0s autopkgtest [08:23:00]: starting date and time: 2024-03-21 08:23:00+0000 0s autopkgtest [08:23:00]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [08:23:00]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.97c1r02y/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-lts,src:alsa-lib,src:cups,src:gnutls28,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-lts/11.0.23~7ea-1ubuntu1 alsa-lib/1.2.11-1build1 cups/2.4.7-1.2ubuntu1 gnutls28/3.8.3-1.1ubuntu2 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@bos01-arm64-2.secgroup --name adt-noble-arm64-picard-tools-20240321-075410-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://us.ports.ubuntu.com/ubuntu-ports/ 146s autopkgtest [08:25:26]: testbed dpkg architecture: arm64 146s autopkgtest [08:25:26]: testbed apt version: 2.7.12 146s autopkgtest [08:25:26]: @@@@@@@@@@@@@@@@@@@@ test bed setup 147s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 148s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 148s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [492 kB] 148s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3769 kB] 148s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [53.9 kB] 148s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [683 kB] 148s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 148s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [41.7 kB] 148s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 148s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4176 kB] 148s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 148s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [67.4 kB] 148s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 154s Fetched 9418 kB in 3s (3579 kB/s) 154s Reading package lists... 163s Reading package lists... 163s Building dependency tree... 163s Reading state information... 166s Calculating upgrade... 166s The following packages will be upgraded: 166s debianutils linux-firmware ubuntu-minimal ubuntu-standard 166s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 166s Need to get 476 MB of archives. 166s After this operation, 5724 kB of additional disk space will be used. 166s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 debianutils arm64 5.17 [90.1 kB] 166s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536build1 [10.7 kB] 166s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536build1 [10.7 kB] 166s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 linux-firmware arm64 20240318.git3b128b60-0ubuntu1 [475 MB] 198s Fetched 476 MB in 29s (16.4 MB/s) 198s (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 ... 75850 files and directories currently installed.) 198s Preparing to unpack .../debianutils_5.17_arm64.deb ... 198s Unpacking debianutils (5.17) over (5.16) ... 198s Setting up debianutils (5.17) ... 198s (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 ... 75850 files and directories currently installed.) 198s Preparing to unpack .../ubuntu-minimal_1.536build1_arm64.deb ... 198s Unpacking ubuntu-minimal (1.536build1) over (1.536) ... 198s Preparing to unpack .../ubuntu-standard_1.536build1_arm64.deb ... 198s Unpacking ubuntu-standard (1.536build1) over (1.536) ... 198s Preparing to unpack .../linux-firmware_20240318.git3b128b60-0ubuntu1_arm64.deb ... 198s Unpacking linux-firmware (20240318.git3b128b60-0ubuntu1) over (20240202.git36777504-0ubuntu1) ... 200s Setting up ubuntu-minimal (1.536build1) ... 200s Setting up linux-firmware (20240318.git3b128b60-0ubuntu1) ... 200s Setting up ubuntu-standard (1.536build1) ... 200s Processing triggers for man-db (2.12.0-3) ... 201s Processing triggers for initramfs-tools (0.142ubuntu20) ... 202s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic 202s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 221s System running in EFI mode, skipping. 221s Reading package lists... 221s Building dependency tree... 221s Reading state information... 222s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 223s sh: Attempting to set up Debian/Ubuntu apt sources automatically 223s sh: Distribution appears to be Ubuntu 226s Reading package lists... 226s Building dependency tree... 226s Reading state information... 226s eatmydata is already the newest version (131-1). 226s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 226s Reading package lists... 227s Building dependency tree... 227s Reading state information... 227s dbus is already the newest version (1.14.10-4ubuntu1). 227s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 227s Reading package lists... 228s Building dependency tree... 228s Reading state information... 228s rng-tools-debian is already the newest version (2.4). 228s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 229s Reading package lists... 229s Building dependency tree... 229s Reading state information... 230s The following packages will be REMOVED: 230s cloud-init* python3-configobj* python3-debconf* 230s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 230s After this operation, 3252 kB disk space will be freed. 230s (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 ... 75912 files and directories currently installed.) 230s Removing cloud-init (24.1.1-0ubuntu1) ... 231s Removing python3-configobj (5.0.8-3) ... 232s Removing python3-debconf (1.5.86) ... 232s Processing triggers for man-db (2.12.0-3) ... 232s (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 ... 75523 files and directories currently installed.) 232s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 234s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 234s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 234s invoke-rc.d: policy-rc.d denied execution of try-restart. 234s Reading package lists... 234s Building dependency tree... 234s Reading state information... 235s linux-generic is already the newest version (6.8.0-11.11+1). 235s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 236s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 236s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 236s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 241s Reading package lists... 241s Reading package lists... 241s Building dependency tree... 241s Reading state information... 242s Calculating upgrade... 242s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 242s Reading package lists... 243s Building dependency tree... 243s Reading state information... 243s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 244s autopkgtest [08:27:04]: rebooting testbed after setup commands that affected boot 411s autopkgtest [08:29:50]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 414s autopkgtest [08:29:54]: @@@@@@@@@@@@@@@@@@@@ apt-source picard-tools 419s Get:1 http://ftpmaster.internal/ubuntu noble/universe picard-tools 3.1.1+dfsg-1 (dsc) [2737 B] 419s Get:2 http://ftpmaster.internal/ubuntu noble/universe picard-tools 3.1.1+dfsg-1 (tar) [20.4 MB] 419s Get:3 http://ftpmaster.internal/ubuntu noble/universe picard-tools 3.1.1+dfsg-1 (diff) [22.8 kB] 419s gpgv: Signature made Sat Dec 16 21:39:31 2023 UTC 419s gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 419s gpgv: Can't check signature: No public key 419s dpkg-source: warning: cannot verify inline signature for ./picard-tools_3.1.1+dfsg-1.dsc: no acceptable signature found 426s autopkgtest [08:30:04]: testing package picard-tools version 3.1.1+dfsg-1 426s autopkgtest [08:30:06]: build not needed 648s autopkgtest [08:33:48]: test run-unit-test: preparing testbed 660s Reading package lists... 660s Building dependency tree... 660s Reading state information... 