Tue Nov 12 23:38:38 UTC 2024 I: starting to build biojava-live/trixie/arm64 on jenkins on '2024-11-12 23:38' Tue Nov 12 23:38:38 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_23/65917/console.log Tue Nov 12 23:38:38 UTC 2024 I: Downloading source for trixie/biojava-live=1:1.9.7+dfsg-2 --2024-11-12 23:38:38-- http://deb.debian.org/debian/pool/main/b/biojava-live/biojava-live_1.9.7%2bdfsg-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2337 (2.3K) [text/prs.lines.tag] Saving to: ‘biojava-live_1.9.7+dfsg-2.dsc’ 0K .. 100% 321M=0s 2024-11-12 23:38:38 (321 MB/s) - ‘biojava-live_1.9.7+dfsg-2.dsc’ saved [2337/2337] Tue Nov 12 23:38:38 UTC 2024 I: biojava-live_1.9.7+dfsg-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: biojava-live Binary: libbiojava1.9-java, libbiojava-java Architecture: all Version: 1:1.9.7+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille , Olivier Sallou , Pierre Gruet Homepage: https://www.biojava.org Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/biojava-live Vcs-Git: https://salsa.debian.org/med-team/biojava-live.git Build-Depends: debhelper-compat (= 13), maven-debian-helper Build-Depends-Indep: default-jdk, junit4 , libcommons-dbcp-java, libjaxb-api-java, libjgrapht0.8-java, libxerces2-java Package-List: libbiojava-java deb java optional arch=all libbiojava1.9-java deb java optional arch=all Checksums-Sha1: 8874aedb4a761cc6e9b1851b4671b86f088e5cc0 3788920 biojava-live_1.9.7+dfsg.orig.tar.xz 07d4c015619996c1ce607eb3749e0a0d4357aeb9 10084 biojava-live_1.9.7+dfsg-2.debian.tar.xz Checksums-Sha256: 9024a431db30ee08fd155031f6d279a708668c6fffd4c63811f990db3a7e9cbd 3788920 biojava-live_1.9.7+dfsg.orig.tar.xz d4d7a803434ece4d62999e1551f8080ea8b32481ebb3d8987bcab470474af8b6 10084 biojava-live_1.9.7+dfsg-2.debian.tar.xz Files: 8a138dacf9f57de4640ec4f46693d293 3788920 biojava-live_1.9.7+dfsg.orig.tar.xz adab9db73b1538f9df38d36abc6e3147 10084 biojava-live_1.9.7+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEuM5N4hCA3PkD4WxA9RPEGeS50KwFAmcDlOgSHGVib3VyZ0Bh cGFjaGUub3JnAAoJEPUTxBnkudCsajcQAKI61OQNkjrQAXyc95/eKLnL+r2kUmqh 79xcbD6CN2o0bcMqOUW5IaR7ZznE1r9VTqB5ymg31i7SK249SLIiJc+VhSmjftTM 9Ipww1fidz8xBG7EtQyVcTJ00AyfygusMmzLg+ym8myfvT8t/7Vwl3QrX+/TSjBL m9254PH8c4MAH24RRU/76avzhewoHbSBftHHCLnbG1rgu7NLQbYd7+acHtOzT77r cM09VE/L3DiP3OIalTPNyDfGRNxmwJg6Vr36bguyGGkhfyO0MhqqbayroQ8IVgCj GhDSEk1xTw7JEbB3zT75TNmiHscBvp6O43WgqlUZtOp0jCfCTeYQJNANrmoVZZJq B7BDqUed5Q73doWNgZsYHVjEJxUu+/zDn1HZEApt3knrebKb7AakJ02TmijUX3sV ibe0tl4x1qyYSyXrXP4cXZy9jhB+tyuElNu8Hw8e6lVoO6/keKyALVgx2bUnVVDn 0TYuAqYS45NCBS3lMmPnaswmZaoVUFBgQ+sj1SICA2xOmnw3vD2Uij2UBREPJogC 6DnqeLTY0jjf7FuCRxyJSKoYhAdPWchkTRFvsWIvpafWZ+Evgub7JOQHNwxq+IhJ gCkW6X6QPIXd7hACWEcKzlLlT96aCL7OMVqKeOX9IhhcingiT/vXLTLAY65X/6sT 86Kpi4t30lPC =CqGb -----END PGP SIGNATURE----- Tue Nov 12 23:38:38 UTC 2024 I: Checking whether the package is not for us Tue Nov 12 23:38:38 UTC 2024 I: Starting 1st build on remote node codethink03-arm64.debian.net. Tue Nov 12 23:38:38 UTC 2024 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Tue Nov 12 23:44:55 UTC 2024 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Dec 15 18:01:41 -12 2025 I: pbuilder-time-stamp: 1765864901 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [biojava-live_1.9.7+dfsg-2.dsc] I: copying [./biojava-live_1.9.7+dfsg.orig.tar.xz] I: copying [./biojava-live_1.9.7+dfsg-2.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Oct 7 07:59:36 2024 gpgv: using RSA key B8CE4DE21080DCF903E16C40F513C419E4B9D0AC gpgv: issuer "ebourg@apache.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./biojava-live_1.9.7+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting biojava-live in biojava-live-1.9.7+dfsg dpkg-source: info: unpacking biojava-live_1.9.7+dfsg.orig.tar.xz dpkg-source: info: unpacking biojava-live_1.9.7+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying omit_tests_with_problematic_data.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3325553/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='29ebe7d1a763456995238647ea496339' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='3325553' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.HGIaNXaC/pbuilderrc_VTD8 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.HGIaNXaC/b1 --logfile b1/build.log biojava-live_1.9.7+dfsg-2.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3325553/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), maven-debian-helper, default-jdk, junit4, libcommons-dbcp-java, libjaxb-api-java, libjgrapht0.8-java, libxerces2-java dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20089 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on maven-debian-helper; however: Package maven-debian-helper is not installed. pbuilder-satisfydepends-dummy depends on default-jdk; however: Package default-jdk is not installed. pbuilder-satisfydepends-dummy depends on junit4; however: Package junit4 is not installed. pbuilder-satisfydepends-dummy depends on libcommons-dbcp-java; however: Package libcommons-dbcp-java is not installed. pbuilder-satisfydepends-dummy depends on libjaxb-api-java; however: Package libjaxb-api-java is not installed. pbuilder-satisfydepends-dummy depends on libjgrapht0.8-java; however: Package libjgrapht0.8-java is not installed. pbuilder-satisfydepends-dummy depends on libxerces2-java; however: Package libxerces2-java is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: adwaita-icon-theme{a} ant{a} at-spi2-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} dbus{a} dbus-bin{a} dbus-daemon{a} dbus-session-bus-common{a} dbus-system-bus-common{a} dbus-user-session{a} dconf-gsettings-backend{a} dconf-service{a} debhelper{a} default-jdk{a} default-jdk-headless{a} default-jre{a} default-jre-headless{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} intltool-debian{a} java-common{a} junit4{a} junit5{a} libactivation-java{a} libaopalliance-java{a} libapache-pom-java{a} libapiguardian-java{a} libapparmor1{a} libarchive-zip-perl{a} libasm-java{a} libasound2-data{a} libasound2t64{a} libatinject-jsr330-api-java{a} libatk-bridge2.0-0t64{a} libatk1.0-0t64{a} libatspi2.0-0t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbrotli1{a} libbsh-java{a} libcairo-gobject2{a} libcairo2{a} libcdi-api-java{a} libcloudproviders0{a} libcolord2{a} libcom-err2{a} libcommons-beanutils-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-compress-java{a} libcommons-dbcp-java{a} libcommons-digester-java{a} libcommons-io-java{a} libcommons-lang-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-parent-java{a} libcommons-pool-java{a} libcommons-text-java{a} libcommons-validator-java{a} libcups2t64{a} libdatrie1{a} libdbus-1-3{a} libdconf1{a} libdebhelper-perl{a} libdeflate0{a} libdom4j-java{a} libdoxia-core-java{a} libdoxia-java{a} libdoxia-sitetools-java{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libel-api-java{a} libelf1t64{a} libepoxy0{a} liberror-prone-java{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgbm1{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libgif7{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0t64{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgtk-3-0t64{a} libgtk-3-common{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{a} libhttpclient-java{a} libhttpcore-java{a} libicu72{a} libjansi-java{a} libjaxb-api-java{a} libjaxen-java{a} libjbig0{a} libjetty9-java{a} libjgraph-java{a} libjgrapht0.8-java{a} libjpeg62-turbo{a} libjsoup-java{a} libjsp-api-java{a} libjsr305-java{a} libjtidy-java{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} liblerc4{a} libllvm19{a} libmagic-mgc{a} libmagic1t64{a} libmaven-archiver-java{a} libmaven-clean-plugin-java{a} libmaven-common-artifact-filters-java{a} libmaven-compiler-plugin-java{a} libmaven-file-management-java{a} libmaven-filtering-java{a} libmaven-jar-plugin-java{a} libmaven-parent-java{a} libmaven-plugin-tools-java{a} libmaven-reporting-api-java{a} libmaven-reporting-exec-java{a} libmaven-resolver-java{a} libmaven-resources-plugin-java{a} libmaven-shared-incremental-java{a} libmaven-shared-io-java{a} libmaven-shared-utils-java{a} libmaven-site-plugin-java{a} libmaven3-core-java{a} libnspr4{a} libnss3{a} libopentest4j-java{a} libopentest4j-reporting-java{a} liboro-java{a} libpam-systemd{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpcsclite1{a} libpicocli-java{a} libpipeline1{a} libpixman-1-0{a} libplexus-ant-factory-java{a} libplexus-archiver-java{a} libplexus-bsh-factory-java{a} libplexus-build-api-java{a} libplexus-cipher-java{a} libplexus-classworlds-java{a} libplexus-compiler-java{a} libplexus-component-annotations-java{a} libplexus-container-default-java{a} libplexus-container-default1.5-java{a} libplexus-i18n-java{a} libplexus-interpolation-java{a} libplexus-io-java{a} libplexus-languages-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libplexus-velocity-java{a} libplexus-xml-java{a} libpng16-16t64{a} libproc2-0{a} libqdox2-java{a} libsensors-config{a} libsensors5{a} libservlet-api-java{a} libsharpyuv0{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libsurefire-java{a} libsystemd-shared{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libunivocity-parsers-java{a} libvelocity-tools-java{a} libvulkan1{a} libwagon-file-java{a} libwagon-http-shaded-java{a} libwagon-provider-api-java{a} libwayland-client0{a} libwayland-cursor0{a} libwayland-egl1{a} libwayland-server0{a} libwebp7{a} libwebsocket-api-java{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxbean-reflect-java{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxerces2-java{a} libxext6{a} libxfixes3{a} libxi6{a} libxinerama1{a} libxkbcommon0{a} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxml2-utils{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxtst6{a} libxxf86vm1{a} libxz-java{a} libz3-4{a} m4{a} man-db{a} maven{a} maven-debian-helper{a} maven-repo-helper{a} mesa-libgallium{a} openjdk-21-jdk{a} openjdk-21-jdk-headless{a} openjdk-21-jre{a} openjdk-21-jre-headless{a} openssl{a} po-debconf{a} procps{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} systemd{a} systemd-sysv{a} unzip{a} velocity{a} x11-common{a} xkb-data{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf