0s autopkgtest [17:43:18]: starting date and time: 2024-03-24 17:43:18+0000 0s autopkgtest [17:43:18]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [17:43:18]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.bwaoww2r/out --timeout-copy=6000 -a i386 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed --apt-upgrade picard-tools --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=openjdk-23/23~15ea-1 openjdk-17/17.0.11~7ea-1 openjdk-22/22+36-1 openjdk-21/21.0.3~7ea-1 openjdk-lts/11.0.23~7ea-1ubuntu1 openjdk-8/8u402-ga-2ubuntu6' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@lcy02-6.secgroup --name adt-noble-i386-picard-tools-20240324-174318-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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/ 63s autopkgtest [17:44:21]: testbed dpkg architecture: amd64 63s autopkgtest [17:44:21]: testbed apt version: 2.7.12 63s autopkgtest [17:44:21]: test architecture: i386 63s autopkgtest [17:44:21]: @@@@@@@@@@@@@@@@@@@@ test bed setup 64s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 64s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3986 kB] 64s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 64s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 64s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 64s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main i386 Packages [490 kB] 64s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [728 kB] 64s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 c-n-f Metadata [3508 B] 64s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted i386 Packages [6700 B] 64s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 Packages [30.5 kB] 64s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 c-n-f Metadata [116 B] 64s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe i386 Packages [1302 kB] 64s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [4421 kB] 64s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 c-n-f Metadata [9396 B] 64s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 Packages [96.4 kB] 64s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/multiverse i386 Packages [27.4 kB] 64s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 c-n-f Metadata [196 B] 67s Fetched 11.8 MB in 2s (7289 kB/s) 67s Reading package lists... 69s Reading package lists... 69s Building dependency tree... 69s Reading state information... 70s Calculating upgrade... 70s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 70s Reading package lists... 70s Building dependency tree... 70s Reading state information... 71s 0 upgraded, 0 newly installed, 0 to remove and 248 not upgraded. 71s sh: Attempting to set up Debian/Ubuntu apt sources automatically 71s sh: Distribution appears to be Ubuntu 72s Reading package lists... 72s Building dependency tree... 72s Reading state information... 73s eatmydata is already the newest version (131-1). 73s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 73s Reading package lists... 73s Building dependency tree... 73s Reading state information... 74s dbus is already the newest version (1.14.10-4ubuntu1). 74s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 74s Reading package lists... 74s Building dependency tree... 74s Reading state information... 75s rng-tools-debian is already the newest version (2.4). 75s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 75s Reading package lists... 75s Building dependency tree... 75s Reading state information... 75s The following packages will be REMOVED: 75s cloud-init* python3-configobj* python3-debconf* 76s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 76s After this operation, 3256 kB disk space will be freed. 76s (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 ... 71864 files and directories currently installed.) 76s Removing cloud-init (24.1.2-0ubuntu1) ... 76s Removing python3-configobj (5.0.8-3) ... 76s Removing python3-debconf (1.5.86) ... 77s Processing triggers for man-db (2.12.0-3) ... 77s (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 ... 71475 files and directories currently installed.) 77s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 78s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 78s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 78s invoke-rc.d: policy-rc.d denied execution of try-restart. 78s Reading package lists... 78s Building dependency tree... 78s Reading state information... 79s linux-generic is already the newest version (6.8.0-11.11+1). 79s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 79s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 79s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 79s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 81s Reading package lists... 81s Reading package lists... 81s Building dependency tree... 81s Reading state information... 82s Calculating upgrade... 82s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 82s Reading package lists... 82s Building dependency tree... 82s Reading state information... 83s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 83s autopkgtest [17:44:41]: rebooting testbed after setup commands that affected boot 101s autopkgtest [17:44:59]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024 102s autopkgtest [17:45:00]: @@@@@@@@@@@@@@@@@@@@ apt-source picard-tools 103s Get:1 http://ftpmaster.internal/ubuntu noble/universe picard-tools 3.1.1+dfsg-1 (dsc) [2737 B] 103s Get:2 http://ftpmaster.internal/ubuntu noble/universe picard-tools 3.1.1+dfsg-1 (tar) [20.4 MB] 103s Get:3 http://ftpmaster.internal/ubuntu noble/universe picard-tools 3.1.1+dfsg-1 (diff) [22.8 kB] 103s gpgv: Signature made Sat Dec 16 21:39:31 2023 UTC 103s gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 103s gpgv: Can't check signature: No public key 103s dpkg-source: warning: cannot verify inline signature for ./picard-tools_3.1.1+dfsg-1.dsc: no acceptable signature found 105s autopkgtest [17:45:03]: testing package picard-tools version 3.1.1+dfsg-1 105s autopkgtest [17:45:03]: build not needed 106s autopkgtest [17:45:04]: test run-unit-test: preparing testbed 110s Note, using file '/tmp/autopkgtest.ntvePJ/1-autopkgtest-satdep.dsc' to get the build dependencies 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 111s Starting pkgProblemResolver with broken count: 0 111s Starting 2 pkgProblemResolver with broken count: 0 111s Done 111s The following NEW packages will be installed: 111s adwaita-icon-theme at-spi2-common build-essential ca-certificates-java cpp 111s cpp-13 cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu default-jre 111s default-jre-headless fontconfig fontconfig-config fonts-dejavu-core 111s fonts-dejavu-mono g++ g++-13 g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu 111s gcc gcc-13 gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu 111s gtk-update-icon-cache hicolor-icon-theme humanity-icon-theme java-common 111s libapache-pom-java libasan8 libasound2 libasound2-data libatk1.0-0 111s libatomic1 libavahi-client3 libavahi-common-data libavahi-common3 111s libbarclay-java libc-dev-bin libc6-dev libcairo2 libcc1-0 111s libcommons-codec-java libcommons-compress-java libcommons-io-java 111s libcommons-jexl2-java libcommons-lang3-java libcommons-logging-java 111s libcommons-math3-java libcommons-parent-java libcrypt-dev libcups2 111s libdatrie1 libdeflate0 libdrm-amdgpu1 libdrm-intel1 libdrm-nouveau2 111s libdrm-radeon1 libfontconfig1 libfreemarker-java 111s libgatk-native-bindings-java libgcc-13-dev libgdk-pixbuf-2.0-0 111s libgdk-pixbuf2.0-common libgif7 libgkl-java libgl1 libgl1-mesa-dri 111s libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libgomp1 libgoogle-gson-java 111s libgraphite2-3 libgtk2.0-0 libgtk2.0-common libharfbuzz0b libhtsjdk-java 111s libhttpclient-java libhttpcore-java libhwasan0 libisl23 libitm1 libjbig0 111s libjoptsimple-java libjpeg-turbo8 libjpeg8 liblcms2-2 liblerc4 111s liblightcouch-java libllvm17 liblog4j2-java liblsan0 libmbedcrypto7 111s libmbedtls14 libmbedx509-1 libmjson-java libmongodb-java libmpc3 111s libncbi-ngs3 libncbi-vdb3 libngs-java libngs-jni libpango-1.0-0 111s libpangocairo-1.0-0 libpangoft2-1.0-0 libpciaccess0 libpcsclite1 111s libpicard-java libpixman-1-0 libquadmath0 librhino-java libsharpyuv0 111s libslf4j-java libsnappy-java libsnappy-jni libsnappy1v5 libstdc++-13-dev 111s libthai-data libthai0 libtiff6 libtsan2 libubsan1 libvulkan1 libwebp7 111s libx11-xcb1 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 111s libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 111s libxcomposite1 libxcursor1 libxdamage1 libxfixes3 libxi6 libxinerama1 111s libxrandr2 libxrender1 libxshmfence1 libxtst6 libxxf86vm1 linux-libc-dev 111s ncbi-vdb-data openjdk-21-jre openjdk-21-jre-headless picard-tools 111s rpcsvc-proto ubuntu-mono x11-common 111s 0 upgraded, 153 newly installed, 0 to remove and 0 not upgraded. 