... 165s Setting up libxcb-dri2-0:arm64 (1.15-1) ... 165s Setting up libgif7:arm64 (5.2.1-2.5) ... 165s Setting up libfreemarker-java (2.3.32-2) ... 165s Setting up libxshmfence1:arm64 (1.3-1build4) ... 165s Setting up at-spi2-common (2.50.0-1) ... 165s Setting up libxcb-randr0:arm64 (1.15-1) ... 165s Setting up libasound2:arm64 (1.2.10-3build1) ... 165s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 165s Setting up ncbi-vdb-data (3.0.2+dfsg-2) ... 165s Setting up libthai-data (0.1.29-2) ... 165s Setting up libcommons-math3-java (3.6.1-3) ... 165s Setting up libgtk2.0-common (2.24.33-2ubuntu2) ... 165s Setting up libatk1.0-0:arm64 (2.50.0-1) ... 165s Setting up libhttpcore-java (4.4.16-1) ... 165s Setting up libjoptsimple-java (5.0.4-4) ... 165s Setting up ca-certificates-java (20240118) ... 165s No JRE found. Skipping Java certificates setup. 165s Setting up libllvm17:arm64 (1:17.0.6-5build1) ... 165s Setting up libsnappy-jni (1.1.10.5-1) ... 165s Setting up libxcomposite1:arm64 (1:0.4.5-1build2) ... 165s Setting up libdrm-amdgpu1:arm64 (2.4.120-2) ... 165s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 165s Setting up libmbedx509-1:arm64 (2.28.7-1ubuntu1) ... 165s Setting up libmbedtls14:arm64 (2.28.7-1ubuntu1) ... 165s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 165s Setting up libxtst6:arm64 (2:1.2.3-1.1) ... 165s Setting up libxcursor1:arm64 (1:1.2.1-1) ... 165s Setting up libgl1-mesa-dri:arm64 (24.0.1-1ubuntu1) ... 165s Setting up libcommons-parent-java (56-1) ... 165s Setting up libavahi-common3:arm64 (0.8-13ubuntu2) ... 165s Setting up libncbi-vdb3:arm64 (3.0.2+dfsg-2) ... 165s Setting up libcommons-logging-java (1.3.0-1ubuntu1) ... 165s Setting up libcommons-jexl2-java (2.1.1-6) ... 165s Setting up libthai0:arm64 (0.1.29-2) ... 165s Setting up libcommons-lang3-java (3.14.0-1) ... 165s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 165s Setting up libgdk-pixbuf-2.0-0:arm64 (2.42.10+dfsg-3) ... 165s Setting up libsnappy-java (1.1.10.5-1) ... 165s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 165s Setting up libcommons-codec-java (1.16.0-1) ... 165s Setting up libavahi-client3:arm64 (0.8-13ubuntu2) ... 165s Setting up libncbi-ngs3:arm64 (3.0.3+dfsg-6ubuntu1) ... 165s Setting up gtk-update-icon-cache (3.24.40-2ubuntu1) ... 165s Setting up fontconfig (2.15.0-1ubuntu1) ... 167s Regenerating fonts cache... done. 167s Setting up libngs-jni:arm64 (3.0.3+dfsg-6ubuntu1) ... 167s Setting up libglx-mesa0:arm64 (24.0.1-1ubuntu1) ... 167s Setting up libglx0:arm64 (1.7.0-1) ... 167s Setting up libcommons-compress-java (1.25.0-1) ... 167s Setting up libcommons-io-java (2.11.0-2) ... 167s Setting up libpango-1.0-0:arm64 (1.51.0+ds-4) ... 167s Setting up libcairo2:arm64 (1.18.0-1) ... 167s Setting up libgl1:arm64 (1.7.0-1) ... 167s Setting up libcups2:arm64 (2.4.6-0ubuntu3) ... 167s Setting up libhttpclient-java (4.5.14-1) ... 167s Setting up liblightcouch-java (0.2.0-1) ... 167s Setting up libngs-java:arm64 (3.0.3+dfsg-6ubuntu1) ... 167s Setting up libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 167s Setting up libhtsjdk-java (4.1.0+dfsg-1) ... 167s Setting up libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 167s Setting up openjdk-21-jre-headless:arm64 (21.0.2+13-2) ... 167s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode 167s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 167s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 167s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 167s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 167s Setting up liblog4j2-java (2.19.0-2) ... 167s Setting up libbarclay-java (5.0.0+dfsg-1) ... 167s Setting up libgkl-java (0.8.11+dfsg-2) ... 167s Setting up libpicard-java (3.1.1+dfsg-1) ... 167s Setting up adwaita-icon-theme (46~rc-1) ... 167s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode 167s Setting up libgtk2.0-0:arm64 (2.24.33-2ubuntu2) ... 