661s Starting pkgProblemResolver with broken count: 0 661s Starting 2 pkgProblemResolver with broken count: 0 661s Done 662s The following additional packages will be installed: 662s adwaita-icon-theme at-spi2-common ca-certificates-java default-jre 662s default-jre-headless fontconfig fontconfig-config fonts-dejavu-core 662s fonts-dejavu-mono gtk-update-icon-cache hicolor-icon-theme 662s humanity-icon-theme java-common libapache-pom-java libasound2 662s libasound2-data libatk1.0-0 libavahi-client3 libavahi-common-data 662s libavahi-common3 libbarclay-java libcairo2 libcommons-codec-java 662s libcommons-compress-java libcommons-io-java libcommons-jexl2-java 662s libcommons-lang3-java libcommons-logging-java libcommons-math3-java 662s libcommons-parent-java libcups2 libdatrie1 libdeflate0 libdrm-amdgpu1 662s libdrm-nouveau2 libdrm-radeon1 libfontconfig1 libfreemarker-java 662s libgatk-native-bindings-java libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common 662s libgif7 libgkl-java libgl1 libgl1-mesa-dri libglapi-mesa libglvnd0 662s libglx-mesa0 libglx0 libgoogle-gson-java libgraphite2-3 libgtk2.0-0 662s libgtk2.0-common libharfbuzz0b libhtsjdk-java libhttpclient-java 662s libhttpcore-java libjbig0 libjoptsimple-java libjpeg-turbo8 libjpeg8 662s liblcms2-2 liblerc4 liblightcouch-java libllvm17 liblog4j2-java 662s libmbedcrypto7 libmbedtls14 libmbedx509-1 libmjson-java libmongodb-java 662s libncbi-ngs3 libncbi-vdb3 libngs-java libngs-jni libpango-1.0-0 662s libpangocairo-1.0-0 libpangoft2-1.0-0 libpcsclite1 libpicard-java 662s libpixman-1-0 librhino-java libsharpyuv0 libslf4j-java libsnappy-java 662s libsnappy-jni libsnappy1v5 libthai-data libthai0 libtiff6 libvulkan1 662s libwebp7 libx11-xcb1 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 662s libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 662s libxcomposite1 libxcursor1 libxdamage1 libxfixes3 libxi6 libxinerama1 662s libxrandr2 libxrender1 libxshmfence1 libxtst6 libxxf86vm1 ncbi-vdb-data 662s openjdk-21-jre openjdk-21-jre-headless picard-tools ubuntu-mono x11-common 662s Suggested packages: 662s libasound2-plugins alsa-utils libasm-java libxz-java libcommons-io-java-doc 662s libavalon-framework-java libexcalibur-logkit-java liblog4j1.2-java 662s cups-common jython libdom4j-java libjaxen-java libjdom1-java libxalan2-java 662s libgoogle-gson-java-doc gvfs libjoptsimple-java-doc liblcms2-utils 662s libactivation-java libcommons-csv-java libconversant-disruptor-java 662s libdisruptor-java libgeronimo-jms-1.1-spec-java 662s libjackson2-dataformat-xml-java libjackson2-dataformat-yaml libjansi-java 662s libjctools-java libjeromq-java libmail-java libwoodstox-java libngs-java-doc 662s pcscd rhino libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic 662s fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic 662s Recommended packages: 662s librsvg2-common alsa-ucm-conf alsa-topology-conf libgdk-pixbuf2.0-bin 662s libgkl-jni libgl1-amber-dri libgail-common libgtk2.0-bin r-base-core 662s mesa-vulkan-drivers | vulkan-icd libatk-wrapper-java-jni fonts-dejavu-extra 662s The following NEW packages will be installed: 662s adwaita-icon-theme at-spi2-common autopkgtest-satdep ca-certificates-java 662s default-jre default-jre-headless fontconfig fontconfig-config 662s fonts-dejavu-core fonts-dejavu-mono gtk-update-icon-cache hicolor-icon-theme 662s humanity-icon-theme java-common libapache-pom-java libasound2 662s libasound2-data libatk1.0-0 libavahi-client3 libavahi-common-data 662s libavahi-common3 libbarclay-java libcairo2 libcommons-codec-java 662s libcommons-compress-java libcommons-io-java libcommons-jexl2-java 662s libcommons-lang3-java libcommons-logging-java libcommons-math3-java 662s libcommons-parent-java libcups2 libdatrie1 libdeflate0 libdrm-amdgpu1 662s libdrm-nouveau2 libdrm-radeon1 libfontconfig1 libfreemarker-java 662s libgatk-native-bindings-java libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common 662s libgif7 libgkl-java libgl1 libgl1-mesa-dri libglapi-mesa libglvnd0 662s libglx-mesa0 libglx0 libgoogle-gson-java libgraphite2-3 libgtk2.0-0 662s libgtk2.0-common libharfbuzz0b libhtsjdk-java libhttpclient-java 662s libhttpcore-java libjbig0 libjoptsimple-java libjpeg-turbo8 libjpeg8 662s liblcms2-2 liblerc4 liblightcouch-java libllvm17 liblog4j2-java 662s libmbedcrypto7 libmbedtls14 libmbedx509-1 libmjson-java libmongodb-java 662s libncbi-ngs3 libncbi-vdb3 libngs-java libngs-jni libpango-1.0-0 662s libpangocairo-1.0-0 libpangoft2-1.0-0 libpcsclite1 libpicard-java 662s libpixman-1-0 librhino-java libsharpyuv0 libslf4j-java libsnappy-java 662s libsnappy-jni libsnappy1v5 libthai-data libthai0 libtiff6 libvulkan1 662s libwebp7 libx11-xcb1 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 662s libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 662s libxcomposite1 libxcursor1 libxdamage1 libxfixes3 libxi6 libxinerama1 662s libxrandr2 libxrender1 libxshmfence1 libxtst6 libxxf86vm1 ncbi-vdb-data 662s openjdk-21-jre openjdk-21-jre-headless picard-tools ubuntu-mono x11-common 662s 0 upgraded, 120 newly installed, 0 to remove and 0 not upgraded. 662s Need to get 110 MB/110 MB of archives. 662s After this operation, 453 MB of additional disk space will be used. 662s Get:1 /tmp/autopkgtest.NqLhrw/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [708 B] 662s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-3 [7624 B] 662s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 663s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 663s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 663s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 663s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 663s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 663s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 663s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 663s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.10+dfsg-3 [144 kB] 663s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 gtk-update-icon-cache arm64 3.24.40-2ubuntu1 [50.5 kB] 663s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 hicolor-icon-theme all 0.17-2 [9976 B] 663s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 humanity-icon-theme all 0.6.16 [1282 kB] 663s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-mono all 24.04-0ubuntu1 [151 kB] 663s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 adwaita-icon-theme all 46~rc-1 [723 kB] 663s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 at-spi2-common all 2.50.0-1 [7864 B] 663s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 ca-certificates-java all 20240118 [11.6 kB] 663s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 java-common all 0.75+exp1 [6798 B] 663s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-common-data arm64 0.8-13ubuntu2 [29.5 kB] 663s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-common3 arm64 0.8-13ubuntu2 [23.2 kB] 663s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-client3 arm64 0.8-13ubuntu2 [27.3 kB] 663s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libcups2 arm64 2.4.6-0ubuntu3 [270 kB] 663s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] 663s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 663s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 666s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 666s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 666s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libasound2-data all 1.2.10-3build1 [20.7 kB] 666s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libasound2 arm64 1.2.10-3build1 [386 kB] 666s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 666s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 666s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libpcsclite1 arm64 2.0.0-1 [21.2 kB] 666s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 openjdk-21-jre-headless arm64 21.0.2+13-2 [45.8 MB] 667s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 default-jre-headless arm64 2:1.21-75+exp1 [3096 B] 667s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libgtk2.0-common all 2.24.33-2ubuntu2 [125 kB] 667s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libatk1.0-0 arm64 2.50.0-1 [53.8 kB] 667s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 667s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 667s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 667s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 667s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 667s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 667s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 667s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 667s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 667s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 667s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 667s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 667s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libxcomposite1 arm64 1:0.4.5-1build2 [7080 B] 667s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libxfixes3 arm64 1:6.0.0-2 [11.0 kB] 667s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 libxcursor1 arm64 1:1.2.1-1 [21.3 kB] 