111s Need to get 179 MB of archives. 111s After this operation, 701 MB of additional disk space will be used. 111s Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-3 [7624 B] 111s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu1 [147 kB] 111s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 111s Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 libdeflate0 amd64 1.19-1 [43.7 kB] 111s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libjbig0 amd64 2.1-6.1ubuntu1 [29.3 kB] 111s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu1 [184 kB] 111s Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 libsharpyuv0 amd64 1.3.2-0.4 [15.6 kB] 111s Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 libwebp7 amd64 1.3.2-0.4 [230 kB] 111s Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libtiff6 amd64 4.5.1+git230720-3ubuntu1 [232 kB] 111s Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.10+dfsg-3 [147 kB] 111s Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 gtk-update-icon-cache amd64 3.24.40-2ubuntu1 [50.3 kB] 111s Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 hicolor-icon-theme all 0.17-2 [9976 B] 111s Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 humanity-icon-theme all 0.6.16 [1282 kB] 111s Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 ubuntu-mono all 24.04-0ubuntu1 [151 kB] 111s Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 adwaita-icon-theme all 46~rc-1 [723 kB] 111s Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 at-spi2-common all 2.50.0-1 [7864 B] 111s Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 libc-dev-bin amd64 2.39-0ubuntu6 [20.4 kB] 111s Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 linux-libc-dev amd64 6.8.0-11.11 [1595 kB] 111s Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt-dev amd64 1:4.4.36-4 [128 kB] 111s Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 rpcsvc-proto amd64 1.4.2-0ubuntu6 [68.5 kB] 111s Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 libc6-dev amd64 2.39-0ubuntu6 [2126 kB] 112s Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 libisl23 amd64 0.26-3 [741 kB] 112s Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libmpc3 amd64 1.3.1-1 [54.1 kB] 112s Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [11.2 MB] 112s Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13 amd64 13.2.0-17ubuntu2 [1030 B] 112s Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B] 112s Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB] 112s Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 libcc1-0 amd64 14-20240303-1ubuntu1 [47.7 kB] 112s Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 libgomp1 amd64 14-20240303-1ubuntu1 [147 kB] 112s Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 libitm1 amd64 14-20240303-1ubuntu1 [29.1 kB] 112s Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 libatomic1 amd64 14-20240303-1ubuntu1 [10.4 kB] 112s Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 libasan8 amd64 14-20240303-1ubuntu1 [3026 kB] 112s Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 liblsan0 amd64 14-20240303-1ubuntu1 [1310 kB] 112s Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 libtsan2 amd64 14-20240303-1ubuntu1 [2732 kB] 112s Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 libubsan1 amd64 14-20240303-1ubuntu1 [1172 kB] 112s Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 libhwasan0 amd64 14-20240303-1ubuntu1 [1629 kB] 112s Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 libquadmath0 amd64 14-20240303-1ubuntu1 [155 kB] 112s Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-13-dev amd64 13.2.0-17ubuntu2 [2687 kB] 112s Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [21.9 MB] 112s Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13 amd64 13.2.0-17ubuntu2 [477 kB] 112s Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B] 112s Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B] 112s Get:43 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++-13-dev amd64 13.2.0-17ubuntu2 [2340 kB] 112s Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [12.5 MB] 112s Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13 amd64 13.2.0-17ubuntu2 [14.5 kB] 112s Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B] 112s Get:47 http://ftpmaster.internal/ubuntu noble/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B] 112s Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 112s Get:49 http://ftpmaster.internal/ubuntu noble/main amd64 ca-certificates-java all 20240118 [11.6 kB] 112s Get:50 http://ftpmaster.internal/ubuntu noble/main amd64 java-common all 0.75+exp1 [6798 B] 112s Get:51 http://ftpmaster.internal/ubuntu noble/main amd64 libavahi-common-data amd64 0.8-13ubuntu2 [29.5 kB] 112s Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 libavahi-common3 amd64 0.8-13ubuntu2 [23.5 kB] 112s Get:53 http://ftpmaster.internal/ubuntu noble/main amd64 libavahi-client3 amd64 0.8-13ubuntu2 [27.4 kB] 112s Get:54 http://ftpmaster.internal/ubuntu noble/main amd64 libcups2 amd64 2.4.6-0ubuntu3 [269 kB] 112s Get:55 http://ftpmaster.internal/ubuntu noble/main amd64 liblcms2-2 amd64 2.14-2 [161 kB] 112s Get:56 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 112s Get:57 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 112s Get:58 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig-config amd64 2.15.0-1ubuntu1 [36.9 kB] 112s Get:59 http://ftpmaster.internal/ubuntu noble/main amd64 libfontconfig1 amd64 2.15.0-1ubuntu1 [139 kB] 112s Get:60 http://ftpmaster.internal/ubuntu noble/main amd64 libasound2-data all 1.2.10-3build1 [20.7 kB] 112s Get:61 http://ftpmaster.internal/ubuntu noble/main amd64 libasound2 amd64 1.2.10-3build1 [396 kB] 112s Get:62 http://ftpmaster.internal/ubuntu noble/main amd64 libgraphite2-3 amd64 1.3.14-2 [83.1 kB] 112s Get:63 http://ftpmaster.internal/ubuntu noble/main amd64 libharfbuzz0b amd64 8.3.0-2 [469 kB] 112s Get:64 http://ftpmaster.internal/ubuntu noble/main amd64 libpcsclite1 amd64 2.0.0-1 [20.6 kB] 112s Get:65 http://ftpmaster.internal/ubuntu noble/main amd64 openjdk-21-jre-headless amd64 21.0.2+13-2 [46.6 MB] 112s Get:66 http://ftpmaster.internal/ubuntu noble/main amd64 default-jre-headless amd64 2:1.21-75+exp1 [3094 B] 112s Get:67 http://ftpmaster.internal/ubuntu noble/main amd64 libgtk2.0-common all 2.24.33-2ubuntu2 [125 kB] 112s Get:68 http://ftpmaster.internal/ubuntu noble/main amd64 libatk1.0-0 amd64 2.50.0-1 [54.2 kB] 112s Get:69 http://ftpmaster.internal/ubuntu noble/main amd64 libpixman-1-0 amd64 0.42.2-1 [268 kB] 112s Get:70 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-render0 amd64 1.15-1 [16.3 kB] 112s Get:71 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-shm0 amd64 1.15-1 [5740 B] 112s Get:72 http://ftpmaster.internal/ubuntu noble/main amd64 libxrender1 amd64 1:0.9.10-1.1 [20.0 kB] 112s Get:73 http://ftpmaster.internal/ubuntu noble/main amd64 libcairo2 amd64 1.18.0-1 [572 kB] 112s Get:74 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig amd64 2.15.0-1ubuntu1 [180 kB] 112s Get:75 http://ftpmaster.internal/ubuntu noble/main amd64 libthai-data all 0.1.29-2 [158 kB] 112s Get:76 http://ftpmaster.internal/ubuntu noble/main amd64 libdatrie1 amd64 0.2.13-3 [20.9 kB] 112s Get:77 http://ftpmaster.internal/ubuntu noble/main amd64 libthai0 amd64 0.1.29-2 [18.8 kB] 112s Get:78 http://ftpmaster.internal/ubuntu noble/main amd64 libpango-1.0-0 amd64 1.51.0+ds-4 [228 kB] 112s Get:79 http://ftpmaster.internal/ubuntu noble/main amd64 libpangoft2-1.0-0 amd64 1.51.0+ds-4 [42.1 kB] 112s Get:80 http://ftpmaster.internal/ubuntu noble/main amd64 libpangocairo-1.0-0 amd64 1.51.0+ds-4 [29.0 kB] 112s Get:81 http://ftpmaster.internal/ubuntu noble/main amd64 libxcomposite1 amd64 1:0.4.5-1build2 [7192 B] 112s Get:82 http://ftpmaster.internal/ubuntu noble/main amd64 libxfixes3 amd64 1:6.0.0-2 [10.9 kB] 112s Get:83 http://ftpmaster.internal/ubuntu noble/main amd64 libxcursor1 amd64 1:1.2.1-1 [21.4 kB] 112s Get:84 http://ftpmaster.internal/ubuntu noble/main amd64 libxdamage1 amd64 1:1.1.6-1 [6098 B] 112s Get:85 http://ftpmaster.internal/ubuntu noble/main amd64 libxi6 amd64 2:1.8.1-1 [32.4 kB] 112s Get:86 http://ftpmaster.internal/ubuntu noble/main amd64 libxinerama1 amd64 2:1.1.4-3 [7382 B] 112s Get:87 http://ftpmaster.internal/ubuntu