167s Setting up humanity-icon-theme (0.6.16) ... 167s Setting up ubuntu-mono (24.04-0ubuntu1) ... 167s Processing triggers for man-db (2.12.0-3) ... 168s Processing triggers for libc-bin (2.39-0ubuntu2) ... 168s Processing triggers for ca-certificates-java (20240118) ... 169s Adding debian:ACCVRAIZ1.pem 169s Adding debian:AC_RAIZ_FNMT-RCM.pem 169s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 169s Adding debian:ANF_Secure_Server_Root_CA.pem 169s Adding debian:Actalis_Authentication_Root_CA.pem 169s Adding debian:AffirmTrust_Commercial.pem 169s Adding debian:AffirmTrust_Networking.pem 169s Adding debian:AffirmTrust_Premium.pem 169s Adding debian:AffirmTrust_Premium_ECC.pem 169s Adding debian:Amazon_Root_CA_1.pem 169s Adding debian:Amazon_Root_CA_2.pem 169s Adding debian:Amazon_Root_CA_3.pem 169s Adding debian:Amazon_Root_CA_4.pem 169s Adding debian:Atos_TrustedRoot_2011.pem 169s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 169s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 169s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 169s Adding debian:BJCA_Global_Root_CA1.pem 169s Adding debian:BJCA_Global_Root_CA2.pem 169s Adding debian:Baltimore_CyberTrust_Root.pem 169s Adding debian:Buypass_Class_2_Root_CA.pem 169s Adding debian:Buypass_Class_3_Root_CA.pem 169s Adding debian:CA_Disig_Root_R2.pem 169s Adding debian:CFCA_EV_ROOT.pem 169s Adding debian:COMODO_Certification_Authority.pem 169s Adding debian:COMODO_ECC_Certification_Authority.pem 169s Adding debian:COMODO_RSA_Certification_Authority.pem 169s Adding debian:Certainly_Root_E1.pem 169s Adding debian:Certainly_Root_R1.pem 169s Adding debian:Certigna.pem 169s Adding debian:Certigna_Root_CA.pem 169s Adding debian:Certum_EC-384_CA.pem 169s Adding debian:Certum_Trusted_Network_CA.pem 169s Adding debian:Certum_Trusted_Network_CA_2.pem 169s Adding debian:Certum_Trusted_Root_CA.pem 169s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 169s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 169s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 169s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 169s Adding debian:Comodo_AAA_Services_root.pem 169s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 169s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 169s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 169s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 169s Adding debian:DigiCert_Assured_ID_Root_CA.pem 169s Adding debian:DigiCert_Assured_ID_Root_G2.pem 169s Adding debian:DigiCert_Assured_ID_Root_G3.pem 169s Adding debian:DigiCert_Global_Root_CA.pem 169s Adding debian:DigiCert_Global_Root_G2.pem 169s Adding debian:DigiCert_Global_Root_G3.pem 169s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 169s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 169s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 169s Adding debian:DigiCert_Trusted_Root_G4.pem 169s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 169s Adding debian:Entrust_Root_Certification_Authority.pem 169s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 169s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 169s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 169s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 169s Adding debian:GLOBALTRUST_2020.pem 169s Adding debian:GTS_Root_R1.pem 169s Adding debian:GTS_Root_R2.pem 169s Adding debian:GTS_Root_R3.pem 169s Adding debian:GTS_Root_R4.pem 169s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 169s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 169s Adding debian:GlobalSign_Root_CA.pem 169s Adding debian:GlobalSign_Root_CA_-_R3.pem 169s Adding debian:GlobalSign_Root_CA_-_R6.pem 169s Adding debian:GlobalSign_Root_E46.pem 169s Adding debian:GlobalSign_Root_R46.pem 169s Adding debian:Go_Daddy_Class_2_CA.pem 