667s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 libxdamage1 arm64 1:1.1.6-1 [6032 B] 667s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libxi6 arm64 2:1.8.1-1 [31.9 kB] 667s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 libxinerama1 arm64 2:1.1.4-3 [7056 B] 667s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 libxrandr2 arm64 2:1.5.2-2 [19.6 kB] 667s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 libgtk2.0-0 arm64 2.24.33-2ubuntu2 [1981 kB] 667s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libglvnd0 arm64 1.7.0-1 [60.0 kB] 667s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libglapi-mesa arm64 24.0.1-1ubuntu1 [57.8 kB] 667s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 libx11-xcb1 arm64 2:1.8.7-1 [7836 B] 667s Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-dri2-0 arm64 1.15-1 [7244 B] 667s Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-dri3-0 arm64 1.15-1 [7108 B] 667s Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-glx0 arm64 1.15-1 [25.2 kB] 667s Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-present0 arm64 1.15-1 [5732 B] 667s Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-randr0 arm64 1.15-1 [18.2 kB] 667s Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-sync1 arm64 1.15-1 [9412 B] 667s Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-xfixes0 arm64 1.15-1 [10.3 kB] 667s Get:68 http://ftpmaster.internal/ubuntu noble/main arm64 libxshmfence1 arm64 1.3-1build4 [5444 B] 667s Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 libxxf86vm1 arm64 1:1.1.4-1build3 [10.3 kB] 667s Get:70 http://ftpmaster.internal/ubuntu noble/main arm64 libvulkan1 arm64 1.3.275.0-1 [150 kB] 667s Get:71 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-amdgpu1 arm64 2.4.120-2 [20.4 kB] 667s Get:72 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-nouveau2 arm64 2.4.120-2 [17.8 kB] 667s Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-radeon1 arm64 2.4.120-2 [20.9 kB] 667s Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 libllvm17 arm64 1:17.0.6-5build1 [25.0 MB] 668s Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 libgl1-mesa-dri arm64 24.0.1-1ubuntu1 [8226 kB] 668s Get:76 http://ftpmaster.internal/ubuntu noble/main arm64 libglx-mesa0 arm64 24.0.1-1ubuntu1 [166 kB] 668s Get:77 http://ftpmaster.internal/ubuntu noble/main arm64 libglx0 arm64 1.7.0-1 [32.4 kB] 668s Get:78 http://ftpmaster.internal/ubuntu noble/main arm64 libgl1 arm64 1.7.0-1 [107 kB] 668s Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 libgif7 arm64 5.2.1-2.5 [34.2 kB] 668s Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 669s Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 libxtst6 arm64 2:1.2.3-1.1 [13.7 kB] 669s Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 openjdk-21-jre arm64 21.0.2+13-2 [226 kB] 669s Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 default-jre arm64 2:1.21-75+exp1 [922 B] 669s Get:84 http://ftpmaster.internal/ubuntu noble/universe arm64 libapache-pom-java all 29-2 [5284 B] 669s Get:85 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-parent-java all 56-1 [10.7 kB] 669s Get:86 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-lang3-java all 3.14.0-1 [586 kB] 669s Get:87 http://ftpmaster.internal/ubuntu noble/universe arm64 libfreemarker-java all 2.3.32-2 [1542 kB] 670s Get:88 http://ftpmaster.internal/ubuntu noble/universe arm64 libgoogle-gson-java all 2.10.1-1 [252 kB] 670s Get:89 http://ftpmaster.internal/ubuntu noble/universe arm64 libjoptsimple-java all 5.0.4-4 [73.1 kB] 670s Get:90 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-codec-java all 1.16.0-1 [306 kB] 670s Get:91 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 670s Get:92 http://ftpmaster.internal/ubuntu noble/universe arm64 libhttpcore-java all 4.4.16-1 [612 kB] 670s Get:93 http://ftpmaster.internal/ubuntu noble/universe arm64 libhttpclient-java all 4.5.14-1 [1241 kB] 670s Get:94 http://ftpmaster.internal/ubuntu noble/universe arm64 liblightcouch-java all 0.2.0-1 [74.2 kB] 670s Get:95 http://ftpmaster.internal/ubuntu noble/universe arm64 libmongodb-java all 3.6.3-2 [1899 kB] 670s Get:96 http://ftpmaster.internal/ubuntu noble/universe arm64 libslf4j-java all 1.7.32-1 [141 kB] 670s Get:97 http://ftpmaster.internal/ubuntu noble/universe arm64 liblog4j2-java all 2.19.0-2 [2294 kB] 670s Get:98 http://ftpmaster.internal/ubuntu noble/universe arm64 libbarclay-java all 5.0.0+dfsg-1 [108 kB] 670s Get:99 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-compress-java all 1.25.0-1 [612 kB] 670s Get:100 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-io-java all 2.11.0-2 [297 kB] 670s Get:101 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-jexl2-java all 2.1.1-6 [250 kB] 670s Get:102 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-math3-java all 3.6.1-3 [2016 kB] 670s Get:103 http://ftpmaster.internal/ubuntu noble/universe arm64 libgatk-native-bindings-java all 1.0.0+dfsg-2 [8014 B] 670s Get:104 http://ftpmaster.internal/ubuntu noble/universe arm64 libmjson-java all 1.4.0-3 [60.4 kB] 670s Get:105 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedcrypto7 arm64 2.28.7-1ubuntu1 [206 kB] 670s Get:106 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedx509-1 arm64 2.28.7-1ubuntu1 [46.8 kB] 670s Get:107 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedtls14 arm64 2.28.7-1ubuntu1 [82.0 kB] 670s Get:108 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-vdb-data all 3.0.2+dfsg-2 [65.8 kB] 670s Get:109 http://ftpmaster.internal/ubuntu noble/universe arm64 libncbi-vdb3 arm64 3.0.2+dfsg-2 [1130 kB] 670s Get:110 http://ftpmaster.internal/ubuntu noble/universe arm64 libncbi-ngs3 arm64 3.0.3+dfsg-6ubuntu1 [146 kB] 670s Get:111 http://ftpmaster.internal/ubuntu noble/universe arm64 libngs-jni arm64 3.0.3+dfsg-6ubuntu1 [4832 B] 670s Get:112 http://ftpmaster.internal/ubuntu noble/universe arm64 libngs-java arm64 3.0.3+dfsg-6ubuntu1 [91.8 kB] 670s Get:113 http://ftpmaster.internal/ubuntu noble/universe arm64 librhino-java all 1.7.14-2.1 [1330 kB] 670s Get:114 http://ftpmaster.internal/ubuntu noble/main arm64 libsnappy1v5 arm64 1.1.10-1 [28.2 kB] 670s Get:115 http://ftpmaster.internal/ubuntu noble/universe arm64 libsnappy-jni arm64 1.1.10.5-1 [6542 B] 670s Get:116 http://ftpmaster.internal/ubuntu noble/universe arm64 libsnappy-java all 1.1.10.5-1 [83.6 kB] 670s Get:117 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtsjdk-java all 4.1.0+dfsg-1 [1821 kB] 670s Get:118 http://ftpmaster.internal/ubuntu noble/universe arm64 libgkl-java all 0.8.11+dfsg-2 [24.8 kB] 670s Get:119 http://ftpmaster.internal/ubuntu noble/universe arm64 libpicard-java all 3.1.1+dfsg-1 [1731 kB] 670s Get:120 http://ftpmaster.internal/ubuntu noble/universe arm64 picard-tools all 3.1.1+dfsg-1 [308 kB] 671s Fetched 110 MB in 8s (14.0 MB/s) 671s Selecting previously unselected package libgdk-pixbuf2.0-common. 671s (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 ... 75468 files and directories currently installed.) 671s Preparing to unpack .../000-libgdk-pixbuf2.0-common_2.42.10+dfsg-3_all.deb ... 671s Unpacking libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ... 671s Selecting previously unselected package libjpeg-turbo8:arm64. 671s Preparing to unpack .../001-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 671s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 671s Selecting previously unselected package libjpeg8:arm64. 671s Preparing to unpack .../002-libjpeg8_8c-2ubuntu11_arm64.deb ... 671s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 671s Selecting previously unselected package libdeflate0:arm64. 671s Preparing to unpack .../003-libdeflate0_1.19-1_arm64.deb ... 671s Unpacking libdeflate0:arm64 (1.19-1) ... 671s Selecting previously unselected package libjbig0:arm64. 671s Preparing to unpack .../004-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 671s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 671s Selecting previously unselected package liblerc4:arm64. 671s Preparing to unpack .../005-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 671s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 671s Selecting previously unselected package libsharpyuv0:arm64. 671s Preparing to unpack .../006-libsharpyuv0_1.3.2-0.4_arm64.deb ... 671s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 671s Selecting previously unselected package libwebp7:arm64. 