noble/main amd64 libxrandr2 amd64 2:1.5.2-2 [20.4 kB] 112s Get:88 http://ftpmaster.internal/ubuntu noble/main amd64 libgtk2.0-0 amd64 2.24.33-2ubuntu2 [2037 kB] 112s Get:89 http://ftpmaster.internal/ubuntu noble/main amd64 libglvnd0 amd64 1.7.0-1 [69.5 kB] 112s Get:90 http://ftpmaster.internal/ubuntu noble/main amd64 libglapi-mesa amd64 24.0.1-1ubuntu1 [40.3 kB] 112s Get:91 http://ftpmaster.internal/ubuntu noble/main amd64 libx11-xcb1 amd64 2:1.8.7-1 [7798 B] 112s Get:92 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-dri2-0 amd64 1.15-1 [7276 B] 112s Get:93 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-dri3-0 amd64 1.15-1 [7174 B] 112s Get:94 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-glx0 amd64 1.15-1 [24.6 kB] 112s Get:95 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-present0 amd64 1.15-1 [5708 B] 112s Get:96 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-randr0 amd64 1.15-1 [18.1 kB] 112s Get:97 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-sync1 amd64 1.15-1 [9358 B] 112s Get:98 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-xfixes0 amd64 1.15-1 [10.2 kB] 112s Get:99 http://ftpmaster.internal/ubuntu noble/main amd64 libxshmfence1 amd64 1.3-1build4 [5394 B] 112s Get:100 http://ftpmaster.internal/ubuntu noble/main amd64 libxxf86vm1 amd64 1:1.1.4-1build3 [10.4 kB] 112s Get:101 http://ftpmaster.internal/ubuntu noble/main amd64 libvulkan1 amd64 1.3.275.0-1 [142 kB] 112s Get:102 http://ftpmaster.internal/ubuntu noble/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [20.4 kB] 112s Get:103 http://ftpmaster.internal/ubuntu noble/main amd64 libpciaccess0 amd64 0.17-3 [18.9 kB] 112s Get:104 http://ftpmaster.internal/ubuntu noble/main amd64 libdrm-intel1 amd64 2.4.120-2 [63.8 kB] 112s Get:105 http://ftpmaster.internal/ubuntu noble/main amd64 libdrm-nouveau2 amd64 2.4.120-2 [17.6 kB] 112s Get:106 http://ftpmaster.internal/ubuntu noble/main amd64 libdrm-radeon1 amd64 2.4.120-2 [20.7 kB] 112s Get:107 http://ftpmaster.internal/ubuntu noble/main amd64 libllvm17 amd64 1:17.0.6-5build1 [26.2 MB] 113s Get:108 http://ftpmaster.internal/ubuntu noble/main amd64 libgl1-mesa-dri amd64 24.0.1-1ubuntu1 [8936 kB] 113s Get:109 http://ftpmaster.internal/ubuntu noble/main amd64 libglx-mesa0 amd64 24.0.1-1ubuntu1 [154 kB] 113s Get:110 http://ftpmaster.internal/ubuntu noble/main amd64 libglx0 amd64 1.7.0-1 [38.7 kB] 113s Get:111 http://ftpmaster.internal/ubuntu noble/main amd64 libgl1 amd64 1.7.0-1 [103 kB] 113s Get:112 http://ftpmaster.internal/ubuntu noble/main amd64 libgif7 amd64 5.2.1-2.5 [34.0 kB] 113s Get:113 http://ftpmaster.internal/ubuntu noble/main amd64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 113s Get:114 http://ftpmaster.internal/ubuntu noble/main amd64 libxtst6 amd64 2:1.2.3-1.1 [13.8 kB] 113s Get:115 http://ftpmaster.internal/ubuntu noble/main amd64 openjdk-21-jre amd64 21.0.2+13-2 [227 kB] 113s Get:116 http://ftpmaster.internal/ubuntu noble/main amd64 default-jre amd64 2:1.21-75+exp1 [922 B] 113s Get:117 http://ftpmaster.internal/ubuntu noble/universe amd64 libapache-pom-java all 29-2 [5284 B] 113s Get:118 http://ftpmaster.internal/ubuntu noble/universe amd64 libcommons-parent-java all 56-1 [10.7 kB] 113s Get:119 http://ftpmaster.internal/ubuntu noble/universe amd64 libcommons-lang3-java all 3.14.0-1 [586 kB] 113s Get:120 http://ftpmaster.internal/ubuntu noble/universe amd64 libfreemarker-java all 2.3.32-2 [1542 kB] 113s Get:121 http://ftpmaster.internal/ubuntu noble/universe amd64 libgoogle-gson-java all 2.10.1-1 [252 kB] 113s Get:122 http://ftpmaster.internal/ubuntu noble/universe amd64 libjoptsimple-java all 5.0.4-4 [73.1 kB] 113s Get:123 http://ftpmaster.internal/ubuntu noble/universe amd64 libcommons-codec-java all 1.16.0-1 [306 kB] 113s Get:124 http://ftpmaster.internal/ubuntu noble/universe amd64 libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 113s Get:125 http://ftpmaster.internal/ubuntu noble/universe amd64 libhttpcore-java all 4.4.16-1 [612 kB] 113s Get:126 http://ftpmaster.internal/ubuntu noble/universe amd64 libhttpclient-java all 4.5.14-1 [1241 kB] 113s Get:127 http://ftpmaster.internal/ubuntu noble/universe amd64 liblightcouch-java all 0.2.0-1 [74.2 kB] 113s Get:128 http://ftpmaster.internal/ubuntu noble/universe amd64 libmongodb-java all 3.6.3-2 [1899 kB] 113s Get:129 http://ftpmaster.internal/ubuntu noble/universe amd64 libslf4j-java all 1.7.32-1 [141 kB] 113s Get:130 http://ftpmaster.internal/ubuntu noble/universe amd64 liblog4j2-java all 2.19.0-2 [2294 kB] 113s Get:131 http://ftpmaster.internal/ubuntu noble/universe amd64 libbarclay-java all 5.0.0+dfsg-1 [108 kB] 113s Get:132 http://ftpmaster.internal/ubuntu noble/universe amd64 libcommons-compress-java all 1.25.0-1 [612 kB] 113s Get:133 http://ftpmaster.internal/ubuntu noble/universe amd64 libcommons-io-java all 2.11.0-2 [297 kB] 113s Get:134 http://ftpmaster.internal/ubuntu noble/universe amd64 libcommons-jexl2-java all 2.1.1-6 [250 kB] 113s Get:135 http://ftpmaster.internal/ubuntu noble/universe amd64 libcommons-math3-java all 3.6.1-3 [2016 kB] 113s Get:136 http://ftpmaster.internal/ubuntu noble/universe amd64 libgatk-native-bindings-java all 1.0.0+dfsg-2 [8014 B] 113s Get:137 http://ftpmaster.internal/ubuntu noble/universe amd64 libmjson-java all 1.4.0-3 [60.4 kB] 113s Get:138 http://ftpmaster.internal/ubuntu noble/universe amd64 libmbedcrypto7 amd64 2.28.7-1ubuntu1 [206 kB] 113s Get:139 http://ftpmaster.internal/ubuntu noble/universe amd64 libmbedx509-1 amd64 2.28.7-1ubuntu1 [46.4 kB] 113s Get:140 http://ftpmaster.internal/ubuntu noble/universe amd64 libmbedtls14 amd64 2.28.7-1ubuntu1 [82.1 kB] 113s Get:141 http://ftpmaster.internal/ubuntu noble/universe amd64 ncbi-vdb-data all 3.0.2+dfsg-2 [65.8 kB] 113s Get:142 http://ftpmaster.internal/ubuntu noble/universe amd64 libncbi-vdb3 amd64 3.0.2+dfsg-2 [1117 kB] 113s Get:143 http://ftpmaster.internal/ubuntu noble/universe amd64 libncbi-ngs3 amd64 3.0.3+dfsg-6ubuntu1 [154 kB] 113s Get:144 http://ftpmaster.internal/ubuntu noble/universe amd64 libngs-jni amd64 3.0.3+dfsg-6ubuntu1 [4838 B] 113s Get:145 http://ftpmaster.internal/ubuntu noble/universe amd64 libngs-java amd64 3.0.3+dfsg-6ubuntu1 [91.8 kB] 113s Get:146 http://ftpmaster.internal/ubuntu noble/universe amd64 librhino-java all 1.7.14-2.1 [1330 kB] 113s Get:147 http://ftpmaster.internal/ubuntu noble/main amd64 libsnappy1v5 amd64 1.1.10-1 [28.4 kB] 113s Get:148 http://ftpmaster.internal/ubuntu noble/universe amd64 libsnappy-jni amd64 1.1.10.5-1 [6538 B] 113s Get:149 http://ftpmaster.internal/ubuntu noble/universe amd64 libsnappy-java all 1.1.10.5-1 [83.6 kB] 113s Get:150 http://ftpmaster.internal/ubuntu noble/universe amd64 libhtsjdk-java all 4.1.0+dfsg-1 [1821 kB] 113s Get:151 http://ftpmaster.internal/ubuntu noble/universe amd64 libgkl-java all 0.8.11+dfsg-2 [24.8 kB] 113s Get:152 http://ftpmaster.internal/ubuntu noble/universe amd64 libpicard-java all 3.1.1+dfsg-1 [1731 kB] 113s Get:153 http://ftpmaster.internal/ubuntu noble/universe amd64 picard-tools all 3.1.1+dfsg-1 [308 kB] 113s Fetched 179 MB in 1s (127 MB/s) 114s Selecting previously unselected package libgdk-pixbuf2.0-common. 114s (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 ... 71420 files and directories currently installed.) 114s Preparing to unpack .../000-libgdk-pixbuf2.0-common_2.42.10+dfsg-3_all.deb ... 114s Unpacking libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ... 114s Selecting previously unselected package libjpeg-turbo8:amd64. 114s Preparing to unpack .../001-libjpeg-turbo8_2.1.5-2ubuntu1_amd64.deb ... 114s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu1) ... 114s Selecting previously unselected package libjpeg8:amd64. 114s Preparing to unpack .../002-libjpeg8_8c-2ubuntu11_amd64.deb ... 114s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 114s Selecting previously unselected package libdeflate0:amd64. 114s Preparing to unpack .../003-libdeflate0_1.19-1_amd64.deb ... 114s Unpacking libdeflate0:amd64 (1.19-1) ... 114s Selecting previously unselected package libjbig0:amd64. 114s Preparing to unpack .../004-libjbig0_2.1-6.1ubuntu1_amd64.deb ... 114s Unpacking libjbig0:amd64 (2.1-6.1ubuntu1) ... 114s Selecting previously unselected package liblerc4:amd64. 114s Preparing to unpack .../005-liblerc4_4.0.0+ds-4ubuntu1_amd64.deb ... 114s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu1) ... 114s Selecting previously unselected package libsharpyuv0:amd64. 114s Preparing to unpack .../006-libsharpyuv0_1.3.2-0.4_amd64.deb ... 114s Unpacking libsharpyuv0:amd64 (1.3.2-0.4) ... 