169s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 169s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 169s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 169s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 169s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 169s Adding debian:HiPKI_Root_CA_-_G1.pem 169s Adding debian:Hongkong_Post_Root_CA_3.pem 169s Adding debian:ISRG_Root_X1.pem 169s Adding debian:ISRG_Root_X2.pem 169s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 169s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 169s Adding debian:Izenpe.com.pem 169s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 169s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 169s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 169s Adding debian:NAVER_Global_Root_Certification_Authority.pem 169s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 169s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 169s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 169s Adding debian:QuoVadis_Root_CA_1_G3.pem 169s Adding debian:QuoVadis_Root_CA_2.pem 169s Adding debian:QuoVadis_Root_CA_2_G3.pem 169s Adding debian:QuoVadis_Root_CA_3.pem 169s Adding debian:QuoVadis_Root_CA_3_G3.pem 169s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 169s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 169s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 169s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 169s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 169s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 169s Adding debian:SZAFIR_ROOT_CA2.pem 169s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 169s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 169s Adding debian:SecureSign_RootCA11.pem 169s Adding debian:SecureTrust_CA.pem 169s Adding debian:Secure_Global_CA.pem 169s Adding debian:Security_Communication_ECC_RootCA1.pem 169s Adding debian:Security_Communication_RootCA2.pem 169s Adding debian:Security_Communication_RootCA3.pem 169s Adding debian:Security_Communication_Root_CA.pem 169s Adding debian:Starfield_Class_2_CA.pem 169s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 169s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 169s Adding debian:SwissSign_Gold_CA_-_G2.pem 169s Adding debian:SwissSign_Silver_CA_-_G2.pem 169s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 169s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 169s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 169s Adding debian:TWCA_Global_Root_CA.pem 169s Adding debian:TWCA_Root_Certification_Authority.pem 169s Adding debian:TeliaSonera_Root_CA_v1.pem 169s Adding debian:Telia_Root_CA_v2.pem 169s Adding debian:TrustAsia_Global_Root_CA_G3.pem 169s Adding debian:TrustAsia_Global_Root_CA_G4.pem 169s Adding debian:Trustwave_Global_Certification_Authority.pem 169s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 169s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 169s Adding debian:TunTrust_Root_CA.pem 169s Adding debian:UCA_Extended_Validation_Root.pem 169s Adding debian:UCA_Global_G2_Root.pem 169s Adding debian:USERTrust_ECC_Certification_Authority.pem 169s Adding debian:USERTrust_RSA_Certification_Authority.pem 169s Adding debian:XRamp_Global_CA_Root.pem 169s Adding debian:certSIGN_ROOT_CA.pem 169s Adding debian:certSIGN_Root_CA_G2.pem 169s Adding debian:e-Szigno_Root_CA_2017.pem 169s Adding debian:ePKI_Root_Certification_Authority.pem 169s Adding debian:emSign_ECC_Root_CA_-_C3.pem 169s Adding debian:emSign_ECC_Root_CA_-_G3.pem 169s Adding debian:emSign_Root_CA_-_C1.pem 169s Adding debian:emSign_Root_CA_-_G1.pem 169s Adding debian:vTrus_ECC_Root_CA.pem 169s Adding debian:vTrus_Root_CA.pem 170s done. 170s Setting up openjdk-21-jre:arm64 (21.0.2+13-2) ... 170s Setting up default-jre-headless (2:1.21-75+exp1) ... 170s Setting up default-jre (2:1.21-75+exp1) ... 