671s Preparing to unpack .../007-libwebp7_1.3.2-0.4_arm64.deb ... 671s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 671s Selecting previously unselected package libtiff6:arm64. 671s Preparing to unpack .../008-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 671s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 671s Selecting previously unselected package libgdk-pixbuf-2.0-0:arm64. 671s Preparing to unpack .../009-libgdk-pixbuf-2.0-0_2.42.10+dfsg-3_arm64.deb ... 671s Unpacking libgdk-pixbuf-2.0-0:arm64 (2.42.10+dfsg-3) ... 671s Selecting previously unselected package gtk-update-icon-cache. 671s Preparing to unpack .../010-gtk-update-icon-cache_3.24.40-2ubuntu1_arm64.deb ... 671s Unpacking gtk-update-icon-cache (3.24.40-2ubuntu1) ... 672s Selecting previously unselected package hicolor-icon-theme. 672s Preparing to unpack .../011-hicolor-icon-theme_0.17-2_all.deb ... 672s Unpacking hicolor-icon-theme (0.17-2) ... 672s Selecting previously unselected package humanity-icon-theme. 672s Preparing to unpack .../012-humanity-icon-theme_0.6.16_all.deb ... 672s Unpacking humanity-icon-theme (0.6.16) ... 673s Selecting previously unselected package ubuntu-mono. 673s Preparing to unpack .../013-ubuntu-mono_24.04-0ubuntu1_all.deb ... 673s Unpacking ubuntu-mono (24.04-0ubuntu1) ... 676s Selecting previously unselected package adwaita-icon-theme. 676s Preparing to unpack .../014-adwaita-icon-theme_46~rc-1_all.deb ... 676s Unpacking adwaita-icon-theme (46~rc-1) ... 676s Selecting previously unselected package at-spi2-common. 676s Preparing to unpack .../015-at-spi2-common_2.50.0-1_all.deb ... 676s Unpacking at-spi2-common (2.50.0-1) ... 676s Selecting previously unselected package ca-certificates-java. 676s Preparing to unpack .../016-ca-certificates-java_20240118_all.deb ... 676s Unpacking ca-certificates-java (20240118) ... 676s Selecting previously unselected package java-common. 676s Preparing to unpack .../017-java-common_0.75+exp1_all.deb ... 676s Unpacking java-common (0.75+exp1) ... 676s Selecting previously unselected package libavahi-common-data:arm64. 676s Preparing to unpack .../018-libavahi-common-data_0.8-13ubuntu2_arm64.deb ... 676s Unpacking libavahi-common-data:arm64 (0.8-13ubuntu2) ... 676s Selecting previously unselected package libavahi-common3:arm64. 676s Preparing to unpack .../019-libavahi-common3_0.8-13ubuntu2_arm64.deb ... 676s Unpacking libavahi-common3:arm64 (0.8-13ubuntu2) ... 676s Selecting previously unselected package libavahi-client3:arm64. 676s Preparing to unpack .../020-libavahi-client3_0.8-13ubuntu2_arm64.deb ... 676s Unpacking libavahi-client3:arm64 (0.8-13ubuntu2) ... 676s Selecting previously unselected package libcups2:arm64. 676s Preparing to unpack .../021-libcups2_2.4.6-0ubuntu3_arm64.deb ... 676s Unpacking libcups2:arm64 (2.4.6-0ubuntu3) ... 676s Selecting previously unselected package liblcms2-2:arm64. 676s Preparing to unpack .../022-liblcms2-2_2.14-2_arm64.deb ... 676s Unpacking liblcms2-2:arm64 (2.14-2) ... 676s Selecting previously unselected package fonts-dejavu-mono. 676s Preparing to unpack .../023-fonts-dejavu-mono_2.37-8_all.deb ... 676s Unpacking fonts-dejavu-mono (2.37-8) ... 676s Selecting previously unselected package fonts-dejavu-core. 676s Preparing to unpack .../024-fonts-dejavu-core_2.37-8_all.deb ... 676s Unpacking fonts-dejavu-core (2.37-8) ... 676s Selecting previously unselected package fontconfig-config. 676s Preparing to unpack .../025-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 676s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 676s Selecting previously unselected package libfontconfig1:arm64. 676s Preparing to unpack .../026-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 676s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 676s Selecting previously unselected package libasound2-data. 676s Preparing to unpack .../027-libasound2-data_1.2.10-3build1_all.deb ... 676s Unpacking libasound2-data (1.2.10-3build1) ... 676s Selecting previously unselected package libasound2:arm64. 676s Preparing to unpack .../028-libasound2_1.2.10-3build1_arm64.deb ... 676s Unpacking libasound2:arm64 (1.2.10-3build1) ... 676s Selecting previously unselected package libgraphite2-3:arm64. 676s Preparing to unpack .../029-libgraphite2-3_1.3.14-2_arm64.deb ... 676s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 676s Selecting previously unselected package libharfbuzz0b:arm64. 676s Preparing to unpack .../030-libharfbuzz0b_8.3.0-2_arm64.deb ... 676s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 676s Selecting previously unselected package libpcsclite1:arm64. 676s Preparing to unpack .../031-libpcsclite1_2.0.0-1_arm64.deb ... 676s Unpacking libpcsclite1:arm64 (2.0.0-1) ... 676s Selecting previously unselected package openjdk-21-jre-headless:arm64. 676s Preparing to unpack .../032-openjdk-21-jre-headless_21.0.2+13-2_arm64.deb ... 676s Unpacking openjdk-21-jre-headless:arm64 (21.0.2+13-2) ... 678s Selecting previously unselected package default-jre-headless. 678s Preparing to unpack .../033-default-jre-headless_2%3a1.21-75+exp1_arm64.deb ... 678s Unpacking default-jre-headless (2:1.21-75+exp1) ... 678s Selecting previously unselected package libgtk2.0-common. 678s Preparing to unpack .../034-libgtk2.0-common_2.24.33-2ubuntu2_all.deb ... 678s Unpacking libgtk2.0-common (2.24.33-2ubuntu2) ... 678s Selecting previously unselected package libatk1.0-0:arm64. 678s Preparing to unpack .../035-libatk1.0-0_2.50.0-1_arm64.deb ... 678s Unpacking libatk1.0-0:arm64 (2.50.0-1) ... 678s Selecting previously unselected package libpixman-1-0:arm64. 678s Preparing to unpack .../036-libpixman-1-0_0.42.2-1_arm64.deb ... 678s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 678s Selecting previously unselected package libxcb-render0:arm64. 678s Preparing to unpack .../037-libxcb-render0_1.15-1_arm64.deb ... 678s Unpacking libxcb-render0:arm64 (1.15-1) ... 678s Selecting previously unselected package libxcb-shm0:arm64. 678s Preparing to unpack .../038-libxcb-shm0_1.15-1_arm64.deb ... 678s Unpacking libxcb-shm0:arm64 (1.15-1) ... 678s Selecting previously unselected package libxrender1:arm64. 678s Preparing to unpack .../039-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 678s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 678s Selecting previously unselected package libcairo2:arm64. 678s Preparing to unpack .../040-libcairo2_1.18.0-1_arm64.deb ... 678s Unpacking libcairo2:arm64 (1.18.0-1) ... 678s Selecting previously unselected package fontconfig. 678s Preparing to unpack .../041-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 678s Unpacking fontconfig (2.15.0-1ubuntu1) ... 678s Selecting previously unselected package libthai-data. 678s Preparing to unpack .../042-libthai-data_0.1.29-2_all.deb ... 678s Unpacking libthai-data (0.1.29-2) ... 678s Selecting previously unselected package libdatrie1:arm64. 678s Preparing to unpack .../043-libdatrie1_0.2.13-3_arm64.deb ... 678s Unpacking libdatrie1:arm64 (0.2.13-3) ... 678s Selecting previously unselected package libthai0:arm64. 679s Preparing to unpack .../044-libthai0_0.1.29-2_arm64.deb ... 679s Unpacking libthai0:arm64 (0.1.29-2) ... 679s Selecting previously unselected package libpango-1.0-0:arm64. 679s Preparing to unpack .../045-libpango-1.0-0_1.51.0+ds-4_arm64.deb ... 679s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ... 679s Selecting previously unselected package libpangoft2-1.0-0:arm64. 679s Preparing to unpack .../046-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 679s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 679s Selecting previously unselected package libpangocairo-1.0-0:arm64. 679s Preparing to unpack .../047-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ... 679s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 679s Selecting previously unselected package libxcomposite1:arm64. 679s Preparing to unpack .../048-libxcomposite1_1%3a0.4.5-1build2_arm64.deb ... 679s Unpacking libxcomposite1:arm64 (1:0.4.5-1build2) ... 679s Selecting previously unselected package libxfixes3:arm64. 679s Preparing to unpack .../049-libxfixes3_1%3a6.0.0-2_arm64.deb ... 679s Unpacking libxfixes3:arm64 (1:6.0.0-2) ... 679s Selecting previously unselected package libxcursor1:arm64. 679s Preparing to unpack .../050-libxcursor1_1%3a1.2.1-1_arm64.deb ... 679s Unpacking libxcursor1:arm64 (1:1.2.1-1) ... 