114s Selecting previously unselected package libwebp7:amd64. 114s Preparing to unpack .../007-libwebp7_1.3.2-0.4_amd64.deb ... 114s Unpacking libwebp7:amd64 (1.3.2-0.4) ... 114s Selecting previously unselected package libtiff6:amd64. 114s Preparing to unpack .../008-libtiff6_4.5.1+git230720-3ubuntu1_amd64.deb ... 114s Unpacking libtiff6:amd64 (4.5.1+git230720-3ubuntu1) ... 114s Selecting previously unselected package libgdk-pixbuf-2.0-0:amd64. 114s Preparing to unpack .../009-libgdk-pixbuf-2.0-0_2.42.10+dfsg-3_amd64.deb ... 114s Unpacking libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-3) ... 114s Selecting previously unselected package gtk-update-icon-cache. 114s Preparing to unpack .../010-gtk-update-icon-cache_3.24.40-2ubuntu1_amd64.deb ... 114s Unpacking gtk-update-icon-cache (3.24.40-2ubuntu1) ... 114s Selecting previously unselected package hicolor-icon-theme. 114s Preparing to unpack .../011-hicolor-icon-theme_0.17-2_all.deb ... 114s Unpacking hicolor-icon-theme (0.17-2) ... 114s Selecting previously unselected package humanity-icon-theme. 114s Preparing to unpack .../012-humanity-icon-theme_0.6.16_all.deb ... 114s Unpacking humanity-icon-theme (0.6.16) ... 115s Selecting previously unselected package ubuntu-mono. 115s Preparing to unpack .../013-ubuntu-mono_24.04-0ubuntu1_all.deb ... 115s Unpacking ubuntu-mono (24.04-0ubuntu1) ... 115s Selecting previously unselected package adwaita-icon-theme. 115s Preparing to unpack .../014-adwaita-icon-theme_46~rc-1_all.deb ... 115s Unpacking adwaita-icon-theme (46~rc-1) ... 116s Selecting previously unselected package at-spi2-common. 116s Preparing to unpack .../015-at-spi2-common_2.50.0-1_all.deb ... 116s Unpacking at-spi2-common (2.50.0-1) ... 116s Selecting previously unselected package libc-dev-bin. 116s Preparing to unpack .../016-libc-dev-bin_2.39-0ubuntu6_amd64.deb ... 116s Unpacking libc-dev-bin (2.39-0ubuntu6) ... 116s Selecting previously unselected package linux-libc-dev:amd64. 116s Preparing to unpack .../017-linux-libc-dev_6.8.0-11.11_amd64.deb ... 116s Unpacking linux-libc-dev:amd64 (6.8.0-11.11) ... 116s Selecting previously unselected package libcrypt-dev:amd64. 116s Preparing to unpack .../018-libcrypt-dev_1%3a4.4.36-4_amd64.deb ... 116s Unpacking libcrypt-dev:amd64 (1:4.4.36-4) ... 116s Selecting previously unselected package rpcsvc-proto. 116s Preparing to unpack .../019-rpcsvc-proto_1.4.2-0ubuntu6_amd64.deb ... 116s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 116s Selecting previously unselected package libc6-dev:amd64. 116s Preparing to unpack .../020-libc6-dev_2.39-0ubuntu6_amd64.deb ... 116s Unpacking libc6-dev:amd64 (2.39-0ubuntu6) ... 116s Selecting previously unselected package libisl23:amd64. 116s Preparing to unpack .../021-libisl23_0.26-3_amd64.deb ... 116s Unpacking libisl23:amd64 (0.26-3) ... 116s Selecting previously unselected package libmpc3:amd64. 116s Preparing to unpack .../022-libmpc3_1.3.1-1_amd64.deb ... 116s Unpacking libmpc3:amd64 (1.3.1-1) ... 116s Selecting previously unselected package cpp-13-x86-64-linux-gnu. 116s Preparing to unpack .../023-cpp-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 116s Unpacking cpp-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 116s Selecting previously unselected package cpp-13. 116s Preparing to unpack .../024-cpp-13_13.2.0-17ubuntu2_amd64.deb ... 116s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 116s Selecting previously unselected package cpp-x86-64-linux-gnu. 116s Preparing to unpack .../025-cpp-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 116s Unpacking cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 116s Selecting previously unselected package cpp. 116s Preparing to unpack .../026-cpp_4%3a13.2.0-7ubuntu1_amd64.deb ... 116s Unpacking cpp (4:13.2.0-7ubuntu1) ... 116s Selecting previously unselected package libcc1-0:amd64. 116s Preparing to unpack .../027-libcc1-0_14-20240303-1ubuntu1_amd64.deb ... 116s Unpacking libcc1-0:amd64 (14-20240303-1ubuntu1) ... 116s Selecting previously unselected package libgomp1:amd64. 116s Preparing to unpack .../028-libgomp1_14-20240303-1ubuntu1_amd64.deb ... 116s Unpacking libgomp1:amd64 (14-20240303-1ubuntu1) ... 116s Selecting previously unselected package libitm1:amd64. 116s Preparing to unpack .../029-libitm1_14-20240303-1ubuntu1_amd64.deb ... 116s Unpacking libitm1:amd64 (14-20240303-1ubuntu1) ... 116s Selecting previously unselected package libatomic1:amd64. 116s Preparing to unpack .../030-libatomic1_14-20240303-1ubuntu1_amd64.deb ... 116s Unpacking libatomic1:amd64 (14-20240303-1ubuntu1) ... 116s Selecting previously unselected package libasan8:amd64. 116s Preparing to unpack .../031-libasan8_14-20240303-1ubuntu1_amd64.deb ... 116s Unpacking libasan8:amd64 (14-20240303-1ubuntu1) ... 117s Selecting previously unselected package liblsan0:amd64. 117s Preparing to unpack .../032-liblsan0_14-20240303-1ubuntu1_amd64.deb ... 117s Unpacking liblsan0:amd64 (14-20240303-1ubuntu1) ... 117s Selecting previously unselected package libtsan2:amd64. 117s Preparing to unpack .../033-libtsan2_14-20240303-1ubuntu1_amd64.deb ... 117s Unpacking libtsan2:amd64 (14-20240303-1ubuntu1) ... 117s Selecting previously unselected package libubsan1:amd64. 117s Preparing to unpack .../034-libubsan1_14-20240303-1ubuntu1_amd64.deb ... 117s Unpacking libubsan1:amd64 (14-20240303-1ubuntu1) ... 117s Selecting previously unselected package libhwasan0:amd64. 117s Preparing to unpack .../035-libhwasan0_14-20240303-1ubuntu1_amd64.deb ... 117s Unpacking libhwasan0:amd64 (14-20240303-1ubuntu1) ... 117s Selecting previously unselected package libquadmath0:amd64. 117s Preparing to unpack .../036-libquadmath0_14-20240303-1ubuntu1_amd64.deb ... 117s Unpacking libquadmath0:amd64 (14-20240303-1ubuntu1) ... 117s Selecting previously unselected package libgcc-13-dev:amd64. 117s Preparing to unpack .../037-libgcc-13-dev_13.2.0-17ubuntu2_amd64.deb ... 117s Unpacking libgcc-13-dev:amd64 (13.2.0-17ubuntu2) ... 117s Selecting previously unselected package gcc-13-x86-64-linux-gnu. 117s Preparing to unpack .../038-gcc-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 117s Unpacking gcc-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 117s Selecting previously unselected package gcc-13. 117s Preparing to unpack .../039-gcc-13_13.2.0-17ubuntu2_amd64.deb ... 117s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 117s Selecting previously unselected package gcc-x86-64-linux-gnu. 117s Preparing to unpack .../040-gcc-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 117s Unpacking gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 117s Selecting previously unselected package gcc. 117s Preparing to unpack .../041-gcc_4%3a13.2.0-7ubuntu1_amd64.deb ... 117s Unpacking gcc (4:13.2.0-7ubuntu1) ... 117s Selecting previously unselected package libstdc++-13-dev:amd64. 117s Preparing to unpack .../042-libstdc++-13-dev_13.2.0-17ubuntu2_amd64.deb ... 117s Unpacking libstdc++-13-dev:amd64 (13.2.0-17ubuntu2) ... 118s Selecting previously unselected package g++-13-x86-64-linux-gnu. 118s Preparing to unpack .../043-g++-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 118s Unpacking g++-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 118s Selecting previously unselected package g++-13. 118s Preparing to unpack .../044-g++-13_13.2.0-17ubuntu2_amd64.deb ... 118s Unpacking g++-13 (13.2.0-17ubuntu2) ... 118s Selecting previously unselected package g++-x86-64-linux-gnu. 118s Preparing to unpack .../045-g++-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 118s Unpacking g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 118s Selecting previously unselected package g++. 118s Preparing to unpack .../046-g++_4%3a13.2.0-7ubuntu1_amd64.deb ... 118s Unpacking g++ (4:13.2.0-7ubuntu1) ... 118s Selecting previously unselected package build-essential. 118s Preparing to unpack .../047-build-essential_12.10ubuntu1_amd64.deb ... 118s Unpacking build-essential (12.10ubuntu1) ... 118s Selecting previously unselected package ca-certificates-java. 118s Preparing to unpack .../048-ca-certificates-java_20240118_all.deb ... 118s Unpacking ca-certificates-java (20240118) ... 118s Selecting previously unselected package java-common. 118s Preparing to unpack .../049-java-common_0.75+exp1_all.deb ... 118s Unpacking java-common (0.75+exp1) ... 118s Selecting previously unselected package libavahi-common-data:amd64. 118s Preparing to unpack .../050-libavahi-common-data_0.8-13ubuntu2_amd64.deb ... 118s Unpacking libavahi-common-data:amd64 (0.8-13ubuntu2) ... 