ant-optional at-spi2-core chrony curl fonts-dejavu-extra krb5-locales libarchive-cpio-perl libatk-wrapper-java-jni libgdk-pixbuf2.0-bin libglib2.0-data libgtk-3-bin libkmod2 libltdl-dev libmail-sendmail-perl libnss-systemd librsvg2-common libxt-dev linux-sysctl-defaults lynx mesa-vulkan-drivers ntpsec openntpd psmisc systemd-cryptsetup systemd-timesyncd wget xdg-user-dirs 0 packages upgraded, 287 newly installed, 0 to remove and 0 not upgraded. Need to get 252 MB of archives. After unpacking 770 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libapparmor1 arm64 3.1.7-1+b2 [41.8 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libsystemd-shared arm64 256.7-3 [1841 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 systemd arm64 256.7-3 [3259 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 systemd-sysv arm64 256.7-3 [58.7 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 libdbus-1-3 arm64 1.14.10-6 [196 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 dbus-bin arm64 1.14.10-6 [105 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 dbus-session-bus-common all 1.14.10-6 [79.2 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.3-2 [90.1 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 dbus-daemon arm64 1.14.10-6 [178 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 dbus-system-bus-common all 1.14.10-6 [80.2 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 dbus arm64 1.14.10-6 [97.4 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 sgml-base all 1.31 [15.4 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 libproc2-0 arm64 2:4.0.4-6 [62.3 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 procps arm64 2:4.0.4-6 [872 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.3.2-2 [1347 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20240203 [158 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libpam-systemd arm64 256.7-3 [260 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-9 [96.6 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [311 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0t64 arm64 2.82.2-2 [1409 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.1 [630 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 shared-mime-info arm64 2.4-5+b1 [755 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libpng16-16t64 arm64 1.6.44-2 [273 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libsharpyuv0 arm64 1.4.0-0.1+b1 [112 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libwebp7 arm64 1.4.0-0.1+b1 [268 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.12+dfsg-1+b1 [131 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 gtk-update-icon-cache arm64 4.16.3+ds-2 [49.7 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 hicolor-icon-theme all 0.18-1 [12.0 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 adwaita-icon-theme all 47.0-2 [463 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 ca-certificates-java all 20240118 [11.6 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 java-common all 0.76 [6776 B] Get: 47 http://deb.debian.org/debian trixie/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libnspr4 arm64 2:4.35-1.1+b1 [101 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libnss3 arm64 2:3.105-2 [1292 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libpcsclite1 arm64 2.3.0-3 [55.1 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 openjdk-21-jre-headless arm64 21.0.5+11-1 [40.6 MB] Get: 52 http://deb.debian.org/debian trixie/main arm64 default-jre-headless arm64 2:1.21-76 [3192 B] Get: 53 http://deb.debian.org/debian trixie/main arm64 ant all 1.10.15-1 [2163 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 at-spi2-common all 2.54.0-1 [170 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 dbus-user-session arm64 1.14.10-6 [79.0 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libdconf1 arm64 0.40.0-4+b3 [40.4 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 dconf-service arm64 0.40.0-4+b3 [31.1 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 dconf-gsettings-backend arm64 0.40.0-4+b3 [27.4 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-8 [517 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 70 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 libatk1.0-0t64 arm64 2.54.0-1 [49.7 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.2-3+b2 [24.4 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 libxi6 arm64 2:1.8.2-1 [77.8 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 libatspi2.0-0t64 arm64 2.54.0-1 [72.9 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libatk-bridge2.0-0t64 arm64 2.54.0-1 [64.4 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b5 [296 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 fontconfig-config arm64 2.15.0-1.1+b1 [318 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 libfontconfig1 arm64 2.15.0-1.1+b1 [387 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libxrender1 arm64 1:0.9.10-1.1+b2 [27.2 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libcairo-gobject2 arm64 1.18.2-2 [130 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libcloudproviders0 arm64 0.3.6-1+b1 [27.7 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libcolord2 arm64 1.4.7-1+b2 [130 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libavahi-common-data arm64 0.8-13+b3 [112 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libavahi-common3 arm64 0.8-13+b3 [42.3 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libavahi-client3 arm64 0.8-13+b3 [46.0 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.1-1+b1 [23.1 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 107 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libcups2t64 arm64 2.4.10-2 [235 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libepoxy0 arm64 1.5.10-2 [200 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libfribidi0 arm64 1.0.15-1 [71.8 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libharfbuzz0b arm64 10.0.1-1 [441 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 fontconfig arm64 2.15.0-1.1+b1 [463 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 libpango-1.0-0 arm64 1.54.0+ds-3 [210 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 libpangoft2-1.0-0 arm64 1.54.0+ds-3 [51.8 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 libpangocairo-1.0-0 arm64 1.54.0+ds-3 [33.5 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 libwayland-client0 arm64 1.23.0-1+b1 [26.0 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 libwayland-cursor0 arm64 1.23.0-1+b1 [11.5 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 libwayland-egl1 arm64 1.23.0-1+b1 [5768 B] Get: 124 http://deb.debian.org/debian trixie/main arm64 libxcomposite1 arm64 1:0.4.6-1 [16.4 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 libxfixes3 arm64 1:6.0.0-2+b2 [20.5 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 libxcursor1 arm64 1:1.2.2-1+b1 [37.1 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 libxdamage1 arm64 1:1.1.6-1+b2 [15.6 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 libxinerama1 arm64 2:1.1.4-3+b2 [16.1 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 xkb-data all 2.42-1 [790 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 libxkbcommon0 arm64 1.6.0-1+b2 [105 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 libxrandr2 arm64 2:1.5.4-1+b1 [36.0 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 libgtk-3-common all 3.24.43-4 [4657 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 libgtk-3-0t64 arm64 3.24.43-4 [2546 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 libglvnd0 arm64 1.7.0-1+b2 [41.6 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 libdrm-common all 2.4.123-1 [8084 B] Get: 136 http://deb.debian.org/debian trixie/main arm64 libdrm2 arm64 2.4.123-1 [38.0 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 libglapi-mesa arm64 24.2.6-1 [47.8 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 libx11-xcb1 arm64 2:1.8.10-2 [241 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 