170s Setting up picard-tools (3.1.1+dfsg-1) ... 170s Setting up autopkgtest-satdep (0) ... 175s (Reading database ... 88886 files and directories currently installed.) 175s Removing autopkgtest-satdep (0) ... 176s autopkgtest [21:35:26]: test run-unit-test: [----------------------- 176s JavOpt: 176s PicardProg: ViewSam 176s PicardOpts: PF_STATUS=All ALIGNMENT_STATUS=All INPUT=unmapped.sam 177s INFO 2024-03-21 21:35:27 ViewSam 177s 177s ********** NOTE: Picard's command line syntax is changing. 177s ********** 177s ********** For more information, please see: 177s ********** 177s https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) 177s ********** 177s ********** The command line looks like this in the new syntax: 177s ********** 177s ********** ViewSam -PF_STATUS All -ALIGNMENT_STATUS All -INPUT unmapped.sam 177s ********** 177s 177s 177s 21:35:27.522 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/aarch64-linux-gnu/jni:/lib/aarch64-linux-gnu:/usr/lib/aarch64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 177s 21:35:27.524 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 177s 21:35:27.524 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Unable to load libgkl_compression.so from /usr/java/packages/lib:/usr/lib/aarch64-linux-gnu/jni:/lib/aarch64-linux-gnu:/usr/lib/aarch64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 177s 21:35:27.526 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/aarch64-linux-gnu/jni:/lib/aarch64-linux-gnu:/usr/lib/aarch64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 177s 21:35:27.526 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 177s 21:35:27.526 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Unable to load libgkl_compression.so from /usr/java/packages/lib:/usr/lib/aarch64-linux-gnu/jni:/lib/aarch64-linux-gnu:/usr/lib/aarch64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 177s [Thu Mar 21 21:35:27 UTC 2024] ViewSam INPUT=unmapped.sam ALIGNMENT_STATUS=All PF_STATUS=All HEADER_ONLY=false RECORDS_ONLY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false 177s [Thu Mar 21 21:35:27 UTC 2024] Executing as ubuntu@autopkgtest on Linux 6.8.0-11-generic aarch64; OpenJDK 64-Bit Server VM 21.0.2+13-Ubuntu-2; Deflater: Jdk; Inflater: Jdk; Provider GCS is available; Picard version: 3.1.1 177s @HD VN:1.0 SO:queryname 177s @RG ID:0 SM:Hi,Mom! PL:ILLUMINA 177s both_reads_align_clip_adapter 77 * 0 0 * * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 aa:Z:Hello ab:Z:ATTCGG ac:B:c,1,2,3 af:B:f,1.0,2.0,3.0 ai:B:i,1,2,3 as:B:s,1,2,3 177s both_reads_align_clip_adapter 141 * 0 0 * * 0 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 aa:Z:Hello ab:Z:ATTCGG ac:B:c,1,2,3 af:B:f,1.0,2.0,3.0 ai:B:i,1,2,3 as:B:s,1,2,3 177s both_reads_align_clip_marked 77 * 0 0 * * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 XT:i:97 aa:Z:Hello ab:Z:ATTCGG ac:B:c,1,2,3 af:B:f,1.0,2.0,3.0 ai:B:i,1,2,3 as:B:s,1,2,3 177s both_reads_align_clip_marked 141 * 0 0 * * 0 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 XT:i:97 aa:Z:Hello ab:Z:ATTCGG ac:B:c,1,2,3 af:B:f,1.0,2.0,3.0 ai:B:i,1,2,3 as:B:s,1,2,3 177s both_reads_present_only_first_aligns 77 * 0 0 * * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 aa:Z:Hello ab:Z:ATTCGG ac:B:c,1,2,3 af:B:f,1.0,2.0,3.0 ai:B:i,1,2,3 as:B:s,1,2,3 177s both_reads_present_only_first_aligns 141 * 0 0 * * 0 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 aa:Z:Hello ab:Z:ATTCGG ac:B:c,1,2,3 af:B:f,1.0,2.0,3.0 ai:B:i,1,2,3 as:B:s,1,2,3 177s neither_read_aligns_or_present 77 * 0 0 * * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 aa:Z:Hello ab:Z:ATTCGG ac:B:c,1,2,3 af:B:f,1.0,2.0,3.0 ai:B:i,1,2,3 as:B:s,1,2,3 177s neither_read_aligns_or_present 141 * 0 0 * * 0 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 aa:Z:Hello ab:Z:ATTCGG ac:B:c,1,2,3 af:B:f,1.0,2.0,3.0 ai:B:i,1,2,3 as:B:s,1,2,3 177s read_2_too_many_gaps 77 * 0 0 * * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 aa:Z:Hello ab:Z:ATTCGG ac:B:c,1,2,3 af:B:f,1.0,2.0,3.0 ai:B:i,1,2,3 as:B:s,1,2,3 177s read_2_too_many_gaps 141 * 0 0 * * 0 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 aa:Z:Hello ab:Z:ATTCGG ac:B:c,1,2,3 af:B:f,1.0,2.0,3.0 ai:B:i,1,2,3 as:B:s,1,2,3 177s [Thu Mar 21 21:35:27 UTC 2024] picard.sam.ViewSam done. Elapsed time: 0.00 minutes. 