118s Selecting previously unselected package libavahi-common3:amd64. 118s Preparing to unpack .../051-libavahi-common3_0.8-13ubuntu2_amd64.deb ... 118s Unpacking libavahi-common3:amd64 (0.8-13ubuntu2) ... 118s Selecting previously unselected package libavahi-client3:amd64. 118s Preparing to unpack .../052-libavahi-client3_0.8-13ubuntu2_amd64.deb ... 118s Unpacking libavahi-client3:amd64 (0.8-13ubuntu2) ... 118s Selecting previously unselected package libcups2:amd64. 118s Preparing to unpack .../053-libcups2_2.4.6-0ubuntu3_amd64.deb ... 118s Unpacking libcups2:amd64 (2.4.6-0ubuntu3) ... 118s Selecting previously unselected package liblcms2-2:amd64. 118s Preparing to unpack .../054-liblcms2-2_2.14-2_amd64.deb ... 118s Unpacking liblcms2-2:amd64 (2.14-2) ... 118s Selecting previously unselected package fonts-dejavu-mono. 118s Preparing to unpack .../055-fonts-dejavu-mono_2.37-8_all.deb ... 118s Unpacking fonts-dejavu-mono (2.37-8) ... 118s Selecting previously unselected package fonts-dejavu-core. 118s Preparing to unpack .../056-fonts-dejavu-core_2.37-8_all.deb ... 118s Unpacking fonts-dejavu-core (2.37-8) ... 118s Selecting previously unselected package fontconfig-config. 118s Preparing to unpack .../057-fontconfig-config_2.15.0-1ubuntu1_amd64.deb ... 118s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 118s Selecting previously unselected package libfontconfig1:amd64. 118s Preparing to unpack .../058-libfontconfig1_2.15.0-1ubuntu1_amd64.deb ... 118s Unpacking libfontconfig1:amd64 (2.15.0-1ubuntu1) ... 118s Selecting previously unselected package libasound2-data. 118s Preparing to unpack .../059-libasound2-data_1.2.10-3build1_all.deb ... 118s Unpacking libasound2-data (1.2.10-3build1) ... 119s Selecting previously unselected package libasound2:amd64. 119s Preparing to unpack .../060-libasound2_1.2.10-3build1_amd64.deb ... 119s Unpacking libasound2:amd64 (1.2.10-3build1) ... 119s Selecting previously unselected package libgraphite2-3:amd64. 119s Preparing to unpack .../061-libgraphite2-3_1.3.14-2_amd64.deb ... 119s Unpacking libgraphite2-3:amd64 (1.3.14-2) ... 119s Selecting previously unselected package libharfbuzz0b:amd64. 119s Preparing to unpack .../062-libharfbuzz0b_8.3.0-2_amd64.deb ... 119s Unpacking libharfbuzz0b:amd64 (8.3.0-2) ... 119s Selecting previously unselected package libpcsclite1:amd64. 119s Preparing to unpack .../063-libpcsclite1_2.0.0-1_amd64.deb ... 119s Unpacking libpcsclite1:amd64 (2.0.0-1) ... 119s Selecting previously unselected package openjdk-21-jre-headless:amd64. 119s Preparing to unpack .../064-openjdk-21-jre-headless_21.0.2+13-2_amd64.deb ... 119s Unpacking openjdk-21-jre-headless:amd64 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unselected package libxcb-shm0:amd64. 120s Preparing to unpack .../070-libxcb-shm0_1.15-1_amd64.deb ... 120s Unpacking libxcb-shm0:amd64 (1.15-1) ... 120s Selecting previously unselected package libxrender1:amd64. 120s Preparing to unpack .../071-libxrender1_1%3a0.9.10-1.1_amd64.deb ... 120s Unpacking libxrender1:amd64 (1:0.9.10-1.1) ... 120s Selecting previously unselected package libcairo2:amd64. 120s Preparing to unpack .../072-libcairo2_1.18.0-1_amd64.deb ... 120s Unpacking libcairo2:amd64 (1.18.0-1) ... 120s Selecting previously unselected package fontconfig. 120s Preparing to unpack .../073-fontconfig_2.15.0-1ubuntu1_amd64.deb ... 120s Unpacking fontconfig (2.15.0-1ubuntu1) ... 120s Selecting previously unselected package libthai-data. 120s Preparing to unpack .../074-libthai-data_0.1.29-2_all.deb ... 120s Unpacking libthai-data (0.1.29-2) ... 120s Selecting previously unselected package libdatrie1:amd64. 120s Preparing to unpack .../075-libdatrie1_0.2.13-3_amd64.deb ... 120s 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libxcomposite1:amd64 (1:0.4.5-1build2) ... 120s Selecting previously unselected package libxfixes3:amd64. 120s Preparing to unpack .../081-libxfixes3_1%3a6.0.0-2_amd64.deb ... 120s Unpacking libxfixes3:amd64 (1:6.0.0-2) ... 120s Selecting previously unselected package libxcursor1:amd64. 120s Preparing to unpack .../082-libxcursor1_1%3a1.2.1-1_amd64.deb ... 120s Unpacking libxcursor1:amd64 (1:1.2.1-1) ... 120s Selecting previously unselected package libxdamage1:amd64. 120s Preparing to unpack .../083-libxdamage1_1%3a1.1.6-1_amd64.deb ... 120s Unpacking libxdamage1:amd64 (1:1.1.6-1) ... 120s Selecting previously unselected package libxi6:amd64. 120s Preparing to unpack .../084-libxi6_2%3a1.8.1-1_amd64.deb ... 120s Unpacking libxi6:amd64 (2:1.8.1-1) ... 120s Selecting previously unselected package libxinerama1:amd64. 120s Preparing to unpack .../085-libxinerama1_2%3a1.1.4-3_amd64.deb ... 120s Unpacking libxinerama1:amd64 (2:1.1.4-3) ... 120s Selecting previously unselected package libxrandr2:amd64. 120s Preparing to unpack .../086-libxrandr2_2%3a1.5.2-2_amd64.deb ... 120s Unpacking libxrandr2:amd64 (2:1.5.2-2) ... 120s Selecting previously unselected package libgtk2.0-0:amd64. 120s Preparing to unpack .../087-libgtk2.0-0_2.24.33-2ubuntu2_amd64.deb ... 120s Unpacking libgtk2.0-0:amd64 (2.24.33-2ubuntu2) ... 120s Selecting previously unselected package libglvnd0:amd64. 120s Preparing to unpack .../088-libglvnd0_1.7.0-1_amd64.deb ... 120s Unpacking libglvnd0:amd64 (1.7.0-1) ... 120s Selecting previously unselected package libglapi-mesa:amd64. 120s Preparing to unpack .../089-libglapi-mesa_24.0.1-1ubuntu1_amd64.deb ... 120s Unpacking libglapi-mesa:amd64 (24.0.1-1ubuntu1) ... 120s Selecting previously unselected package libx11-xcb1:amd64. 120s Preparing to unpack .../090-libx11-xcb1_2%3a1.8.7-1_amd64.deb ... 120s Unpacking libx11-xcb1:amd64 (2:1.8.7-1) ... 120s Selecting previously unselected package libxcb-dri2-0:amd64. 120s Preparing to unpack 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121s Selecting previously unselected package libxcb-xfixes0:amd64. 121s Preparing to unpack .../097-libxcb-xfixes0_1.15-1_amd64.deb ... 121s Unpacking libxcb-xfixes0:amd64 (1.15-1) ... 121s Selecting previously unselected package libxshmfence1:amd64. 121s Preparing to unpack .../098-libxshmfence1_1.3-1build4_amd64.deb ... 121s Unpacking libxshmfence1:amd64 (1.3-1build4) ... 121s Selecting previously unselected package libxxf86vm1:amd64. 121s Preparing to unpack .../099-libxxf86vm1_1%3a1.1.4-1build3_amd64.deb ... 121s Unpacking libxxf86vm1:amd64 (1:1.1.4-1build3) ... 121s Selecting previously unselected package libvulkan1:amd64. 121s Preparing to unpack .../100-libvulkan1_1.3.275.0-1_amd64.deb ... 121s Unpacking libvulkan1:amd64 (1.3.275.0-1) ... 121s Selecting previously unselected package libdrm-amdgpu1:amd64. 121s Preparing to unpack .../101-libdrm-amdgpu1_2.4.120-2_amd64.deb ... 121s Unpacking libdrm-amdgpu1:amd64 (2.4.120-2) ... 121s Selecting previously unselected package libpciaccess0:amd64. 121s Preparing to unpack .../102-libpciaccess0_0.17-3_amd64.deb ... 121s Unpacking libpciaccess0:amd64 (0.17-3) ... 121s Selecting previously unselected package libdrm-intel1:amd64. 121s Preparing to unpack .../103-libdrm-intel1_2.4.120-2_amd64.deb ... 121s Unpacking libdrm-intel1:amd64 (2.4.120-2) ... 121s Selecting previously unselected package libdrm-nouveau2:amd64. 121s Preparing to unpack .../104-libdrm-nouveau2_2.4.120-2_amd64.deb ... 121s Unpacking libdrm-nouveau2:amd64 (2.4.120-2) ... 121s Selecting previously unselected package libdrm-radeon1:amd64. 121s Preparing to unpack .../105-libdrm-radeon1_2.4.120-2_amd64.deb ... 121s Unpacking libdrm-radeon1:amd64 (2.4.120-2) ... 121s Selecting previously unselected package libllvm17:amd64. 121s Preparing to unpack .../106-libllvm17_1%3a17.0.6-5build1_amd64.deb ... 121s Unpacking libllvm17:amd64 (1:17.0.6-5build1) ... 122s Selecting previously unselected package libgl1-mesa-dri:amd64. 122s Preparing to unpack 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previously unselected package libcommons-math3-java. 123s Preparing to unpack .../134-libcommons-math3-java_3.6.1-3_all.deb ... 123s Unpacking libcommons-math3-java (3.6.1-3) ... 123s Selecting previously unselected package libgatk-native-bindings-java. 123s Preparing to unpack .../135-libgatk-native-bindings-java_1.0.0+dfsg-2_all.deb ... 123s Unpacking libgatk-native-bindings-java (1.0.0+dfsg-2) ... 123s Selecting previously unselected package libmjson-java. 123s Preparing to unpack .../136-libmjson-java_1.4.0-3_all.deb ... 123s Unpacking libmjson-java (1.4.0-3) ... 123s Selecting previously unselected package libmbedcrypto7:amd64. 123s Preparing to unpack .../137-libmbedcrypto7_2.28.7-1ubuntu1_amd64.deb ... 