libxcb-dri2-0 arm64 1.17.0-2+b1 [107 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 libxcb-dri3-0 arm64 1.17.0-2+b1 [107 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 libxcb-glx0 arm64 1.17.0-2+b1 [123 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 libxcb-present0 arm64 1.17.0-2+b1 [106 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 libxcb-randr0 arm64 1.17.0-2+b1 [117 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 libxcb-sync1 arm64 1.17.0-2+b1 [109 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 libxcb-xfixes0 arm64 1.17.0-2+b1 [110 kB] Get: 146 http://deb.debian.org/debian trixie/main arm64 libxshmfence1 arm64 1.3-1+b2 [9076 B] Get: 147 http://deb.debian.org/debian trixie/main arm64 libxxf86vm1 arm64 1:1.1.4-1+b3 [19.2 kB] Get: 148 http://deb.debian.org/debian trixie/main arm64 libdrm-amdgpu1 arm64 2.4.123-1 [21.6 kB] Get: 149 http://deb.debian.org/debian trixie/main arm64 libdrm-radeon1 arm64 2.4.123-1 [21.3 kB] Get: 150 http://deb.debian.org/debian trixie/main arm64 libedit2 arm64 3.1-20240808-1 [89.2 kB] Get: 151 http://deb.debian.org/debian trixie/main arm64 libz3-4 arm64 4.13.3-1 [7507 kB] Get: 152 http://deb.debian.org/debian trixie/main arm64 libllvm19 arm64 1:19.1.3-1 [23.3 MB] Get: 153 http://deb.debian.org/debian trixie/main arm64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get: 154 http://deb.debian.org/debian trixie/main arm64 libsensors5 arm64 1:3.6.0-10+b1 [34.3 kB] Get: 155 http://deb.debian.org/debian trixie/main arm64 mesa-libgallium arm64 24.2.6-1 [7688 kB] Get: 156 http://deb.debian.org/debian trixie/main arm64 libvulkan1 arm64 1.3.296.0-1 [123 kB] Get: 157 http://deb.debian.org/debian trixie/main arm64 libwayland-server0 arm64 1.23.0-1+b1 [33.4 kB] Get: 158 http://deb.debian.org/debian trixie/main arm64 libgbm1 arm64 24.2.6-1 [42.0 kB] Get: 159 http://deb.debian.org/debian trixie/main arm64 libgl1-mesa-dri arm64 24.2.6-1 [43.6 kB] Get: 160 http://deb.debian.org/debian trixie/main arm64 libglx-mesa0 arm64 24.2.6-1 [152 kB] Get: 161 http://deb.debian.org/debian trixie/main arm64 libglx0 arm64 1.7.0-1+b2 [31.1 kB] Get: 162 http://deb.debian.org/debian trixie/main arm64 libgl1 arm64 1.7.0-1+b2 [90.9 kB] Get: 163 http://deb.debian.org/debian trixie/main arm64 libasound2-data all 1.2.12-1 [21.0 kB] Get: 164 http://deb.debian.org/debian trixie/main arm64 libasound2t64 arm64 1.2.12-1+b1 [336 kB] Get: 165 http://deb.debian.org/debian trixie/main arm64 libgif7 arm64 5.2.2-1+b1 [44.2 kB] Get: 166 http://deb.debian.org/debian trixie/main arm64 x11-common all 1:7.7+23.1 [216 kB] Get: 167 http://deb.debian.org/debian trixie/main arm64 libxtst6 arm64 2:1.2.3-1.1+b2 [26.0 kB] Get: 168 http://deb.debian.org/debian trixie/main arm64 openjdk-21-jre arm64 21.0.5+11-1 [193 kB] Get: 169 http://deb.debian.org/debian trixie/main arm64 default-jre arm64 2:1.21-76 [1068 B] Get: 170 http://deb.debian.org/debian trixie/main arm64 openjdk-21-jdk-headless arm64 21.0.5+11-1 [81.9 MB] Get: 171 http://deb.debian.org/debian trixie/main arm64 default-jdk-headless arm64 2:1.21-76 [1124 B] Get: 172 http://deb.debian.org/debian trixie/main arm64 openjdk-21-jdk arm64 21.0.5+11-1 [3422 kB] Get: 173 http://deb.debian.org/debian trixie/main arm64 default-jdk arm64 2:1.21-76 [1076 B] Get: 174 http://deb.debian.org/debian trixie/main arm64 libhamcrest-java all 2.2-2 [121 kB] Get: 175 http://deb.debian.org/debian trixie/main arm64 junit4 all 4.13.2-5 [350 kB] Get: 176 http://deb.debian.org/debian trixie/main arm64 libapiguardian-java all 1.1.2-1 [4656 B] Get: 177 http://deb.debian.org/debian trixie/main arm64 libopentest4j-java all 1.2.0-4 [9516 B] Get: 178 http://deb.debian.org/debian trixie/main arm64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 179 http://deb.debian.org/debian trixie/main arm64 libpicocli-java all 4.6.2-2 [390 kB] Get: 180 http://deb.debian.org/debian trixie/main arm64 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 181 http://deb.debian.org/debian trixie/main arm64 junit5 all 5.10.3-1 [2459 kB] Get: 182 http://deb.debian.org/debian trixie/main arm64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 183 http://deb.debian.org/debian trixie/main arm64 libaopalliance-java all 20070526-7 [8572 B] Get: 184 http://deb.debian.org/debian trixie/main arm64 libapache-pom-java all 33-2 [5852 B] Get: 185 http://deb.debian.org/debian trixie/main arm64 libasm-java all 9.7.1-1 [391 kB] Get: 186 http://deb.debian.org/debian trixie/main arm64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 187 http://deb.debian.org/debian trixie/main arm64 libbsh-java all 2.0b4-20 [291 kB] Get: 188 http://deb.debian.org/debian trixie/main arm64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 189 http://deb.debian.org/debian trixie/main arm64 libcdi-api-java all 1.2-4 [55.3 kB] Get: 190 http://deb.debian.org/debian trixie/main arm64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 191 http://deb.debian.org/debian trixie/main arm64 libcommons-parent-java all 56-1 [10.8 kB] Get: 192 http://deb.debian.org/debian trixie/main arm64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 193 http://deb.debian.org/debian trixie/main arm64 libcommons-beanutils-java all 1.9.4-2 [233 kB] Get: 194 http://deb.debian.org/debian trixie/main arm64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 195 http://deb.debian.org/debian trixie/main arm64 libcommons-codec-java all 1.17.1-1 [303 kB] Get: 196 http://deb.debian.org/debian trixie/main arm64 libcommons-io-java all 2.17.0-1 [488 kB] Get: 197 http://deb.debian.org/debian trixie/main arm64 libcommons-compress-java all 1.27.1-2 [641 kB] Get: 198 http://deb.debian.org/debian trixie/main arm64 libcommons-pool-java all 1.6-5 [109 kB] Get: 199 http://deb.debian.org/debian trixie/main arm64 libcommons-dbcp-java all 1.4-8 [157 kB] Get: 200 http://deb.debian.org/debian trixie/main arm64 libcommons-digester-java all 1.8.1-7 [138 kB] Get: 201 http://deb.debian.org/debian trixie/main arm64 libcommons-lang-java all 2.6-10 [273 kB] Get: 202 http://deb.debian.org/debian trixie/main arm64 libcommons-lang3-java all 3.17.0-1 [641 kB] Get: 203 http://deb.debian.org/debian trixie/main arm64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 204 http://deb.debian.org/debian trixie/main arm64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 205 http://deb.debian.org/debian trixie/main arm64 libslf4j-java all 1.7.32-1 [144 kB] Get: 206 http://deb.debian.org/debian trixie/main arm64 libsnappy1v5 arm64 1.2.1-1+b1 [28.7 kB] Get: 207 http://deb.debian.org/debian trixie/main arm64 libsnappy-jni arm64 1.1.10.5-2+b1 [6712 B] Get: 208 http://deb.debian.org/debian trixie/main arm64 libsnappy-java all 1.1.10.5-2 [87.5 kB] Get: 209 http://deb.debian.org/debian trixie/main arm64 libxz-java all 1.9-1 [143 kB] Get: 210 http://deb.debian.org/debian trixie/main arm64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 211 http://deb.debian.org/debian trixie/main arm64 libplexus-interpolation-java all 1.27-1 [76.8 kB] Get: 212 http://deb.debian.org/debian trixie/main arm64 libmaven-archiver-java all 3.6.2-1 [26.1 kB] Get: 213 http://deb.debian.org/debian trixie/main arm64 libmaven-shared-utils-java all 3.4.2-1 [137 kB] Get: 214 http://deb.debian.org/debian trixie/main arm64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 215 http://deb.debian.org/debian trixie/main arm64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 216 http://deb.debian.org/debian trixie/main arm64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 217 http://deb.debian.org/debian trixie/main arm64 libguava-java all 32.0.1-1 [2708 kB] Get: 218 http://deb.debian.org/debian trixie/main arm64 libguice-java all 4.2.3-2 [1435 kB] Get: 219 http://deb.debian.org/debian trixie/main arm64 libmaven-parent-java all 43-2 [6252 B] Get: 220 http://deb.debian.org/debian trixie/main arm64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 221 http://deb.debian.org/debian trixie/main arm64 libmaven-resolver-java all 1.6.3-1 [548 kB] Get: 222 http://deb.debian.org/debian trixie/main arm64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 223 http://deb.debian.org/debian trixie/main arm64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 224 http://deb.debian.org/debian trixie/main arm64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 225 http://deb.debian.org/debian trixie/main arm64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 226 http://deb.debian.org/debian trixie/main arm64 libsisu-inject-java all 0.3.4-2 [347 kB] Get: 227 http://deb.debian.org/debian trixie/main arm64 libsisu-plexus-java all 0.3.4-3 [181 kB] Get: 228 http://deb.debian.org/debian trixie/main arm64 libmaven3-core-java all 3.8.8-1 [1579 kB] Get: 229 http://deb.debian.org/debian trixie/main arm64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 230 http://deb.debian.org/debian trixie/main arm64 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 231 http://deb.debian.org/debian trixie/main arm64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 232 http://deb.debian.org/debian trixie/main arm64 libcommons-text-java all 1.12.0-1 [222 kB] Get: 233 http://deb.debian.org/debian