679s Selecting previously unselected package libxdamage1:arm64. 679s Preparing to unpack .../051-libxdamage1_1%3a1.1.6-1_arm64.deb ... 679s Unpacking libxdamage1:arm64 (1:1.1.6-1) ... 679s Selecting previously unselected package libxi6:arm64. 679s Preparing to unpack .../052-libxi6_2%3a1.8.1-1_arm64.deb ... 679s Unpacking libxi6:arm64 (2:1.8.1-1) ... 679s Selecting previously unselected package libxinerama1:arm64. 679s Preparing to unpack .../053-libxinerama1_2%3a1.1.4-3_arm64.deb ... 679s Unpacking libxinerama1:arm64 (2:1.1.4-3) ... 679s Selecting previously unselected package libxrandr2:arm64. 679s Preparing to unpack .../054-libxrandr2_2%3a1.5.2-2_arm64.deb ... 679s Unpacking libxrandr2:arm64 (2:1.5.2-2) ... 679s Selecting previously unselected package libgtk2.0-0:arm64. 679s Preparing to unpack .../055-libgtk2.0-0_2.24.33-2ubuntu2_arm64.deb ... 679s Unpacking libgtk2.0-0:arm64 (2.24.33-2ubuntu2) ... 679s Selecting previously unselected package libglvnd0:arm64. 679s Preparing to unpack .../056-libglvnd0_1.7.0-1_arm64.deb ... 679s Unpacking libglvnd0:arm64 (1.7.0-1) ... 679s Selecting previously unselected package libglapi-mesa:arm64. 679s Preparing to unpack .../057-libglapi-mesa_24.0.1-1ubuntu1_arm64.deb ... 679s Unpacking libglapi-mesa:arm64 (24.0.1-1ubuntu1) ... 679s Selecting previously unselected package libx11-xcb1:arm64. 679s Preparing to unpack .../058-libx11-xcb1_2%3a1.8.7-1_arm64.deb ... 679s Unpacking libx11-xcb1:arm64 (2:1.8.7-1) ... 679s Selecting previously unselected package libxcb-dri2-0:arm64. 679s Preparing to unpack .../059-libxcb-dri2-0_1.15-1_arm64.deb ... 679s Unpacking libxcb-dri2-0:arm64 (1.15-1) ... 679s Selecting previously unselected package libxcb-dri3-0:arm64. 679s Preparing to unpack .../060-libxcb-dri3-0_1.15-1_arm64.deb ... 679s Unpacking libxcb-dri3-0:arm64 (1.15-1) ... 679s Selecting previously unselected package libxcb-glx0:arm64. 679s Preparing to unpack .../061-libxcb-glx0_1.15-1_arm64.deb ... 679s Unpacking libxcb-glx0:arm64 (1.15-1) ... 679s Selecting previously unselected package libxcb-present0:arm64. 679s Preparing to unpack .../062-libxcb-present0_1.15-1_arm64.deb ... 679s Unpacking libxcb-present0:arm64 (1.15-1) ... 679s Selecting previously unselected package libxcb-randr0:arm64. 680s Preparing to unpack .../063-libxcb-randr0_1.15-1_arm64.deb ... 680s Unpacking libxcb-randr0:arm64 (1.15-1) ... 680s Selecting previously unselected package libxcb-sync1:arm64. 680s Preparing to unpack .../064-libxcb-sync1_1.15-1_arm64.deb ... 680s Unpacking libxcb-sync1:arm64 (1.15-1) ... 680s Selecting previously unselected package libxcb-xfixes0:arm64. 680s Preparing to unpack .../065-libxcb-xfixes0_1.15-1_arm64.deb ... 680s Unpacking libxcb-xfixes0:arm64 (1.15-1) ... 680s Selecting previously unselected package libxshmfence1:arm64. 680s Preparing to unpack .../066-libxshmfence1_1.3-1build4_arm64.deb ... 680s Unpacking libxshmfence1:arm64 (1.3-1build4) ... 680s Selecting previously unselected package libxxf86vm1:arm64. 680s Preparing to unpack .../067-libxxf86vm1_1%3a1.1.4-1build3_arm64.deb ... 680s Unpacking libxxf86vm1:arm64 (1:1.1.4-1build3) ... 680s Selecting previously unselected package libvulkan1:arm64. 680s Preparing to unpack .../068-libvulkan1_1.3.275.0-1_arm64.deb ... 680s Unpacking libvulkan1:arm64 (1.3.275.0-1) ... 680s Selecting previously unselected package libdrm-amdgpu1:arm64. 680s Preparing to unpack .../069-libdrm-amdgpu1_2.4.120-2_arm64.deb ... 680s Unpacking libdrm-amdgpu1:arm64 (2.4.120-2) ... 680s Selecting previously unselected package libdrm-nouveau2:arm64. 680s Preparing to unpack .../070-libdrm-nouveau2_2.4.120-2_arm64.deb ... 680s Unpacking libdrm-nouveau2:arm64 (2.4.120-2) ... 680s Selecting previously unselected package libdrm-radeon1:arm64. 680s Preparing to unpack .../071-libdrm-radeon1_2.4.120-2_arm64.deb ... 680s Unpacking libdrm-radeon1:arm64 (2.4.120-2) ... 680s Selecting previously unselected package libllvm17:arm64. 680s Preparing to unpack .../072-libllvm17_1%3a17.0.6-5build1_arm64.deb ... 680s Unpacking libllvm17:arm64 (1:17.0.6-5build1) ... 691s Selecting previously unselected package libgl1-mesa-dri:arm64. 691s Preparing to unpack .../073-libgl1-mesa-dri_24.0.1-1ubuntu1_arm64.deb ... 691s Unpacking libgl1-mesa-dri:arm64 (24.0.1-1ubuntu1) ... 691s Selecting previously unselected package libglx-mesa0:arm64. 691s Preparing to unpack .../074-libglx-mesa0_24.0.1-1ubuntu1_arm64.deb ... 691s Unpacking libglx-mesa0:arm64 (24.0.1-1ubuntu1) ... 691s Selecting previously unselected package libglx0:arm64. 691s Preparing to unpack .../075-libglx0_1.7.0-1_arm64.deb ... 691s Unpacking libglx0:arm64 (1.7.0-1) ... 691s Selecting previously unselected package libgl1:arm64. 691s Preparing to unpack .../076-libgl1_1.7.0-1_arm64.deb ... 691s Unpacking libgl1:arm64 (1.7.0-1) ... 691s Selecting previously unselected package libgif7:arm64. 691s Preparing to unpack .../077-libgif7_5.2.1-2.5_arm64.deb ... 691s Unpacking libgif7:arm64 (5.2.1-2.5) ... 691s Selecting previously unselected package x11-common. 691s Preparing to unpack .../078-x11-common_1%3a7.7+23ubuntu2_all.deb ... 691s Unpacking x11-common (1:7.7+23ubuntu2) ... 691s Selecting previously unselected package libxtst6:arm64. 691s Preparing to unpack .../079-libxtst6_2%3a1.2.3-1.1_arm64.deb ... 691s Unpacking libxtst6:arm64 (2:1.2.3-1.1) ... 691s Selecting previously unselected package openjdk-21-jre:arm64. 691s Preparing to unpack .../080-openjdk-21-jre_21.0.2+13-2_arm64.deb ... 691s Unpacking openjdk-21-jre:arm64 (21.0.2+13-2) ... 691s Selecting previously unselected package default-jre. 691s Preparing to unpack .../081-default-jre_2%3a1.21-75+exp1_arm64.deb ... 691s Unpacking default-jre (2:1.21-75+exp1) ... 691s Selecting previously unselected package libapache-pom-java. 691s Preparing to unpack .../082-libapache-pom-java_29-2_all.deb ... 691s Unpacking libapache-pom-java (29-2) ... 691s Selecting previously unselected package libcommons-parent-java. 691s Preparing to unpack .../083-libcommons-parent-java_56-1_all.deb ... 691s Unpacking libcommons-parent-java (56-1) ... 691s Selecting previously unselected package libcommons-lang3-java. 691s Preparing to unpack .../084-libcommons-lang3-java_3.14.0-1_all.deb ... 691s Unpacking libcommons-lang3-java (3.14.0-1) ... 691s Selecting previously unselected package libfreemarker-java. 691s Preparing to unpack .../085-libfreemarker-java_2.3.32-2_all.deb ... 691s Unpacking libfreemarker-java (2.3.32-2) ... 691s Selecting previously unselected package libgoogle-gson-java. 691s Preparing to unpack .../086-libgoogle-gson-java_2.10.1-1_all.deb ... 691s Unpacking libgoogle-gson-java (2.10.1-1) ... 691s Selecting previously unselected package libjoptsimple-java. 691s Preparing to unpack .../087-libjoptsimple-java_5.0.4-4_all.deb ... 691s Unpacking libjoptsimple-java (5.0.4-4) ... 691s Selecting previously unselected package libcommons-codec-java. 691s Preparing to unpack .../088-libcommons-codec-java_1.16.0-1_all.deb ... 691s Unpacking libcommons-codec-java (1.16.0-1) ... 691s Selecting previously unselected package libcommons-logging-java. 691s Preparing to unpack .../089-libcommons-logging-java_1.3.0-1ubuntu1_all.deb ... 691s Unpacking libcommons-logging-java (1.3.0-1ubuntu1) ... 691s Selecting previously unselected package libhttpcore-java. 691s Preparing to unpack .../090-libhttpcore-java_4.4.16-1_all.deb ... 691s Unpacking libhttpcore-java (4.4.16-1) ... 691s Selecting previously unselected package libhttpclient-java. 691s Preparing to unpack .../091-libhttpclient-java_4.5.14-1_all.deb ... 691s Unpacking libhttpclient-java (4.5.14-1) ... 691s Selecting previously unselected package liblightcouch-java. 691s Preparing to unpack .../092-liblightcouch-java_0.2.0-1_all.deb ... 691s Unpacking liblightcouch-java (0.2.0-1) ... 691s Selecting previously unselected package libmongodb-java. 691s Preparing to unpack .../093-libmongodb-java_3.6.3-2_all.deb ... 691s Unpacking libmongodb-java (3.6.3-2) ... 691s Selecting previously unselected package libslf4j-java. 691s Preparing to unpack .../094-libslf4j-java_1.7.32-1_all.deb ... 691s Unpacking libslf4j-java (1.7.32-1) ... 691s Selecting previously unselected package liblog4j2-java. 691s Preparing to unpack .../095-liblog4j2-java_2.19.0-2_all.deb ... 691s Unpacking liblog4j2-java (2.19.0-2) ... 691s Selecting previously unselected package libbarclay-java. 691s Preparing to unpack .../096-libbarclay-java_5.0.0+dfsg-1_all.deb ... 