177s Runtime.totalMemory()=67108864 177s JavOpt: 177s PicardProg: CollectSequencingArtifactMetrics 177s PicardOpts: I=test.sam O=test R=test.fasta 178s INFO 2024-03-21 21:35:28 CollectSequencingArtifactMetrics 178s 178s ********** NOTE: Picard's command line syntax is changing. 178s ********** 178s ********** For more information, please see: 178s ********** 178s https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) 178s ********** 178s ********** The command line looks like this in the new syntax: 178s ********** 178s ********** CollectSequencingArtifactMetrics -I test.sam -O test -R test.fasta 178s ********** 178s 178s 178s 21:35:28.526 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/aarch64-linux-gnu/jni:/lib/aarch64-linux-gnu:/usr/lib/aarch64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 178s 21:35:28.528 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 178s 21:35:28.529 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Unable to load libgkl_compression.so from /usr/java/packages/lib:/usr/lib/aarch64-linux-gnu/jni:/lib/aarch64-linux-gnu:/usr/lib/aarch64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 178s 21:35:28.530 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/aarch64-linux-gnu/jni:/lib/aarch64-linux-gnu:/usr/lib/aarch64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 178s 21:35:28.530 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 178s 21:35:28.530 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Unable to load libgkl_compression.so from /usr/java/packages/lib:/usr/lib/aarch64-linux-gnu/jni:/lib/aarch64-linux-gnu:/usr/lib/aarch64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 178s [Thu Mar 21 21:35:28 UTC 2024] CollectSequencingArtifactMetrics INPUT=test.sam OUTPUT=test REFERENCE_SEQUENCE=test.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 MINIMUM_INSERT_SIZE=60 MAXIMUM_INSERT_SIZE=600 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true CONTEXT_SIZE=1 ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false 178s [Thu Mar 21 21:35:28 UTC 2024] Executing as ubuntu@autopkgtest on Linux 6.8.0-11-generic aarch64; OpenJDK 64-Bit Server VM 21.0.2+13-Ubuntu-2; Deflater: Jdk; Inflater: Jdk; Provider GCS is available; Picard version: 3.1.1 178s [Thu Mar 21 21:35:28 UTC 2024] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes. 178s Runtime.totalMemory()=67108864 178s All output files generated 178s JavOpt: 178s PicardProg: SortVcf 178s PicardOpts: I=mini.vcf O=mini_sorted.vcf 179s INFO 2024-03-21 21:35:29 SortVcf 179s 179s ********** NOTE: Picard's command line syntax is changing. 179s ********** 179s ********** For more information, please see: 179s ********** 179s https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) 179s ********** 179s ********** The command line looks like this in the new syntax: 179s ********** 179s ********** SortVcf -I mini.vcf -O mini_sorted.vcf 179s ********** 179s 179s 179s 21:35:29.852 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/aarch64-linux-gnu/jni:/lib/aarch64-linux-gnu:/usr/lib/aarch64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 179s 21:35:29.854 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 179s 21:35:29.855 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Unable to load libgkl_compression.so from /usr/java/packages/lib:/usr/lib/aarch64-linux-gnu/jni:/lib/aarch64-linux-gnu:/usr/lib/aarch64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 