trixie/main arm64 libcommons-validator-java all 1:1.7-1 [181 kB] Get: 234 http://deb.debian.org/debian trixie/main arm64 libjaxen-java all 1.1.6-5 [214 kB] Get: 235 http://deb.debian.org/debian trixie/main arm64 libdom4j-java all 2.1.4-1 [312 kB] Get: 236 http://deb.debian.org/debian trixie/main arm64 libdoxia-core-java all 2.0.0-1 [149 kB] Get: 237 http://deb.debian.org/debian trixie/main arm64 libplexus-xml-java all 3.0.1-2 [93.7 kB] Get: 238 http://deb.debian.org/debian trixie/main arm64 libdoxia-java all 2.0.0-1 [113 kB] Get: 239 http://deb.debian.org/debian trixie/main arm64 libmaven-reporting-api-java all 4.0.0-1 [6724 B] Get: 240 http://deb.debian.org/debian trixie/main arm64 libxbean-reflect-java all 4.5-9 [132 kB] Get: 241 http://deb.debian.org/debian trixie/main arm64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 242 http://deb.debian.org/debian trixie/main arm64 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB] Get: 243 http://deb.debian.org/debian trixie/main arm64 velocity all 1.7-7 [431 kB] Get: 244 http://deb.debian.org/debian trixie/main arm64 libplexus-velocity-java all 1.2-4 [9676 B] Get: 245 http://deb.debian.org/debian trixie/main arm64 liboro-java all 2.0.8a-14 [70.5 kB] Get: 246 http://deb.debian.org/debian trixie/main arm64 libvelocity-tools-java all 2.0-9 [311 kB] Get: 247 http://deb.debian.org/debian trixie/main arm64 libdoxia-sitetools-java all 2.0.0-1 [176 kB] Get: 248 http://deb.debian.org/debian trixie/main arm64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 249 http://deb.debian.org/debian trixie/main arm64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 250 http://deb.debian.org/debian trixie/main arm64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 251 http://deb.debian.org/debian trixie/main arm64 libjansi-java all 2.4.1-2 [100 kB] Get: 252 http://deb.debian.org/debian trixie/main arm64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 253 http://deb.debian.org/debian trixie/main arm64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 254 http://deb.debian.org/debian trixie/main arm64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 255 http://deb.debian.org/debian trixie/main arm64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 256 http://deb.debian.org/debian trixie/main arm64 libjetty9-java all 9.4.56-1 [2964 kB] Get: 257 http://deb.debian.org/debian trixie/main arm64 libjgraph-java all 5.12.4.2+dfsg-7 [207 kB] Get: 258 http://deb.debian.org/debian trixie/main arm64 libjgrapht0.8-java all 0.8.3-7 [216 kB] Get: 259 http://deb.debian.org/debian trixie/main arm64 libjsoup-java all 1.15.3-1 [431 kB] Get: 260 http://deb.debian.org/debian trixie/main arm64 libjtidy-java all 7+svn20110807-5 [250 kB] Get: 261 http://deb.debian.org/debian trixie/main arm64 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB] Get: 262 http://deb.debian.org/debian trixie/main arm64 libmaven-common-artifact-filters-java all 3.4.0-1 [47.7 kB] Get: 263 http://deb.debian.org/debian trixie/main arm64 libmaven-shared-incremental-java all 1.1-6 [9916 B] Get: 264 http://deb.debian.org/debian trixie/main arm64 libplexus-compiler-java all 2.13.0-1 [99.5 kB] Get: 265 http://deb.debian.org/debian trixie/main arm64 libqdox2-java all 2.0.3-1 [296 kB] Get: 266 http://deb.debian.org/debian trixie/main arm64 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 267 http://deb.debian.org/debian trixie/main arm64 libmaven-compiler-plugin-java all 3.13.0-1 [78.8 kB] Get: 268 http://deb.debian.org/debian trixie/main arm64 libplexus-build-api-java all 0.0.7-4 [10.3 kB] Get: 269 http://deb.debian.org/debian trixie/main arm64 libmaven-filtering-java all 3.4.0-1 [51.4 kB] Get: 270 http://deb.debian.org/debian trixie/main arm64 libplexus-container-default1.5-java all 2.1.1-1 [4476 B] Get: 271 http://deb.debian.org/debian trixie/main arm64 libplexus-ant-factory-java all 1.0~alpha2.1-4 [11.4 kB] Get: 272 http://deb.debian.org/debian trixie/main arm64 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B] Get: 273 http://deb.debian.org/debian trixie/main arm64 libmaven-plugin-tools-java all 3.10.2-1 [245 kB] Get: 274 http://deb.debian.org/debian trixie/main arm64 libmaven-reporting-exec-java all 2.0.0-1 [23.9 kB] Get: 275 http://deb.debian.org/debian trixie/main arm64 libmaven-resources-plugin-java all 3.3.1-1 [27.5 kB] Get: 276 http://deb.debian.org/debian trixie/main arm64 libmaven-site-plugin-java all 3.21.0-1 [106 kB] Get: 277 http://deb.debian.org/debian trixie/main arm64 libsurefire-java all 2.22.3-3 [1284 kB] Get: 278 http://deb.debian.org/debian trixie/main arm64 libwagon-file-java all 3.5.3-1 [8388 B] Get: 279 http://deb.debian.org/debian trixie/main arm64 libwagon-http-shaded-java all 3.5.3-1 [1341 kB] Get: 280 http://deb.debian.org/debian trixie/main arm64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 281 http://deb.debian.org/debian trixie/main arm64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 282 http://deb.debian.org/debian trixie/main arm64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 283 http://deb.debian.org/debian trixie/main arm64 libxml2-utils arm64 2.12.7+dfsg+really2.9.14-0.1 [97.4 kB] Get: 284 http://deb.debian.org/debian trixie/main arm64 maven all 3.8.8-1 [19.3 kB] Get: 285 http://deb.debian.org/debian trixie/main arm64 maven-repo-helper all 1.11 [142 kB] Get: 286 http://deb.debian.org/debian trixie/main arm64 unzip arm64 6.0-28+b1 [158 kB] Get: 287 http://deb.debian.org/debian trixie/main arm64 maven-debian-helper all 2.6.5 [108 kB] Fetched 252 MB in 2s (127 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libapparmor1:arm64. (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 ... 20089 files and directories currently installed.) Preparing to unpack .../libapparmor1_3.1.7-1+b2_arm64.deb ... Unpacking libapparmor1:arm64 (3.1.7-1+b2) ... Selecting previously unselected package libsystemd-shared:arm64. Preparing to unpack .../libsystemd-shared_256.7-3_arm64.deb ... Unpacking libsystemd-shared:arm64 (256.7-3) ... Selecting previously unselected package systemd. Preparing to unpack .../systemd_256.7-3_arm64.deb ... Unpacking systemd (256.7-3) ... Setting up libapparmor1:arm64 (3.1.7-1+b2) ... Setting up libsystemd-shared:arm64 (256.7-3) ... Setting up systemd (256.7-3) ... Created symlink '/etc/systemd/system/getty.target.wants/getty@tty1.service' -> '/usr/lib/systemd/system/getty@.service'. Created symlink '/etc/systemd/system/multi-user.target.wants/remote-fs.target' -> '/usr/lib/systemd/system/remote-fs.target'. Created symlink '/etc/systemd/system/sysinit.target.wants/systemd-pstore.service' -> '/usr/lib/systemd/system/systemd-pstore.service'. Initializing machine ID from random generator. Creating group 'systemd-journal' with GID 999. Creating group 'systemd-network' with GID 998. Creating user 'systemd-network' (systemd Network Management) with UID 998 and GID 998. /usr/lib/tmpfiles.d/legacy.conf:13: Duplicate line for path "/run/lock", ignoring. Selecting previously unselected package systemd-sysv. (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 ... 21040 files and directories currently installed.) Preparing to unpack .../000-systemd-sysv_256.7-3_arm64.deb ... Unpacking systemd-sysv (256.7-3) ... Selecting previously unselected package libdbus-1-3:arm64. Preparing to unpack .../001-libdbus-1-3_1.14.10-6_arm64.deb ... Unpacking libdbus-1-3:arm64 (1.14.10-6) ... Selecting previously unselected package dbus-bin. Preparing to unpack .../002-dbus-bin_1.14.10-6_arm64.deb ... Unpacking dbus-bin (1.14.10-6) ... Selecting previously unselected package dbus-session-bus-common. Preparing to unpack .../003-dbus-session-bus-common_1.14.10-6_all.deb ... Unpacking dbus-session-bus-common (1.14.10-6) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../004-libexpat1_2.6.3-2_arm64.deb ... Unpacking libexpat1:arm64 (2.6.3-2) ... Selecting previously unselected package dbus-daemon. Preparing to unpack .../005-dbus-daemon_1.14.10-6_arm64.deb ... Unpacking dbus-daemon (1.14.10-6) ... Selecting previously unselected package dbus-system-bus-common. Preparing to unpack .../006-dbus-system-bus-common_1.14.10-6_all.deb ... Unpacking dbus-system-bus-common (1.14.10-6) ... Selecting previously unselected package dbus. Preparing to unpack .../007-dbus_1.14.10-6_arm64.deb ... Unpacking dbus (1.14.10-6) ... Selecting previously unselected package sgml-base. Preparing to unpack .../008-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../009-libproc2-0_2%3a4.0.4-6_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../010-procps_2%3a4.0.4-6_arm64.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../011-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../012-openssl_3.3.2-2_arm64.