691s Unpacking libbarclay-java (5.0.0+dfsg-1) ... 691s Selecting previously unselected package libcommons-compress-java. 691s Preparing to unpack .../097-libcommons-compress-java_1.25.0-1_all.deb ... 691s Unpacking libcommons-compress-java (1.25.0-1) ... 691s Selecting previously unselected package libcommons-io-java. 691s Preparing to unpack .../098-libcommons-io-java_2.11.0-2_all.deb ... 691s Unpacking libcommons-io-java (2.11.0-2) ... 691s Selecting previously unselected package libcommons-jexl2-java. 691s Preparing to unpack .../099-libcommons-jexl2-java_2.1.1-6_all.deb ... 691s Unpacking libcommons-jexl2-java (2.1.1-6) ... 691s Selecting previously unselected package libcommons-math3-java. 691s Preparing to unpack .../100-libcommons-math3-java_3.6.1-3_all.deb ... 691s Unpacking libcommons-math3-java (3.6.1-3) ... 691s Selecting previously unselected package libgatk-native-bindings-java. 691s Preparing to unpack .../101-libgatk-native-bindings-java_1.0.0+dfsg-2_all.deb ... 691s Unpacking libgatk-native-bindings-java (1.0.0+dfsg-2) ... 691s Selecting previously unselected package libmjson-java. 691s Preparing to unpack .../102-libmjson-java_1.4.0-3_all.deb ... 691s Unpacking libmjson-java (1.4.0-3) ... 691s Selecting previously unselected package libmbedcrypto7:arm64. 691s Preparing to unpack .../103-libmbedcrypto7_2.28.7-1ubuntu1_arm64.deb ... 691s Unpacking libmbedcrypto7:arm64 (2.28.7-1ubuntu1) ... 691s Selecting previously unselected package libmbedx509-1:arm64. 691s Preparing to unpack .../104-libmbedx509-1_2.28.7-1ubuntu1_arm64.deb ... 691s Unpacking libmbedx509-1:arm64 (2.28.7-1ubuntu1) ... 691s Selecting previously unselected package libmbedtls14:arm64. 691s Preparing to unpack .../105-libmbedtls14_2.28.7-1ubuntu1_arm64.deb ... 691s Unpacking libmbedtls14:arm64 (2.28.7-1ubuntu1) ... 691s Selecting previously unselected package ncbi-vdb-data. 691s Preparing to unpack .../106-ncbi-vdb-data_3.0.2+dfsg-2_all.deb ... 691s Unpacking ncbi-vdb-data (3.0.2+dfsg-2) ... 691s Selecting previously unselected package libncbi-vdb3:arm64. 691s Preparing to unpack .../107-libncbi-vdb3_3.0.2+dfsg-2_arm64.deb ... 691s Unpacking libncbi-vdb3:arm64 (3.0.2+dfsg-2) ... 691s Selecting previously unselected package libncbi-ngs3:arm64. 691s Preparing to unpack .../108-libncbi-ngs3_3.0.3+dfsg-6ubuntu1_arm64.deb ... 691s Unpacking libncbi-ngs3:arm64 (3.0.3+dfsg-6ubuntu1) ... 691s Selecting previously unselected package libngs-jni:arm64. 691s Preparing to unpack .../109-libngs-jni_3.0.3+dfsg-6ubuntu1_arm64.deb ... 691s Unpacking libngs-jni:arm64 (3.0.3+dfsg-6ubuntu1) ... 691s Selecting previously unselected package libngs-java:arm64. 691s Preparing to unpack .../110-libngs-java_3.0.3+dfsg-6ubuntu1_arm64.deb ... 691s Unpacking libngs-java:arm64 (3.0.3+dfsg-6ubuntu1) ... 691s Selecting previously unselected package librhino-java. 691s Preparing to unpack .../111-librhino-java_1.7.14-2.1_all.deb ... 691s Unpacking librhino-java (1.7.14-2.1) ... 691s Selecting previously unselected package libsnappy1v5:arm64. 691s Preparing to unpack .../112-libsnappy1v5_1.1.10-1_arm64.deb ... 691s Unpacking libsnappy1v5:arm64 (1.1.10-1) ... 691s Selecting previously unselected package libsnappy-jni. 691s Preparing to unpack .../113-libsnappy-jni_1.1.10.5-1_arm64.deb ... 691s Unpacking libsnappy-jni (1.1.10.5-1) ... 691s Selecting previously unselected package libsnappy-java. 691s Preparing to unpack .../114-libsnappy-java_1.1.10.5-1_all.deb ... 691s Unpacking libsnappy-java (1.1.10.5-1) ... 691s Selecting previously unselected package libhtsjdk-java. 691s Preparing to unpack .../115-libhtsjdk-java_4.1.0+dfsg-1_all.deb ... 691s Unpacking libhtsjdk-java (4.1.0+dfsg-1) ... 691s Selecting previously unselected package libgkl-java. 691s Preparing to unpack .../116-libgkl-java_0.8.11+dfsg-2_all.deb ... 691s Unpacking libgkl-java (0.8.11+dfsg-2) ... 691s Selecting previously unselected package libpicard-java. 691s Preparing to unpack .../117-libpicard-java_3.1.1+dfsg-1_all.deb ... 691s Unpacking libpicard-java (3.1.1+dfsg-1) ... 691s Selecting previously unselected package picard-tools. 691s Preparing to unpack .../118-picard-tools_3.1.1+dfsg-1_all.deb ... 691s Unpacking picard-tools (3.1.1+dfsg-1) ... 691s Selecting previously unselected package autopkgtest-satdep. 691s Preparing to unpack .../119-1-autopkgtest-satdep.deb ... 691s Unpacking autopkgtest-satdep (0) ... 691s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 691s Setting up libxcb-dri3-0:arm64 (1.15-1) ... 691s Setting up liblcms2-2:arm64 (2.14-2) ... 691s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 691s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 691s Setting up libx11-xcb1:arm64 (2:1.8.7-1) ... 691s Setting up libslf4j-java (1.7.32-1) ... 691s Setting up libdrm-nouveau2:arm64 (2.4.120-2) ... 691s Setting up libxdamage1:arm64 (1:1.1.6-1) ... 691s Setting up libxcb-xfixes0:arm64 (1.15-1) ... 691s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 691s Setting up hicolor-icon-theme (0.17-2) ... 691s Setting up libxi6:arm64 (2:1.8.1-1) ... 691s Setting up libgatk-native-bindings-java (1.0.0+dfsg-2) ... 691s Setting up java-common (0.75+exp1) ... 691s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 691s Setting up libdatrie1:arm64 (0.2.13-3) ... 691s Setting up libxcb-render0:arm64 (1.15-1) ... 691s Setting up libdrm-radeon1:arm64 (2.4.120-2) ... 691s Setting up libglvnd0:arm64 (1.7.0-1) ... 691s Setting up libgoogle-gson-java (2.10.1-1) ... 691s Setting up libmjson-java (1.4.0-3) ... 691s Setting up libxcb-glx0:arm64 (1.15-1) ... 691s Setting up libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ... 691s Setting up x11-common (1:7.7+23ubuntu2) ... 691s Setting up libdeflate0:arm64 (1.19-1) ... 691s Setting up libxcb-shm0:arm64 (1.15-1) ... 691s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 691s Setting up libxxf86vm1:arm64 (1:1.1.4-1build3) ... 691s Setting up libsnappy1v5:arm64 (1.1.10-1) ... 691s Setting up libxcb-present0:arm64 (1.15-1) ... 691s Setting up libasound2-data (1.2.10-3build1) ... 691s Setting up librhino-java (1.7.14-2.1) ... 691s Setting up libmbedcrypto7:arm64 (2.28.7-1ubuntu1) ... 691s Setting up libxfixes3:arm64 (1:6.0.0-2) ... 691s Setting up libxcb-sync1:arm64 (1.15-1) ... 691s Setting up libapache-pom-java (29-2) ... 691s Setting up libavahi-common-data:arm64 (0.8-13ubuntu2) ... 691s Setting up libxinerama1:arm64 (2:1.1.4-3) ... 691s Setting up fonts-dejavu-mono (2.37-8) ... 691s Setting up libxrandr2:arm64 (2:1.5.2-2) ... 691s Setting up fonts-dejavu-core (2.37-8) ... 691s Setting up libpcsclite1:arm64 (2.0.0-1) ... 691s Setting up libmongodb-java (3.6.3-2) ... 691s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 691s Setting up libglapi-mesa:arm64 (24.0.1-1ubuntu1) ... 691s Setting up libvulkan1:arm64 (1.3.275.0-1) ... 691s Setting up libwebp7:arm64 (1.3.2-0.4) ... 691s Setting up libxcb-dri2-0:arm64 (1.15-1) ... 691s Setting up libgif7:arm64 (5.2.1-2.5) ... 691s Setting up libfreemarker-java (2.3.32-2) ... 691s Setting up libxshmfence1:arm64 (1.3-1build4) ... 691s Setting up at-spi2-common (2.50.0-1) ... 691s Setting up libxcb-randr0:arm64 (1.15-1) ... 691s Setting up libasound2:arm64 (1.2.10-3build1) ... 691s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 691s Setting up ncbi-vdb-data (3.0.2+dfsg-2) ... 691s Setting up libthai-data (0.1.29-2) ... 691s Setting up libcommons-math3-java (3.6.1-3) ... 691s Setting up libgtk2.0-common (2.24.33-2ubuntu2) ... 691s Setting up libatk1.0-0:arm64 (2.50.0-1) ... 691s Setting up libhttpcore-java (4.4.16-1) ... 691s Setting up libjoptsimple-java (5.0.4-4) ... 691s Setting up ca-certificates-java (20240118) ... 691s No JRE found. Skipping Java certificates setup. 691s Setting up libllvm17:arm64 (1:17.0.6-5build1) ... 691s Setting up libsnappy-jni (1.1.10.5-1) ... 691s Setting up libxcomposite1:arm64 (1:0.4.5-1build2) ... 691s Setting up libdrm-amdgpu1:arm64 (2.4.120-2) ... 691s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 691s Setting up libmbedx509-1:arm64 (2.28.7-1ubuntu1) ... 691s Setting up libmbedtls14:arm64 (2.28.7-1ubuntu1) ... 691s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 691s Setting up libxtst6:arm64 (2:1.2.3-1.1) ... 691s Setting up libxcursor1:arm64 (1:1.2.1-1) ... 691s Setting up libgl1-mesa-dri:arm64 (24.0.1-1ubuntu1) ... 691s Setting up libcommons-parent-java (56-1) ... 