123s Unpacking libmbedcrypto7:amd64 (2.28.7-1ubuntu1) ... 123s Selecting previously unselected package libmbedx509-1:amd64. 123s Preparing to unpack .../138-libmbedx509-1_2.28.7-1ubuntu1_amd64.deb ... 123s Unpacking libmbedx509-1:amd64 (2.28.7-1ubuntu1) ... 123s Selecting previously unselected package libmbedtls14:amd64. 123s Preparing to unpack .../139-libmbedtls14_2.28.7-1ubuntu1_amd64.deb ... 123s Unpacking libmbedtls14:amd64 (2.28.7-1ubuntu1) ... 123s Selecting previously unselected package ncbi-vdb-data. 123s Preparing to unpack .../140-ncbi-vdb-data_3.0.2+dfsg-2_all.deb ... 123s Unpacking ncbi-vdb-data (3.0.2+dfsg-2) ... 123s Selecting previously unselected package libncbi-vdb3:amd64. 123s Preparing to unpack .../141-libncbi-vdb3_3.0.2+dfsg-2_amd64.deb ... 123s Unpacking libncbi-vdb3:amd64 (3.0.2+dfsg-2) ... 123s Selecting previously unselected package libncbi-ngs3:amd64. 123s Preparing to unpack .../142-libncbi-ngs3_3.0.3+dfsg-6ubuntu1_amd64.deb ... 123s Unpacking libncbi-ngs3:amd64 (3.0.3+dfsg-6ubuntu1) ... 123s Selecting previously unselected package libngs-jni:amd64. 123s Preparing to unpack .../143-libngs-jni_3.0.3+dfsg-6ubuntu1_amd64.deb ... 123s Unpacking libngs-jni:amd64 (3.0.3+dfsg-6ubuntu1) ... 123s Selecting previously unselected 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libslf4j-java (1.7.32-1) ... 124s Setting up libdrm-nouveau2:amd64 (2.4.120-2) ... 124s Setting up libxdamage1:amd64 (1:1.1.6-1) ... 124s Setting up libxcb-xfixes0:amd64 (1.15-1) ... 124s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu1) ... 124s Setting up hicolor-icon-theme (0.17-2) ... 124s Setting up libxi6:amd64 (2:1.8.1-1) ... 124s Setting up libgatk-native-bindings-java (1.0.0+dfsg-2) ... 124s Setting up java-common (0.75+exp1) ... 124s Setting up libxrender1:amd64 (1:0.9.10-1.1) ... 124s Setting up libdatrie1:amd64 (0.2.13-3) ... 124s Setting up libxcb-render0:amd64 (1.15-1) ... 124s Setting up libdrm-radeon1:amd64 (2.4.120-2) ... 124s Setting up libglvnd0:amd64 (1.7.0-1) ... 124s Setting up libgoogle-gson-java (2.10.1-1) ... 124s Setting up libmjson-java (1.4.0-3) ... 124s Setting up libxcb-glx0:amd64 (1.15-1) ... 124s Setting up libdrm-intel1:amd64 (2.4.120-2) ... 124s Setting up libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ... 124s Setting up x11-common (1:7.7+23ubuntu2) ... 124s Setting up libdeflate0:amd64 (1.19-1) ... 124s Setting up linux-libc-dev:amd64 (6.8.0-11.11) ... 124s Setting up libxcb-shm0:amd64 (1.15-1) ... 124s Setting up libgomp1:amd64 (14-20240303-1ubuntu1) ... 124s Setting up libjbig0:amd64 (2.1-6.1ubuntu1) ... 124s Setting up libxxf86vm1:amd64 (1:1.1.4-1build3) ... 124s Setting up libsnappy1v5:amd64 (1.1.10-1) ... 124s Setting up libxcb-present0:amd64 (1.15-1) ... 124s Setting up libasound2-data (1.2.10-3build1) ... 124s Setting up librhino-java (1.7.14-2.1) ... 124s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 124s Setting up libmbedcrypto7:amd64 (2.28.7-1ubuntu1) ... 124s Setting up libxfixes3:amd64 (1:6.0.0-2) ... 124s Setting up libxcb-sync1:amd64 (1.15-1) ... 124s Setting up libapache-pom-java (29-2) ... 124s Setting up libavahi-common-data:amd64 (0.8-13ubuntu2) ... 124s Setting up libquadmath0:amd64 (14-20240303-1ubuntu1) ... 124s Setting up libxinerama1:amd64 (2:1.1.4-3) ... 124s Setting up fonts-dejavu-mono (2.37-8) ... 124s Setting up libmpc3:amd64 (1.3.1-1) ... 124s Setting up libatomic1:amd64 (14-20240303-1ubuntu1) ... 124s Setting up libxrandr2:amd64 (2:1.5.2-2) ... 124s Setting up fonts-dejavu-core (2.37-8) ... 124s Setting up libpcsclite1:amd64 (2.0.0-1) ... 124s Setting up libmongodb-java (3.6.3-2) ... 124s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu1) ... 124s Setting up libglapi-mesa:amd64 (24.0.1-1ubuntu1) ... 124s Setting up libvulkan1:amd64 (1.3.275.0-1) ... 124s Setting up libwebp7:amd64 (1.3.2-0.4) ... 124s Setting up libubsan1:amd64 (14-20240303-1ubuntu1) ... 124s Setting up libxcb-dri2-0:amd64 (1.15-1) ... 124s Setting up libgif7:amd64 (5.2.1-2.5) ... 124s Setting up libfreemarker-java (2.3.32-2) ... 124s Setting up libxshmfence1:amd64 (1.3-1build4) ... 124s Setting up libhwasan0:amd64 (14-20240303-1ubuntu1) ... 124s Setting up at-spi2-common (2.50.0-1) ... 124s Setting up libcrypt-dev:amd64 (1:4.4.36-4) ... 124s Setting up libxcb-randr0:amd64 (1.15-1) ... 124s Setting up libasan8:amd64 (14-20240303-1ubuntu1) ... 124s Setting up libasound2:amd64 (1.2.10-3build1) ... 124s Setting up libharfbuzz0b:amd64 (8.3.0-2) ... 124s Setting up ncbi-vdb-data (3.0.2+dfsg-2) ... 124s Setting up libthai-data (0.1.29-2) ... 124s Setting up libcommons-math3-java (3.6.1-3) ... 124s Setting up libgtk2.0-common (2.24.33-2ubuntu2) ... 124s Setting up libatk1.0-0:amd64 (2.50.0-1) ... 124s Setting up libhttpcore-java (4.4.16-1) ... 124s Setting up libtsan2:amd64 (14-20240303-1ubuntu1) ... 124s Setting up libjoptsimple-java (5.0.4-4) ... 124s Setting up ca-certificates-java (20240118) ... 124s No JRE found. Skipping Java certificates setup. 124s Setting up libisl23:amd64 (0.26-3) ... 124s Setting up libc-dev-bin (2.39-0ubuntu6) ... 124s Setting up libllvm17:amd64 (1:17.0.6-5build1) ... 124s Setting up libsnappy-jni (1.1.10.5-1) ... 124s Setting up libxcomposite1:amd64 (1:0.4.5-1build2) ... 124s Setting up libcc1-0:amd64 (14-20240303-1ubuntu1) ... 124s Setting up liblsan0:amd64 (14-20240303-1ubuntu1) ... 124s Setting up libitm1:amd64 (14-20240303-1ubuntu1) ... 124s Setting up libdrm-amdgpu1:amd64 (2.4.120-2) ... 124s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 124s Setting up libmbedx509-1:amd64 (2.28.7-1ubuntu1) ... 124s Setting up libmbedtls14:amd64 (2.28.7-1ubuntu1) ... 124s Setting up cpp-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 124s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 124s Setting up libxtst6:amd64 (2:1.2.3-1.1) ... 124s Setting up libxcursor1:amd64 (1:1.2.1-1) ... 124s Setting up libgl1-mesa-dri:amd64 (24.0.1-1ubuntu1) ... 124s Setting up libcommons-parent-java (56-1) ... 124s Setting up libavahi-common3:amd64 (0.8-13ubuntu2) ... 124s Setting up libncbi-vdb3:amd64 (3.0.2+dfsg-2) ... 124s Setting up libcommons-logging-java (1.3.0-1ubuntu1) ... 124s Setting up libcommons-jexl2-java (2.1.1-6) ... 124s Setting up libthai0:amd64 (0.1.29-2) ... 124s Setting up libcommons-lang3-java (3.14.0-1) ... 124s Setting up libgcc-13-dev:amd64 (13.2.0-17ubuntu2) ... 124s Setting up libtiff6:amd64 (4.5.1+git230720-3ubuntu1) ... 124s Setting up libc6-dev:amd64 (2.39-0ubuntu6) ... 124s Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-3) ... 125s Setting up libsnappy-java (1.1.10.5-1) ... 125s Setting up libfontconfig1:amd64 (2.15.0-1ubuntu1) ... 125s Setting up libcommons-codec-java (1.16.0-1) ... 125s Setting up libavahi-client3:amd64 (0.8-13ubuntu2) ... 125s Setting up libstdc++-13-dev:amd64 (13.2.0-17ubuntu2) ... 125s Setting up cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 125s Setting up libncbi-ngs3:amd64 (3.0.3+dfsg-6ubuntu1) ... 125s Setting up gtk-update-icon-cache (3.24.40-2ubuntu1) ... 125s Setting up fontconfig (2.15.0-1ubuntu1) ... 127s Regenerating fonts cache... done. 127s Setting up libngs-jni:amd64 (3.0.3+dfsg-6ubuntu1) ... 127s Setting up libglx-mesa0:amd64 (24.0.1-1ubuntu1) ... 127s Setting up libglx0:amd64 (1.7.0-1) ... 127s Setting up cpp-13 (13.2.0-17ubuntu2) ... 127s Setting up libcommons-compress-java (1.25.0-1) ... 127s Setting up libcommons-io-java (2.11.0-2) ... 127s Setting up gcc-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 127s Setting up libpango-1.0-0:amd64 (1.51.0+ds-4) ... 127s Setting up libcairo2:amd64 (1.18.0-1) ... 127s Setting up libgl1:amd64 (1.7.0-1) ... 127s Setting up gcc-13 (13.2.0-17ubuntu2) ... 127s Setting up libcups2:amd64 (2.4.6-0ubuntu3) ... 127s Setting up libhttpclient-java (4.5.14-1) ... 127s Setting up cpp (4:13.2.0-7ubuntu1) ... 127s Setting up liblightcouch-java (0.2.0-1) ... 127s Setting up libngs-java:amd64 (3.0.3+dfsg-6ubuntu1) ... 127s Setting up libpangoft2-1.0-0:amd64 (1.51.0+ds-4) ... 127s Setting up libhtsjdk-java (4.1.0+dfsg-1) ... 127s Setting up libpangocairo-1.0-0:amd64 (1.51.0+ds-4) ... 127s Setting up openjdk-21-jre-headless:amd64 (21.0.2+13-2) ... 127s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode 127s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 127s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 127s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 127s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 127s Setting up g++-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 127s Setting up gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 127s Setting up liblog4j2-java (2.19.0-2) ... 