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../013-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../014-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../015-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../016-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../017-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../018-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../019-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package libpam-systemd:arm64. Preparing to unpack .../020-libpam-systemd_256.7-3_arm64.deb ... Unpacking libpam-systemd:arm64 (256.7-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../021-bsdextrautils_2.40.2-9_arm64.deb ... Unpacking bsdextrautils (2.40.2-9) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../022-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../023-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package libgdk-pixbuf2.0-common. Preparing to unpack .../024-libgdk-pixbuf2.0-common_2.42.12+dfsg-1_all.deb ... Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ... Selecting previously unselected package libglib2.0-0t64:arm64. Preparing to unpack .../025-libglib2.0-0t64_2.82.2-2_arm64.deb ... Unpacking libglib2.0-0t64:arm64 (2.82.2-2) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../026-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../027-libxml2_2.12.7+dfsg+really2.9.14-0.1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.1) ... Selecting previously unselected package shared-mime-info. Preparing to unpack .../028-shared-mime-info_2.4-5+b1_arm64.deb ... Unpacking shared-mime-info (2.4-5+b1) ... Selecting previously unselected package libjpeg62-turbo:arm64. Preparing to unpack .../029-libjpeg62-turbo_1%3a2.1.5-3+b1_arm64.deb ... Unpacking libjpeg62-turbo:arm64 (1:2.1.5-3+b1) ... Selecting previously unselected package libpng16-16t64:arm64. Preparing to unpack .../030-libpng16-16t64_1.6.44-2_arm64.deb ... Unpacking libpng16-16t64:arm64 (1.6.44-2) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../031-libdeflate0_1.22-1_arm64.deb ... Unpacking libdeflate0:arm64 (1.22-1) ... Selecting previously unselected package libjbig0:arm64. Preparing to unpack .../032-libjbig0_2.1-6.1+b2_arm64.deb ... Unpacking libjbig0:arm64 (2.1-6.1+b2) ... Selecting previously unselected package liblerc4:arm64. Preparing to unpack .../033-liblerc4_4.0.0+ds-5_arm64.deb ... Unpacking liblerc4:arm64 (4.0.0+ds-5) ... Selecting previously unselected package libsharpyuv0:arm64. Preparing to unpack .../034-libsharpyuv0_1.4.0-0.1+b1_arm64.deb ... Unpacking libsharpyuv0:arm64 (1.4.0-0.1+b1) ... Selecting previously unselected package libwebp7:arm64. Preparing to unpack .../035-libwebp7_1.4.0-0.1+b1_arm64.deb ... Unpacking libwebp7:arm64 (1.4.0-0.1+b1) ... Selecting previously unselected package libtiff6:arm64. Preparing to unpack .../036-libtiff6_4.5.1+git230720-5_arm64.deb ... Unpacking libtiff6:arm64 (4.5.1+git230720-5) ... Selecting previously unselected package libgdk-pixbuf-2.0-0:arm64. Preparing to unpack .../037-libgdk-pixbuf-2.0-0_2.42.12+dfsg-1+b1_arm64.deb ... Unpacking libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-1+b1) ... Selecting previously unselected package gtk-update-icon-cache. Preparing to unpack .../038-gtk-update-icon-cache_4.16.3+ds-2_arm64.deb ... No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. No diversion 'diversion of /usr/share/man/man8/update-icon-caches.8.gz to /usr/share/man/man8/update-icon-caches.gtk2.8.gz by libgtk-3-bin', none removed. Unpacking gtk-update-icon-cache (4.16.3+ds-2) ... Selecting previously unselected package hicolor-icon-theme. Preparing to unpack .../039-hicolor-icon-theme_0.18-1_all.deb ... Unpacking hicolor-icon-theme (0.18-1) ... Selecting previously unselected package adwaita-icon-theme. Preparing to unpack .../040-adwaita-icon-theme_47.0-2_all.deb ... Unpacking adwaita-icon-theme (47.0-2) ... Selecting previously unselected package ca-certificates-java. Preparing to unpack .../041-ca-certificates-java_20240118_all.deb ... Unpacking ca-certificates-java (20240118) ... Selecting previously unselected package java-common. Preparing to unpack .../042-java-common_0.76_all.deb ... Unpacking java-common (0.76) ... Selecting previously unselected package liblcms2-2:arm64. Preparing to unpack .../043-liblcms2-2_2.16-2_arm64.deb ... Unpacking liblcms2-2:arm64 (2.16-2) ... Selecting previously unselected package libnspr4:arm64. Preparing to unpack .../044-libnspr4_2%3a4.35-1.1+b1_arm64.deb ... Unpacking libnspr4:arm64 (2:4.35-1.1+b1) ... Selecting previously unselected package libnss3:arm64. Preparing to unpack .../045-libnss3_2%3a3.105-2_arm64.deb ... Unpacking libnss3:arm64 (2:3.105-2) ... Selecting previously unselected package libpcsclite1:arm64. Preparing to unpack .../046-libpcsclite1_2.3.0-3_arm64.deb ... Unpacking libpcsclite1:arm64 (2.3.0-3) ... Selecting previously unselected package openjdk-21-jre-headless:arm64. Preparing to unpack .../047-openjdk-21-jre-headless_21.0.5+11-1_arm64.deb ... Unpacking openjdk-21-jre-headless:arm64 (21.0.5+11-1) ... 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Preparing to unpack .../283-maven-debian-helper_2.6.5_all.deb ... Unpacking maven-debian-helper (2.6.5) ... Setting up libexpat1:arm64 (2.6.3-2) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libgraphite2-3:arm64 (1.3.14-2+b1) ... Setting up liblcms2-2:arm64 (2.16-2) ... Setting up libpixman-1-0:arm64 (0.42.2-1+b1) ... Setting up libsharpyuv0:arm64 (1.4.0-0.1+b1) ... Setting up libwayland-server0:arm64 (1.23.0-1+b1) ... Setting up libslf4j-java (1.7.32-1) ... Setting up systemd-sysv (256.7-3) ... Setting up libxau6:arm64 (1:1.0.11-1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3+b2) ... Setting up libplexus-utils2-java (3.4.2-1) ... Setting up libkeyutils1:arm64 (1.6.3-4) ... Setting up libplexus-classworlds-java (2.7.0-1) ... Setting up libxcb1:arm64 (1.17.0-2+b1) ... Setting up libopentest4j-reporting-java (0.1.0-M1-2) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up libplexus-build-api-java (0.0.7-4) ... Setting up libxcb-xfixes0:arm64 (1.17.0-2+b1) ... Setting up liblerc4:arm64 (4.0.0+ds-5) ... Setting up libjsr305-java (0.1~+svn49-11) ... Setting up bsdextrautils (2.40.2-9) ... Setting up hicolor-icon-theme (0.18-1) ... Setting up java-common (0.76) ... Setting up libdatrie1:arm64 (0.2.13-3+b1) ... Setting up libqdox2-java (2.0.3-1) ... Setting up libaopalliance-java (20070526-7) ... Setting up libcommons-cli-java (1.6.0-1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libxcb-render0:arm64 (1.17.0-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglvnd0:arm64 (1.7.0-1+b2) ... Setting up libxcb-glx0:arm64 (1.17.0-2+b1) ... Setting up unzip (6.0-28+b1) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:arm64 (1.1.0-2+b5) ... Setting up libedit2:arm64 (3.1-20240808-1) ... Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up libpicocli-java (4.6.2-2) ... Setting up libasm-java (9.7.1-1) ... Setting up x11-common (1:7.7+23.1) ... Running in chroot, ignoring request. Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libsensors-config (1:3.6.0-10) ... Setting up libdeflate0:arm64 (1.22-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libel-api-java (3.0.0-3) ... Setting up xkb-data (2.42-1) ... Setting up libplexus-component-annotations-java (2.1.1-1) ... Setting up libxcb-shm0:arm64 (1.17.0-2+b1) ... Setting up libcom-err2:arm64 (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libunivocity-parsers-java (2.9.1-1) ... Setting up libjbig0:arm64 (2.1-6.1+b2) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up liboro-java (2.0.8a-14) ... Setting up libsnappy1v5:arm64 (1.2.1-1+b1) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up libxcb-present0:arm64 (1.17.0-2+b1) ... Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... Setting up libgeronimo-interceptor-3.0-spec-java (1.0.1-4) ... Setting up libcommons-collections3-java (3.2.2-3) ... Setting up libasound2-data (1.2.12-1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:arm64 (4.13.3-1) ... Setting up libglib2.0-0t64:arm64 (2.82.2-2) ... Setting up libasound2t64:arm64 (1.2.12-1+b1) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-3+b1) ... Setting up libjaxen-java (1.1.6-5) ... Setting up libapiguardian-java (1.1.2-1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libepoxy0:arm64 (1.5.10-2) ... Setting up libnspr4:arm64 (2:4.35-1.1+b1) ... Setting up libxcb-sync1:arm64 (1.17.0-2+b1) ... Setting up libjtidy-java (7+svn20110807-5) ... Setting up libjansi-java (2.4.1-2) ... Setting up libapache-pom-java (33-2) ... Setting up libavahi-common-data:arm64 (0.8-13+b3) ... Setting up libatinject-jsr330-api-java (1.0+ds1-5) ... Setting up libdbus-1-3:arm64 (1.14.10-6) ... Setting up libwebsocket-api-java (1.1-2) ... Setting up libfribidi0:arm64 (1.0.15-1) ... Setting up libproc2-0:arm64 (2:4.0.4-6) ... Setting up libplexus-interpolation-java (1.27-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.44-2) ... Setting up libxml-commons-resolver1.1-java (1.2-11) ... Setting up libxz-java (1.9-1) ... Setting up libcommons-pool-java (1.6-5) ... Setting up autopoint (0.22.5-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libpcsclite1:arm64 (2.3.0-3) ... Setting up libsensors5:arm64 (1:3.6.0-10+b1) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up libjgraph-java (5.12.4.2+dfsg-7) ... Setting up libactivation-java (1.2.0-2) ... Setting up libhamcrest-java (2.2-2) ... Setting up libglapi-mesa:arm64 (24.2.6-1) ... Setting