691s Setting up libavahi-common3:arm64 (0.8-13ubuntu2) ... 691s Setting up libncbi-vdb3:arm64 (3.0.2+dfsg-2) ... 691s Setting up libcommons-logging-java (1.3.0-1ubuntu1) ... 691s Setting up libcommons-jexl2-java (2.1.1-6) ... 691s Setting up libthai0:arm64 (0.1.29-2) ... 691s Setting up libcommons-lang3-java (3.14.0-1) ... 691s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 691s Setting up libgdk-pixbuf-2.0-0:arm64 (2.42.10+dfsg-3) ... 691s Setting up libsnappy-java (1.1.10.5-1) ... 691s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 691s Setting up libcommons-codec-java (1.16.0-1) ... 691s Setting up libavahi-client3:arm64 (0.8-13ubuntu2) ... 691s Setting up libncbi-ngs3:arm64 (3.0.3+dfsg-6ubuntu1) ... 691s Setting up gtk-update-icon-cache (3.24.40-2ubuntu1) ... 691s Setting up fontconfig (2.15.0-1ubuntu1) ... 691s Regenerating fonts cache... done. 691s Setting up libngs-jni:arm64 (3.0.3+dfsg-6ubuntu1) ... 691s Setting up libglx-mesa0:arm64 (24.0.1-1ubuntu1) ... 691s Setting up libglx0:arm64 (1.7.0-1) ... 691s Setting up libcommons-compress-java (1.25.0-1) ... 691s Setting up libcommons-io-java (2.11.0-2) ... 691s Setting up libpango-1.0-0:arm64 (1.51.0+ds-4) ... 691s Setting up libcairo2:arm64 (1.18.0-1) ... 691s Setting up libgl1:arm64 (1.7.0-1) ... 691s Setting up libcups2:arm64 (2.4.6-0ubuntu3) ... 691s Setting up libhttpclient-java (4.5.14-1) ... 691s Setting up liblightcouch-java (0.2.0-1) ... 691s Setting up libngs-java:arm64 (3.0.3+dfsg-6ubuntu1) ... 691s Setting up libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 691s Setting up libhtsjdk-java (4.1.0+dfsg-1) ... 691s Setting up libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 691s Setting up openjdk-21-jre-headless:arm64 (21.0.2+13-2) ... 691s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode 691s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 691s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 691s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 691s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 691s Setting up liblog4j2-java (2.19.0-2) ... 691s Setting up libbarclay-java (5.0.0+dfsg-1) ... 691s Setting up libgkl-java (0.8.11+dfsg-2) ... 691s Setting up libpicard-java (3.1.1+dfsg-1) ... 691s Setting up adwaita-icon-theme (46~rc-1) ... 691s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode 691s Setting up libgtk2.0-0:arm64 (2.24.33-2ubuntu2) ... 691s Setting up humanity-icon-theme (0.6.16) ... 691s Setting up ubuntu-mono (24.04-0ubuntu1) ... 691s Processing triggers for man-db (2.12.0-3) ... 691s Processing triggers for libc-bin (2.39-0ubuntu2) ... 691s Processing triggers for ca-certificates-java (20240118) ... 691s Adding debian:ACCVRAIZ1.pem 691s Adding debian:AC_RAIZ_FNMT-RCM.pem 691s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 691s Adding debian:ANF_Secure_Server_Root_CA.pem 691s Adding debian:Actalis_Authentication_Root_CA.pem 691s Adding debian:AffirmTrust_Commercial.pem 691s Adding debian:AffirmTrust_Networking.pem 691s Adding debian:AffirmTrust_Premium.pem 691s Adding debian:AffirmTrust_Premium_ECC.pem 691s Adding debian:Amazon_Root_CA_1.pem 691s Adding debian:Amazon_Root_CA_2.pem 691s Adding debian:Amazon_Root_CA_3.pem 691s Adding debian:Amazon_Root_CA_4.pem 691s Adding debian:Atos_TrustedRoot_2011.pem 691s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 691s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 691s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 691s Adding debian:BJCA_Global_Root_CA1.pem 691s Adding debian:BJCA_Global_Root_CA2.pem 691s Adding debian:Baltimore_CyberTrust_Root.pem 691s Adding debian:Buypass_Class_2_Root_CA.pem 691s Adding debian:Buypass_Class_3_Root_CA.pem 691s Adding debian:CA_Disig_Root_R2.pem 691s Adding debian:CFCA_EV_ROOT.pem 691s Adding debian:COMODO_Certification_Authority.pem 691s Adding debian:COMODO_ECC_Certification_Authority.pem 691s Adding debian:COMODO_RSA_Certification_Authority.pem 691s Adding debian:Certainly_Root_E1.pem 691s Adding debian:Certainly_Root_R1.pem 691s Adding debian:Certigna.pem 691s Adding debian:Certigna_Root_CA.pem 691s Adding debian:Certum_EC-384_CA.pem 691s Adding debian:Certum_Trusted_Network_CA.pem 691s Adding debian:Certum_Trusted_Network_CA_2.pem 691s Adding debian:Certum_Trusted_Root_CA.pem 691s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 691s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 691s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 691s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 691s Adding debian:Comodo_AAA_Services_root.pem 691s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 691s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 691s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 691s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 691s Adding debian:DigiCert_Assured_ID_Root_CA.pem 691s Adding debian:DigiCert_Assured_ID_Root_G2.pem 691s Adding debian:DigiCert_Assured_ID_Root_G3.pem 691s Adding debian:DigiCert_Global_Root_CA.pem 691s Adding debian:DigiCert_Global_Root_G2.pem 691s Adding debian:DigiCert_Global_Root_G3.pem 691s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 691s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 691s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 691s Adding debian:DigiCert_Trusted_Root_G4.pem 691s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 691s Adding debian:Entrust_Root_Certification_Authority.pem 691s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 691s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 691s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 691s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 691s Adding debian:GLOBALTRUST_2020.pem 691s Adding debian:GTS_Root_R1.pem 691s Adding debian:GTS_Root_R2.pem 691s Adding debian:GTS_Root_R3.pem 691s Adding debian:GTS_Root_R4.pem 691s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 691s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 691s Adding debian:GlobalSign_Root_CA.pem 691s Adding debian:GlobalSign_Root_CA_-_R3.pem 691s Adding debian:GlobalSign_Root_CA_-_R6.pem 691s Adding debian:GlobalSign_Root_E46.pem 691s Adding debian:GlobalSign_Root_R46.pem 691s Adding debian:Go_Daddy_Class_2_CA.pem 691s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 691s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 691s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 691s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 691s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 691s Adding debian:HiPKI_Root_CA_-_G1.pem 691s Adding debian:Hongkong_Post_Root_CA_3.pem 691s Adding debian:ISRG_Root_X1.pem 691s Adding debian:ISRG_Root_X2.pem 691s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 691s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 691s Adding debian:Izenpe.com.pem 691s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 691s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 691s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 691s Adding debian:NAVER_Global_Root_Certification_Authority.pem 691s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 691s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 691s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 691s Adding debian:QuoVadis_Root_CA_1_G3.pem 691s Adding debian:QuoVadis_Root_CA_2.pem 691s Adding debian:QuoVadis_Root_CA_2_G3.pem 691s Adding debian:QuoVadis_Root_CA_3.pem 691s Adding debian:QuoVadis_Root_CA_3_G3.pem 691s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 691s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 691s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 691s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 691s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 691s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 691s Adding debian:SZAFIR_ROOT_CA2.pem 691s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 691s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 691s Adding debian:SecureSign_RootCA11.pem 691s Adding debian:SecureTrust_CA.pem 691s Adding debian:Secure_Global_CA.pem 691s Adding debian:Security_Communication_ECC_RootCA1.pem 691s Adding debian:Security_Communication_RootCA2.pem 691s Adding debian:Security_Communication_RootCA3.pem 691s Adding debian:Security_Communication_Root_CA.pem 691s Adding debian:Starfield_Class_2_CA.pem 691s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 