127s Setting up gcc (4:13.2.0-7ubuntu1) ... 127s Setting up g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 127s Setting up libbarclay-java (5.0.0+dfsg-1) ... 127s Setting up g++-13 (13.2.0-17ubuntu2) ... 127s Setting up libgkl-java (0.8.11+dfsg-2) ... 127s Setting up libpicard-java (3.1.1+dfsg-1) ... 127s Setting up g++ (4:13.2.0-7ubuntu1) ... 127s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 127s Setting up build-essential (12.10ubuntu1) ... 127s Setting up adwaita-icon-theme (46~rc-1) ... 127s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode 127s Setting up libgtk2.0-0:amd64 (2.24.33-2ubuntu2) ... 127s Setting up humanity-icon-theme (0.6.16) ... 127s Setting up ubuntu-mono (24.04-0ubuntu1) ... 127s Processing triggers for man-db (2.12.0-3) ... 128s Processing triggers for libc-bin (2.39-0ubuntu6) ... 128s Processing triggers for ca-certificates-java (20240118) ... 129s Adding debian:ACCVRAIZ1.pem 129s Adding debian:AC_RAIZ_FNMT-RCM.pem 129s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 129s Adding debian:ANF_Secure_Server_Root_CA.pem 129s Adding debian:Actalis_Authentication_Root_CA.pem 129s Adding debian:AffirmTrust_Commercial.pem 129s Adding debian:AffirmTrust_Networking.pem 129s Adding debian:AffirmTrust_Premium.pem 129s Adding debian:AffirmTrust_Premium_ECC.pem 129s Adding debian:Amazon_Root_CA_1.pem 129s Adding debian:Amazon_Root_CA_2.pem 129s Adding debian:Amazon_Root_CA_3.pem 129s Adding debian:Amazon_Root_CA_4.pem 129s Adding debian:Atos_TrustedRoot_2011.pem 129s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 129s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 129s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 129s Adding debian:BJCA_Global_Root_CA1.pem 129s Adding debian:BJCA_Global_Root_CA2.pem 129s Adding debian:Baltimore_CyberTrust_Root.pem 129s Adding debian:Buypass_Class_2_Root_CA.pem 129s Adding debian:Buypass_Class_3_Root_CA.pem 129s Adding debian:CA_Disig_Root_R2.pem 129s Adding debian:CFCA_EV_ROOT.pem 129s Adding debian:COMODO_Certification_Authority.pem 129s Adding debian:COMODO_ECC_Certification_Authority.pem 129s Adding debian:COMODO_RSA_Certification_Authority.pem 129s Adding debian:Certainly_Root_E1.pem 129s Adding debian:Certainly_Root_R1.pem 129s Adding debian:Certigna.pem 129s Adding debian:Certigna_Root_CA.pem 129s Adding debian:Certum_EC-384_CA.pem 129s Adding debian:Certum_Trusted_Network_CA.pem 129s Adding debian:Certum_Trusted_Network_CA_2.pem 129s Adding debian:Certum_Trusted_Root_CA.pem 129s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 129s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 129s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 129s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 129s Adding debian:Comodo_AAA_Services_root.pem 129s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 129s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 129s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 129s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 129s Adding debian:DigiCert_Assured_ID_Root_CA.pem 129s Adding debian:DigiCert_Assured_ID_Root_G2.pem 129s Adding debian:DigiCert_Assured_ID_Root_G3.pem 129s Adding debian:DigiCert_Global_Root_CA.pem 129s Adding debian:DigiCert_Global_Root_G2.pem 129s Adding debian:DigiCert_Global_Root_G3.pem 129s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 129s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 129s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 129s Adding debian:DigiCert_Trusted_Root_G4.pem 129s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 129s Adding debian:Entrust_Root_Certification_Authority.pem 129s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 129s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 129s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 129s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 129s Adding debian:GLOBALTRUST_2020.pem 129s Adding debian:GTS_Root_R1.pem 129s Adding debian:GTS_Root_R2.pem 129s Adding debian:GTS_Root_R3.pem 129s Adding debian:GTS_Root_R4.pem 129s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 129s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 129s Adding debian:GlobalSign_Root_CA.pem 129s Adding debian:GlobalSign_Root_CA_-_R3.pem 129s Adding debian:GlobalSign_Root_CA_-_R6.pem 129s Adding debian:GlobalSign_Root_E46.pem 129s Adding debian:GlobalSign_Root_R46.pem 129s Adding debian:Go_Daddy_Class_2_CA.pem 129s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 129s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 129s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 129s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 129s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 129s Adding debian:HiPKI_Root_CA_-_G1.pem 129s Adding debian:Hongkong_Post_Root_CA_3.pem 129s Adding debian:ISRG_Root_X1.pem 129s Adding debian:ISRG_Root_X2.pem 129s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 129s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 129s Adding debian:Izenpe.com.pem 129s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 129s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 129s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 129s Adding debian:NAVER_Global_Root_Certification_Authority.pem 129s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 129s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 129s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 129s Adding debian:QuoVadis_Root_CA_1_G3.pem 129s Adding debian:QuoVadis_Root_CA_2.pem 129s Adding debian:QuoVadis_Root_CA_2_G3.pem 129s Adding debian:QuoVadis_Root_CA_3.pem 129s Adding debian:QuoVadis_Root_CA_3_G3.pem 129s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 129s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 129s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 129s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 129s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 129s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 129s Adding debian:SZAFIR_ROOT_CA2.pem 129s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 129s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 129s Adding debian:SecureSign_RootCA11.pem 129s Adding debian:SecureTrust_CA.pem 129s Adding debian:Secure_Global_CA.pem 129s Adding debian:Security_Communication_ECC_RootCA1.pem 129s Adding debian:Security_Communication_RootCA2.pem 129s Adding debian:Security_Communication_RootCA3.pem 129s Adding debian:Security_Communication_Root_CA.pem 129s Adding debian:Starfield_Class_2_CA.pem 129s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 129s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 129s Adding debian:SwissSign_Gold_CA_-_G2.pem 129s Adding debian:SwissSign_Silver_CA_-_G2.pem 129s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 129s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 129s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 129s Adding debian:TWCA_Global_Root_CA.pem 129s Adding debian:TWCA_Root_Certification_Authority.pem 129s Adding debian:TeliaSonera_Root_CA_v1.pem 129s Adding debian:Telia_Root_CA_v2.pem 129s Adding debian:TrustAsia_Global_Root_CA_G3.pem 129s Adding debian:TrustAsia_Global_Root_CA_G4.pem 129s Adding debian:Trustwave_Global_Certification_Authority.pem 129s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 129s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 129s Adding debian:TunTrust_Root_CA.pem 129s Adding debian:UCA_Extended_Validation_Root.pem 129s Adding debian:UCA_Global_G2_Root.pem 129s Adding debian:USERTrust_ECC_Certification_Authority.pem 129s Adding debian:USERTrust_RSA_Certification_Authority.pem 129s Adding debian:XRamp_Global_CA_Root.pem 129s Adding debian:certSIGN_ROOT_CA.pem 129s Adding debian:certSIGN_Root_CA_G2.pem 129s Adding debian:e-Szigno_Root_CA_2017.pem 129s Adding debian:ePKI_Root_Certification_Authority.pem 129s Adding debian:emSign_ECC_Root_CA_-_C3.pem 129s Adding debian:emSign_ECC_Root_CA_-_G3.pem 129s Adding debian:emSign_Root_CA_-_C1.pem 129s Adding debian:emSign_Root_CA_-_G1.pem 129s Adding debian:vTrus_ECC_Root_CA.pem 129s Adding debian:vTrus_Root_CA.pem 129s done. 129s Setting up openjdk-21-jre:amd64 (21.0.2+13-2) ... 129s Setting up default-jre-headless (2:1.21-75+exp1) ... 129s Setting up default-jre (2:1.21-75+exp1) ... 129s Setting up picard-tools (3.1.1+dfsg-1) ... 130s Reading package lists... 130s Building dependency tree... 130s Reading state information... 