up libbsh-java (2.0b4-20) ... Setting up libjsp-api-java (2.3.4-3) ... Setting up libvulkan1:arm64 (1.3.296.0-1) ... Setting up autoconf (2.72-3) ... Setting up libwebp7:arm64 (1.4.0-0.1+b1) ... Setting up libxcb-dri2-0:arm64 (1.17.0-2+b1) ... Setting up libgif7:arm64 (5.2.2-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libxshmfence1:arm64 (1.3-1+b2) ... Setting up libjsoup-java (1.15.3-1) ... Setting up at-spi2-common (2.54.0-1) ... Setting up libtiff6:arm64 (4.5.1+git230720-5) ... Setting up libxcb-randr0:arm64 (1.17.0-2+b1) ... Setting up dbus-session-bus-common (1.14.10-6) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libxml-commons-external-java (1.4.01-6) ... Setting up procps (2:4.0.4-6) ... Setting up libxbean-reflect-java (4.5-9) ... Setting up libservlet-api-java (4.0.1-2) ... Setting up libplexus-xml-java (3.0.1-2) ... Setting up libopentest4j-java (1.2.0-4) ... Setting up libx11-6:arm64 (2:1.8.10-2) ... Setting up libthai-data (0.1.29-2) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up libwagon-http-shaded-java (3.5.3-1) ... Setting up libwayland-egl1:arm64 (1.23.0-1+b1) ... Setting up libhttpcore-java (4.4.16-1) ... Setting up libxerces2-java (2.12.2-1) ... Setting up dbus-system-bus-common (1.14.10-6) ... useradd: Warning: missing or non-executable shell '/usr/sbin/nologin' Setting up openssl (3.3.2-2) ... Setting up libdrm-common (2.4.123-1) ... Setting up libcdi-api-java (1.2-4) ... Setting up libsnappy-jni (1.1.10.5-2+b1) ... Setting up libxcomposite1:arm64 (1:0.4.6-1) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.1) ... Setting up dbus-bin (1.14.10-6) ... Setting up libxkbcommon0:arm64 (1.6.0-1+b2) ... Setting up libwayland-client0:arm64 (1.23.0-1+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libdom4j-java (2.1.4-1) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libxcb-dri3-0:arm64 (1.17.0-2+b1) ... Setting up libwagon-provider-api-java (3.5.3-1) ... Setting up libcommons-dbcp-java (1.4-8) ... Setting up libllvm19:arm64 (1:19.1.3-1) ... Setting up libx11-xcb1:arm64 (2:1.8.10-2) ... Setting up gettext (0.22.5-2) ... Setting up libjetty9-java (9.4.56-1) ... Setting up libxdamage1:arm64 (1:1.1.6-1+b2) ... Setting up libatk1.0-0t64:arm64 (2.54.0-1) ... Setting up libplexus-languages-java (1.1.1-2) ... Setting up libjgrapht0.8-java (0.8.3-7) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b2) ... Setting up libtool (2.4.7-8) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libmaven-parent-java (43-2) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:arm64 (0.8-13+b3) ... Setting up libcloudproviders0:arm64 (0.3.6-1+b1) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxext6:arm64 (2:1.3.4-1+b2) ... Setting up libsisu-inject-java (0.3.4-2) ... Setting up libnss3:arm64 (2:3.105-2) ... Setting up dbus-daemon (1.14.10-6) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libcolord2:arm64 (1.4.7-1+b2) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up libxxf86vm1:arm64 (1:1.1.4-1+b3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libdconf1:arm64 (0.40.0-4+b3) ... Setting up dh-autoreconf (20) ... Setting up libthai0:arm64 (0.1.29-2+b1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.4-3) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libxfixes3:arm64 (1:6.0.0-2+b2) ... Setting up dbus (1.14.10-6) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up shared-mime-info (2.4-5+b1) ... Setting up libxinerama1:arm64 (2:1.1.4-3+b2) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up libxrandr2:arm64 (2:1.5.4-1+b1) ... Setting up libcommons-lang3-java (3.17.0-1) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libdrm2:arm64 (2.4.123-1) ... Setting up groff-base (1.23.0-5) ... Setting up libwayland-cursor0:arm64 (1.23.0-1+b1) ... Setting up libpam-systemd:arm64 (256.7-3) ... Setting up libcommons-beanutils-java (1.9.4-2) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libharfbuzz0b:arm64 (10.0.1-1) ... Setting up libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-1+b1) ... Setting up libsnappy-java (1.1.10.5-2) ... Setting up libfontconfig1:arm64 (2.15.0-1.1+b1) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libwagon-file-java (3.5.3-1) ... Setting up libxml2-utils (2.12.7+dfsg+really2.9.14-0.1) ... Setting up libcommons-codec-java (1.17.1-1) ... Setting up libavahi-client3:arm64 (0.8-13+b3) ... Setting up libdrm-amdgpu1:arm64 (2.4.123-1) ... Setting up gtk-update-icon-cache (4.16.3+ds-2) ... Setting up velocity (1.7-7) ... Setting up fontconfig (2.15.0-1.1+b1) ... Regenerating fonts cache... done. Setting up openjdk-21-jre-headless:arm64 (21.0.5+11-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libxi6:arm64 (2:1.8.2-1) ... Setting up libcommons-io-java (2.17.0-1) ... Setting up libdrm-radeon1:arm64 (2.4.123-1) ... Setting up libcommons-digester-java (1.8.1-7) ... Setting up libxtst6:arm64 (2:1.2.3-1.1+b2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxcursor1:arm64 (1:1.2.2-1+b1) ... Setting up libpango-1.0-0:arm64 (1.54.0+ds-3) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink '/etc/systemd/system/timers.target.wants/man-db.timer' -> '/usr/lib/systemd/system/man-db.timer'. Setting up libcairo2:arm64 (1.18.2-2) ... Setting up libmaven-filtering-java (3.4.0-1) ... Setting up dbus-user-session (1.14.10-6) ... Setting up libmaven-resolver-java (1.6.3-1) ... Setting up adwaita-icon-theme (47.0-2) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up libatspi2.0-0t64:arm64 (2.54.0-1) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up libmaven-common-artifact-filters-java (3.4.0-1) ... Setting up libcairo-gobject2:arm64 (1.18.2-2) ... Setting up libmaven-shared-utils-java (3.4.2-1) ... Setting up libpangoft2-1.0-0:arm64 (1.54.0+ds-3) ... Setting up libmaven-resources-plugin-java (3.3.1-1) ... Setting up libcups2t64:arm64 (2.4.10-2) ... Setting up libpangocairo-1.0-0:arm64 (1.54.0+ds-3) ... Setting up libatk-bridge2.0-0t64:arm64 (2.54.0-1) ... Setting up mesa-libgallium:arm64 (24.2.6-1) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up libcommons-compress-java (1.27.1-2) ... Setting up libcommons-validator-java (1:1.7-1) ... Setting up libgbm1:arm64 (24.2.6-1) ... Setting up libgl1-mesa-dri:arm64 (24.2.6-1) ... Setting up debhelper (13.20) ... Setting up dconf-service (0.40.0-4+b3) ... Setting up libmaven-clean-plugin-java (3.2.0-2) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libglx-mesa0:arm64 (24.2.6-1) ... Setting up libglx0:arm64 (1.7.0-1+b2) ... Setting up dconf-gsettings-backend:arm64 (0.40.0-4+b3) ... Setting up libmaven-archiver-java (3.6.2-1) ... Setting up libgl1:arm64 (1.7.0-1+b2) ... Setting up libgtk-3-common (3.24.43-4) ... Setting up libgtk-3-0t64:arm64 (3.24.43-4) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libguava-java (32.0.1-1) ... Setting up libplexus-container-default-java (2.1.1-1) ... Setting up libguice-java (4.2.3-2) ... Setting up libplexus-i18n-java (1.0-beta-10-6) ... Setting up libplexus-container-default1.5-java (2.1.1-1) ... Setting up libplexus-velocity-java (1.2-4) ... Setting up libmaven3-core-java (3.8.8-1) ... Setting up libmaven-shared-incremental-java (1.1-6) ... Setting up libmaven-shared-io-java (3.0.0-4) ... Setting up libplexus-bsh-factory-java (1.0~alpha7-5) ... Setting up libplexus-compiler-java (2.13.0-1) ... Setting up libmaven-compiler-plugin-java (3.13.0-1) ... Setting up libmaven-file-management-java (3.0.0-1) ... Setting up libmaven-jar-plugin-java (3.3.0-2) ... Setting up libcommons-text-java (1.12.0-1) ... Setting up libdoxia-core-java (2.0.0-1) ... Setting up libdoxia-java (2.0.0-1) ... Setting up libmaven-reporting-api-java (4.0.0-1) ... Setting up libmaven-reporting-exec-java (2.0.0-1) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up maven-repo-helper (1.11) ... Setting up maven (3.8.8-1) ... update-alternatives: using /usr/share/maven/bin/mvn to provide /usr/bin/mvn (mvn) in auto mode Setting up openjdk-21-jre:arm64 (21.0.5+11-1) ... Setting up ant (1.10.15-1) ... Setting up junit4 (4.13.2-5) ... Setting up openjdk-21-jdk-headless:arm64 (21.0.5+11-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jwebserver to provide /usr/bin/jwebserver (jwebserver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jre-headless (2:1.21-76) ... Setting up default-jre (2:1.21-76) ... Setting up libplexus-ant-factory-java (1.0~alpha2.1-4) ... Setting up openjdk-21-jdk:arm64 (21.0.5+11-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up default-jdk-headless (2:1.21-76) ... Setting up junit5 (5.10.3-1) ... Setting up libmaven-plugin-tools-java (3.10.2-1) ... Setting up default-jdk (2:1.21-76) ... Setting up libsurefire-java (2.22.3-3) ... Processing triggers for sgml-base (1.31) ... Setting up libvelocity-tools-java (2.0-9) ... Setting up libdoxia-sitetools-java (2.0.0-1) ... Setting up libmaven-site-plugin-java (3.21.0-1) ... Setting up maven-debian-helper (2.6.5) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/biojava-live-1.9.7+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../biojava-live_1.9.7+dfsg-2_source.changes dpkg-buildpackage: info: source package biojava-live