691s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 691s Adding debian:SwissSign_Gold_CA_-_G2.pem 691s Adding debian:SwissSign_Silver_CA_-_G2.pem 691s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 691s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 691s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 691s Adding debian:TWCA_Global_Root_CA.pem 691s Adding debian:TWCA_Root_Certification_Authority.pem 691s Adding debian:TeliaSonera_Root_CA_v1.pem 691s Adding debian:Telia_Root_CA_v2.pem 691s Adding debian:TrustAsia_Global_Root_CA_G3.pem 691s Adding debian:TrustAsia_Global_Root_CA_G4.pem 691s Adding debian:Trustwave_Global_Certification_Authority.pem 691s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 691s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 691s Adding debian:TunTrust_Root_CA.pem 691s Adding debian:UCA_Extended_Validation_Root.pem 691s Adding debian:UCA_Global_G2_Root.pem 691s Adding debian:USERTrust_ECC_Certification_Authority.pem 691s Adding debian:USERTrust_RSA_Certification_Authority.pem 691s Adding debian:XRamp_Global_CA_Root.pem 691s Adding debian:certSIGN_ROOT_CA.pem 691s Adding debian:certSIGN_Root_CA_G2.pem 691s Adding debian:e-Szigno_Root_CA_2017.pem 691s Adding debian:ePKI_Root_Certification_Authority.pem 691s Adding debian:emSign_ECC_Root_CA_-_C3.pem 691s Adding debian:emSign_ECC_Root_CA_-_G3.pem 691s Adding debian:emSign_Root_CA_-_C1.pem 693s Adding debian:emSign_Root_CA_-_G1.pem 693s Adding debian:vTrus_ECC_Root_CA.pem 693s Adding debian:vTrus_Root_CA.pem 693s done. 693s Setting up openjdk-21-jre:arm64 (21.0.2+13-2) ... 693s Setting up default-jre-headless (2:1.21-75+exp1) ... 693s Setting up default-jre (2:1.21-75+exp1) ... 693s Setting up picard-tools (3.1.1+dfsg-1) ... 693s Setting up autopkgtest-satdep (0) ... 700s (Reading database ... 89964 files and directories currently installed.) 700s Removing autopkgtest-satdep (0) ... 700s autopkgtest [08:34:40]: test run-unit-test: [----------------------- 701s JavOpt: 701s PicardProg: ViewSam 701s PicardOpts: PF_STATUS=All ALIGNMENT_STATUS=All INPUT=unmapped.sam 704s INFO 2024-03-21 08:34:44 ViewSam 704s 704s ********** NOTE: Picard's command line syntax is changing. 704s ********** 704s ********** For more information, please see: 704s ********** 704s https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) 704s ********** 704s ********** The command line looks like this in the new syntax: 704s ********** 704s ********** ViewSam -PF_STATUS All -ALIGNMENT_STATUS All -INPUT unmapped.sam 704s ********** 704s 704s 704s 08:34:44.402 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 704s 08:34:44.412 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 704s 08:34:44.416 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 704s 08:34:44.419 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 704s 08:34:44.423 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 704s 08:34:44.424 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 704s [Thu Mar 21 08:34:44 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 704s [Thu Mar 21 08:34:44 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 704s @HD VN:1.0 SO:queryname 704s @RG ID:0 SM:Hi,Mom! PL:ILLUMINA 704s 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 704s 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 704s 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 704s 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 704s 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 704s 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 704s 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 704s 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 704s 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 704s 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 704s [Thu Mar 21 08:34:44 UTC 2024] picard.sam.ViewSam done. Elapsed time: 0.01 minutes. 704s Runtime.totalMemory()=24379392 704s JavOpt: 704s PicardProg: CollectSequencingArtifactMetrics 704s PicardOpts: I=test.sam O=test R=test.fasta 708s INFO 2024-03-21 08:34:47 CollectSequencingArtifactMetrics 708s 708s ********** NOTE: Picard's command line syntax is changing. 708s ********** 708s ********** For more information, please see: 708s ********** 708s https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) 708s ********** 708s ********** The command line looks like this in the new syntax: 708s ********** 708s ********** CollectSequencingArtifactMetrics -I test.sam -O test -R test.fasta 708s ********** 708s 708s 708s 08:34:48.085 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 708s 08:34:48.106 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 708s 08:34:48.107 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 708s 08:34:48.114 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 708s 08:34:48.114 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 708s 08:34:48.115 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 708s [Thu Mar 21 08:34:48 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 708s [Thu Mar 21 08:34:48 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 708s [Thu Mar 21 08:34:48 UTC 2024] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.01 minutes. 708s Runtime.totalMemory()=24379392 708s All output files generated 708s JavOpt: 708s PicardProg: SortVcf 708s PicardOpts: I=mini.vcf O=mini_sorted.vcf 714s INFO 2024-03-21 08:34:51 SortVcf 714s 714s ********** NOTE: Picard's command line syntax is changing. 714s ********** 714s ********** For more information, please see: 714s ********** 714s https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) 714s ********** 714s ********** The command line looks like this in the new syntax: 714s ********** 714s ********** SortVcf -I mini.vcf -O mini_sorted.vcf 714s ********** 714s 714s 714s JavOpt: 714s PicardProg: SplitVcfs 714s PicardOpts: I=mini.vcf SNP_OUTPUT=snp.vcf INDEL_OUTPUT=indel.vcf 714s 08:34:52.114 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 714s 08:34:52.118 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 714s 08:34:52.119 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 714s 08:34:52.121 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 714s 08:34:52.122 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 714s 08:34:52.122 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 714s [Thu Mar 21 08:34:52 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 714s [Thu Mar 21 08:34:52 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 714s INFO 2024-03-21 08:34:52 SortVcf Reading entries from input file 1 714s [Thu Mar 21 08:34:53 UTC 2024] picard.vcf.SortVcf done. Elapsed time: 0.03 minutes. 714s Runtime.totalMemory()=24379392 714s sorted vcf generated 717s INFO 2024-03-21 08:34:56 SplitVcfs 717s 717s ********** NOTE: Picard's command line syntax is changing. 717s ********** 717s ********** For more information, please see: 717s ********** 717s https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) 717s ********** 717s ********** The command line looks like this in the new syntax: 717s ********** 717s ********** SplitVcfs -I mini.vcf -SNP_OUTPUT snp.vcf -INDEL_OUTPUT indel.vcf 717s ********** 717s 717s 717s 08:34:57.122 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 717s 08:34:57.128 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 717s 08:34:57.129 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 717s 08:34:57.133 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 717s 08:34:57.135 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 717s 08:34:57.136 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 717s [Thu Mar 21 08:34:57 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 717s [Thu Mar 21 08:34:57 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 718s [Thu Mar 21 08:34:58 UTC 2024] picard.vcf.SplitVcfs done. Elapsed time: 0.03 minutes. 718s Runtime.totalMemory()=24379392 718s snp and indel vcfs generated 719s autopkgtest [08:34:59]: test run-unit-test: -----------------------] 719s autopkgtest [08:34:59]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 719s run-unit-test PASS 719s autopkgtest [08:34:59]: @@@@@@@@@@@@@@@@@@@@ summary 719s run-unit-test PASS 735s Creating nova instance adt-noble-arm64-picard-tools-20240321-075410-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240319.img (UUID bd25b89b-8264-4402-95d9-d9c88f21f275)...