130s Starting pkgProblemResolver with broken count: 0 131s Starting 2 pkgProblemResolver with broken count: 0 131s Done 131s The following NEW packages will be installed: 131s autopkgtest-satdep 131s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 131s Need to get 0 B/696 B of archives. 131s After this operation, 0 B of additional disk space will be used. 131s Get:1 /tmp/autopkgtest.ntvePJ/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [696 B] 131s Selecting previously unselected package autopkgtest-satdep. 131s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 88776 files and directories currently installed.) 131s Preparing to unpack .../2-autopkgtest-satdep.deb ... 131s Unpacking autopkgtest-satdep (0) ... 131s Setting up autopkgtest-satdep (0) ... 132s autopkgtest: WARNING: package picard-tools:i386 is not installed though it should be 133s (Reading database ... 88776 files and directories currently installed.) 133s Removing autopkgtest-satdep (0) ... 133s autopkgtest [17:45:31]: test run-unit-test: [----------------------- 133s JavOpt: 133s PicardProg: ViewSam 133s PicardOpts: PF_STATUS=All ALIGNMENT_STATUS=All INPUT=unmapped.sam 134s INFO 2024-03-24 17:45:32 ViewSam 134s 134s ********** NOTE: Picard's command line syntax is changing. 134s ********** 134s ********** For more information, please see: 134s ********** 134s https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) 134s ********** 134s ********** The command line looks like this in the new syntax: 134s ********** 134s ********** ViewSam -PF_STATUS All -ALIGNMENT_STATUS All -INPUT unmapped.sam 134s ********** 134s 134s 134s 17:45:32.502 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 134s 17:45:32.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 134s 17:45:32.504 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Unable to load libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 134s 17:45:32.506 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 134s 17:45:32.506 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 134s 17:45:32.506 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Unable to load libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 134s [Sun Mar 24 17:45:32 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 134s [Sun Mar 24 17:45:32 UTC 2024] Executing as ubuntu@autopkgtest on Linux 6.8.0-11-generic amd64; OpenJDK 64-Bit Server VM 21.0.2+13-Ubuntu-2; Deflater: Jdk; Inflater: Jdk; Provider GCS is available; Picard version: 3.1.1 134s @HD VN:1.0 SO:queryname 134s @RG ID:0 SM:Hi,Mom! PL:ILLUMINA 134s 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 134s 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 134s 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 134s 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 134s 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 134s 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 134s 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 134s 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 134s 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 134s 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 134s [Sun Mar 24 17:45:32 UTC 2024] picard.sam.ViewSam done. Elapsed time: 0.00 minutes. 134s Runtime.totalMemory()=67108864 134s JavOpt: 134s PicardProg: CollectSequencingArtifactMetrics 134s PicardOpts: I=test.sam O=test R=test.fasta 135s INFO 2024-03-24 17:45:33 CollectSequencingArtifactMetrics 135s 135s ********** NOTE: Picard's command line syntax is changing. 135s ********** 135s ********** For more information, please see: 135s ********** 135s https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) 135s ********** 135s ********** The command line looks like this in the new syntax: 135s ********** 135s ********** CollectSequencingArtifactMetrics -I test.sam -O test -R test.fasta 135s ********** 135s 135s 135s 17:45:33.339 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 135s 17:45:33.341 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 135s 17:45:33.341 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Unable to load libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 135s 17:45:33.342 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 135s 17:45:33.342 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 135s 17:45:33.343 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Unable to load libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 135s [Sun Mar 24 17:45:33 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 135s [Sun Mar 24 17:45:33 UTC 2024] Executing as ubuntu@autopkgtest on Linux 6.8.0-11-generic amd64; OpenJDK 64-Bit Server VM 21.0.2+13-Ubuntu-2; Deflater: Jdk; Inflater: Jdk; Provider GCS is available; Picard version: 3.1.1 135s [Sun Mar 24 17:45:33 UTC 2024] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes. 135s Runtime.totalMemory()=67108864 135s All output files generated 135s JavOpt: 135s PicardProg: SortVcf 135s PicardOpts: I=mini.vcf O=mini_sorted.vcf 136s INFO 2024-03-24 17:45:34 SortVcf 136s 136s ********** NOTE: Picard's command line syntax is changing. 136s ********** 136s ********** For more information, please see: 136s ********** 136s https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) 136s ********** 136s ********** The command line looks like this in the new syntax: 136s ********** 136s ********** SortVcf -I mini.vcf -O mini_sorted.vcf 136s ********** 136s 136s 136s 17:45:34.282 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 136s 17:45:34.284 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 136s 17:45:34.284 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Unable to load libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 136s 17:45:34.285 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 136s 17:45:34.285 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 136s 17:45:34.286 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Unable to load libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 136s [Sun Mar 24 17:45:34 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 136s [Sun Mar 24 17:45:34 UTC 2024] Executing as ubuntu@autopkgtest on Linux 6.8.0-11-generic amd64; OpenJDK 64-Bit Server VM 21.0.2+13-Ubuntu-2; Deflater: Jdk; Inflater: Jdk; Provider GCS is available; Picard version: 3.1.1 136s INFO 2024-03-24 17:45:34 SortVcf Reading entries from input file 1 136s [Sun Mar 24 17:45:34 UTC 2024] picard.vcf.SortVcf done. Elapsed time: 0.01 minutes. 136s Runtime.totalMemory()=67108864 136s sorted vcf generated 136s JavOpt: 136s PicardProg: SplitVcfs 136s PicardOpts: I=mini.vcf SNP_OUTPUT=snp.vcf INDEL_OUTPUT=indel.vcf 137s INFO 2024-03-24 17:45:35 SplitVcfs 137s 137s ********** NOTE: Picard's command line syntax is changing. 137s ********** 137s ********** For more information, please see: 137s ********** 137s https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) 137s ********** 137s ********** The command line looks like this in the new syntax: 137s ********** 137s ********** SplitVcfs -I mini.vcf -SNP_OUTPUT snp.vcf -INDEL_OUTPUT indel.vcf 137s ********** 137s 137s 137s 17:45:35.405 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 137s 17:45:35.407 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 137s 17:45:35.407 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Unable to load libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 137s 17:45:35.408 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 137s 17:45:35.408 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 137s 17:45:35.408 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Unable to load libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 137s [Sun Mar 24 17:45:35 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 137s [Sun Mar 24 17:45:35 UTC 2024] Executing as ubuntu@autopkgtest on Linux 6.8.0-11-generic amd64; OpenJDK 64-Bit Server VM 21.0.2+13-Ubuntu-2; Deflater: Jdk; Inflater: Jdk; Provider GCS is available; Picard version: 3.1.1 137s [Sun Mar 24 17:45:35 UTC 2024] picard.vcf.SplitVcfs done. Elapsed time: 0.01 minutes. 137s Runtime.totalMemory()=67108864 137s snp and indel vcfs generated 138s autopkgtest [17:45:36]: test run-unit-test: -----------------------] 138s autopkgtest [17:45:36]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 138s run-unit-test PASS 138s autopkgtest [17:45:36]: @@@@@@@@@@@@@@@@@@@@ summary 138s run-unit-test PASS 150s Creating nova instance adt-noble-i386-picard-tools-20240324-174318-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-amd64-server-20240324.img (UUID 4e56ccec-954f-4884-8b9c-3e1a29e50308)...