dpkg-buildpackage: info: source version 1:1.9.7+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Emmanuel Bourg dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean bash -c "for dir in \$(find . -name target -type d); do if [ -f \$(echo \$dir | sed -e s/target\$/pom.xml/) ]; then rm -Rf \$dir; fi done" mh_unpatchpoms -plibbiojava1.9-java dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure mh_patchpoms -plibbiojava1.9-java --debian-build --keep-pom-version --maven-repo=/build/reproducible-path/biojava-live-1.9.7\+dfsg/debian/maven-repo dh_auto_build /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/biojava-live-1.9.7\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/biojava-live-1.9.7\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/biojava-live-1.9.7\+dfsg/debian/maven-repo --batch-mode package -DskipTests -Dnotimestamp=true -Dlocale=en_US OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release. [INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] biojava-legacy [pom] [INFO] bytecode [jar] [INFO] core [jar] [INFO] alignment [jar] [INFO] biosql [jar] [INFO] blast [jar] [INFO] sequencing [jar] [INFO] gui [jar] [INFO] phylo [jar] [INFO] [INFO] ---------------------< org.biojava:biojava-legacy >--------------------- [INFO] Building biojava-legacy 1.9.7 [1/9] [INFO] from pom.xml [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] ------------------------< org.biojava:bytecode >------------------------ [INFO] Building bytecode 1.9.7 [2/9] [INFO] from bytecode/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ bytecode --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ bytecode --- [INFO] Recompiling the module because of changed source code. [INFO] Compiling 44 source files with javac [debug target 1.8] to target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/MethodRootContext.java:[104,25] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/MethodRootContext.java:[117,28] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/ChildContext.java:[83,25] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/ChildContext.java:[140,28] Integer(int) in java.lang.Integer has been deprecated and marked for removal [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/IntrospectedCodeClass.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/IntrospectedCodeClass.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ bytecode --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ bytecode --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ bytecode --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ bytecode --- [INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/target/bytecode-1.9.7.jar [INFO] [INFO] --------------------------< org.biojava:core >-------------------------- [INFO] Building core 1.9.7 [3/9] [INFO] from core/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ core --- [INFO] Copying 29 resources from src/main/resources to target/classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ core --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 1063 source files with javac [debug target 1.8] to target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/SuffixTree.java:[147,22] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/SuffixTree.java:[150,18] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dist/DistributionTools.java:[237,24] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dist/DistributionTools.java:[240,24] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dist/DistributionTools.java:[269,25] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dist/AbstractDistribution.java:[124,28] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dist/AbstractDistribution.java:[125,28] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/db/emblcd/RecordParser.java:[156,30] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/db/emblcd/RecordParser.java:[184,30] Long(long) in java.lang.Long has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/db/emblcd/RecordParser.java:[185,30] Long(long) in java.lang.Long has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/db/emblcd/RecordParser.java:[186,30] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/db/emblcd/RecordParser.java:[211,25] Long(long) in java.lang.Long has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/db/emblcd/RecordParser.java:[212,25] Long(long) in java.lang.Long has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/db/emblcd/RecordParser.java:[230,24] Long(long) in java.lang.Long has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:[949,39] Boolean(java.lang.String) in java.lang.Boolean has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/SimpleRankedDocRef.java:[92,21] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/SimpleRankedDocRef.java:[93,21] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/SimpleRankedDocRef.java:[152,22] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/SimpleRankedDocRef.java:[153,20] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dp/twohead/DPCompiler.java:[1455,19] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dist/SimpleDistributionTrainer.java:[77,16] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dist/SimpleDistributionTrainer.java:[132,23] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dist/IndexedCount.java:[85,29] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dist/IndexedCount.java:[86,29] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dist/IndexedCount.java:[107,29] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dist/IndexedCount.java:[108,29] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/SimpleSymbolPropertyTable.java:[55,30] Double(java.lang.String) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/agave/AGAVESeqLocationPropHandler.java:[61,14] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/agave/AGAVESeqLocationPropHandler.java:[62,13] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/IntegerAlphabet.java:[157,19] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/RichSequence.java:[558,80] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/RichSequence.java:[585,89] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/proteomics/MassCalc.java:[150,25] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/proteomics/MassCalc.java:[190,38] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/proteomics/MassCalc.java:[224,26] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/proteomics/MassCalc.java:[459,33] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/proteomics/MassCalc.java:[466,37] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/ChunkedSymbolList.java:[52,18] finalize() in java.lang.Object has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/ChunkedSymbolList.java:[53,10] finalize() in java.lang.Object has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/SimpleRankedCrossRef.java:[74,21] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/SimpleRankedCrossRef.java:[75,21] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dp/BaumWelchTrainer.java:[145,29] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/UkkonenSuffixTree.java:[254,54] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/UkkonenSuffixTree.java:[345,54] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/UkkonenSuffixTree.java:[483,25] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/UkkonenSuffixTree.java:[495,17] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/UkkonenSuffixTree.java:[500,17] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/ThinRichSequence.java:[127,41] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/ThinRichSequence.java:[127,64] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/SimpleRichLocation.java:[261,21] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/SimpleRichLocation.java:[262,21] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/SimpleRichLocation.java:[302,21] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/SimpleRichLocation.java:[303,21] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.java:[429,108] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/agave/AGAVEMatchRegionPropHandler.java:[72,29] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/agave/AGAVEMatchRegionPropHandler.java:[73,27] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/taxa/io/SimpleNCBITaxonomyLoader.java:[71,52] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/taxa/io/SimpleNCBITaxonomyLoader.java:[73,36] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/taxa/io/SimpleNCBITaxonomyLoader.java:[74,33] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/ga/functions/AbstractCrossOverFunction.java:[59,40] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/ga/functions/AbstractCrossOverFunction.java:[60,40] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/ByLocationMinMaxComparator.java:[50,22] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/ByLocationMinMaxComparator.java:[51,22] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/ByLocationMinMaxComparator.java:[58,14] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/ByLocationMinMaxComparator.java:[59,14] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/EmblLikeLocationParser.java:[505,32] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/EmblLikeLocationParser.java:[516,36] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/EmblLikeLocationParser.java:[558,20] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/tagvalue/ChangeTable.java:[41,14] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/io/UniProtCommentParser.java:[208,85] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/NameTokenization.java:[64,20] finalize() in