179s 21:35:29.856 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/aarch64-linux-gnu/jni:/lib/aarch64-linux-gnu:/usr/lib/aarch64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 179s 21:35:29.856 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 179s 21:35:29.857 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Unable to load libgkl_compression.so from /usr/java/packages/lib:/usr/lib/aarch64-linux-gnu/jni:/lib/aarch64-linux-gnu:/usr/lib/aarch64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 179s [Thu Mar 21 21:35:29 UTC 2024] SortVcf INPUT=[mini.vcf] OUTPUT=mini_sorted.vcf VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=true CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false 179s [Thu Mar 21 21:35:29 UTC 2024] Executing as ubuntu@autopkgtest on Linux 6.8.0-11-generic aarch64; OpenJDK 64-Bit Server VM 21.0.2+13-Ubuntu-2; Deflater: Jdk; Inflater: Jdk; Provider GCS is available; Picard version: 3.1.1 179s INFO 2024-03-21 21:35:29 SortVcf Reading entries from input file 1 180s [Thu Mar 21 21:35:30 UTC 2024] picard.vcf.SortVcf done. Elapsed time: 0.01 minutes. 180s Runtime.totalMemory()=67108864 180s sorted vcf generated 180s JavOpt: 180s PicardProg: SplitVcfs 180s PicardOpts: I=mini.vcf SNP_OUTPUT=snp.vcf INDEL_OUTPUT=indel.vcf 181s INFO 2024-03-21 21:35:31 SplitVcfs 181s 181s ********** NOTE: Picard's command line syntax is changing. 181s ********** 181s ********** For more information, please see: 181s ********** 181s https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) 181s ********** 181s ********** The command line looks like this in the new syntax: 181s ********** 181s ********** SplitVcfs -I mini.vcf -SNP_OUTPUT snp.vcf -INDEL_OUTPUT indel.vcf 181s ********** 181s 181s 181s 21:35:31.096 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/aarch64-linux-gnu/jni:/lib/aarch64-linux-gnu:/usr/lib/aarch64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 181s 21:35:31.098 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 181s 21:35:31.098 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Unable to load libgkl_compression.so from /usr/java/packages/lib:/usr/lib/aarch64-linux-gnu/jni:/lib/aarch64-linux-gnu:/usr/lib/aarch64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 181s 21:35:31.100 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/aarch64-linux-gnu/jni:/lib/aarch64-linux-gnu:/usr/lib/aarch64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 181s 21:35:31.100 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 181s 21:35:31.100 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Unable to load libgkl_compression.so from /usr/java/packages/lib:/usr/lib/aarch64-linux-gnu/jni:/lib/aarch64-linux-gnu:/usr/lib/aarch64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 181s [Thu Mar 21 21:35:31 UTC 2024] SplitVcfs INPUT=mini.vcf SNP_OUTPUT=snp.vcf INDEL_OUTPUT=indel.vcf STRICT=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=true CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false 181s [Thu Mar 21 21:35:31 UTC 2024] Executing as ubuntu@autopkgtest on Linux 6.8.0-11-generic aarch64; OpenJDK 64-Bit Server VM 21.0.2+13-Ubuntu-2; Deflater: Jdk; Inflater: Jdk; Provider GCS is available; Picard version: 3.1.1 181s [Thu Mar 21 21:35:31 UTC 2024] picard.vcf.SplitVcfs done. Elapsed time: 0.01 minutes. 181s Runtime.totalMemory()=67108864 181s snp and indel vcfs generated 181s autopkgtest [21:35:31]: test run-unit-test: -----------------------] 182s autopkgtest [21:35:32]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 182s run-unit-test PASS 182s autopkgtest [21:35:32]: @@@@@@@@@@@@@@@@@@@@ summary 182s run-unit-test PASS 187s Creating nova instance adt-noble-arm64-picard-tools-20240321-213230-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240321.img (UUID 28ecccfc-4cb0-4cc6-a280-209e2d140e10)...