java.lang.Object has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/NameTokenization.java:[65,14] finalize() in java.lang.Object has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/process/ExternalProcess.java:[604,20] finalize() in java.lang.Object has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/indexdb/BioStoreFactory.java:[214,27] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/io/INSDseqFormat.java:[892,146] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/io/INSDseqFormat.java:[936,58] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/io/INSDseqFormat.java:[946,136] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/io/INSDseqFormat.java:[996,74] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/io/INSDseqFormat.java:[996,89] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/io/INSDseqFormat.java:[1034,143] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/SimpleRichFeatureRelationship.java:[82,21] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/SimpleRichFeatureRelationship.java:[83,21] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:[76,33] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:[76,53] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:[77,33] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:[77,53] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:[78,33] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:[78,53] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:[79,33] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:[79,53] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:[80,33] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:[80,53] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:[81,33] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:[81,53] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:[82,33] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:[82,54] Character(char) in java.lang.Character has been deprecated and marked for removal [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dist/DistributionTools.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dist/DistributionTools.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java: Some input files additionally use or override a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/regex/Search.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/regex/Search.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ core --- [INFO] Copying 53 resources from src/test/resources to target/test-classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ core --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 148 source files with javac [debug target 1.8] to target/test-classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/ontology/SimpleComparableTermTest.java:[308,28] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojava/utils/walker/WalkerTest.java:[106,34] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojava/utils/walker/WalkerTest.java:[109,36] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojava/utils/walker/WalkerTest.java:[153,14] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/SimpleCommentTest.java:[82,26] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/SimpleCommentTest.java:[84,27] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojava/bio/symbol/UkkonenSuffixTreeTest.java:[88,40] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojava/bio/symbol/UkkonenSuffixTreeTest.java:[89,40] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/bio/SimpleBioEntryTest.java:[625,17] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/bio/SimpleBioEntryTest.java:[625,33] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/bio/SimpleBioEntryTest.java:[663,17] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/bio/SimpleBioEntryTest.java:[663,33] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/bio/SimpleBioEntryTest.java:[794,31] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/bio/SimpleBioEntryTest.java:[835,31] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/SimpleRankedDocRefTest.java:[40,17] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/SimpleRankedDocRefTest.java:[41,15] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/SimpleRankedDocRefTest.java:[76,26] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/SimpleRankedDocRefTest.java:[78,27] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/SimpleRankedDocRefTest.java:[174,43] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/SimpleRankedDocRefTest.java:[174,60] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/SimpleRankedDocRefTest.java:[203,43] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/SimpleRankedDocRefTest.java:[203,60] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/SimpleRankedDocRefTest.java:[227,43] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/SimpleRankedDocRefTest.java:[227,60] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/SimpleRankedCrossRefTest.java:[76,26] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/SimpleRankedCrossRefTest.java:[78,27] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/ga/util/WeightedSetTest.java:[89,29] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/ga/util/WeightedSetTest.java:[135,29] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/ga/util/WeightedSetTest.java:[139,27] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/ga/util/WeightedSetTest.java:[149,29] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/ga/util/WeightedSetTest.java:[150,27] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:[163,46] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:[164,22] Double(double) in java.lang.Double has been deprecated and marked for removal [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojava/bio/seq/io/SeqIOToolsTest.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojava/bio/seq/io/SeqIOToolsTest.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojava/bio/search/SimpleSeqSimilaritySearchHitTest.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojava/bio/search/SimpleSeqSimilaritySearchHitTest.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ core --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ core --- [INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/core/target/core-1.9.7.jar [INFO] [INFO] -----------------------< org.biojava:alignment >------------------------ [INFO] Building alignment 1.9.7 [4/9] [INFO] from alignment/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ alignment --- [INFO] Copying 89 resources from src/main/resources to target/classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ alignment --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 14 source files with javac [debug target 1.8] to target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/main/java/org/biojava/bio/alignment/SubstitutionMatrix.java:[180,48] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/main/java/org/biojava/bio/alignment/SubstitutionMatrix.java:[181,48] Integer(int) in java.lang.Integer has been deprecated and marked for removal [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ alignment --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ alignment --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 5 source files with javac [debug target 1.8] to target/test-classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/test/java/org/biojava/bio/alignment/FlexibleAlignmentTest.java: /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/test/java/org/biojava/bio/alignment/FlexibleAlignmentTest.java uses unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/test/java/org/biojava/bio/alignment/FlexibleAlignmentTest.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ alignment --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ alignment --- [INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/target/alignment-1.9.7.jar [INFO] [INFO] -------------------------< org.biojava:biosql >------------------------- [INFO] Building biosql 1.9.7 [5/9] [INFO] from biosql/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biosql --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biosql --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 35 source files with javac [debug target 1.8] to target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.java:[530,48] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.java:[618,35] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.java:[722,45] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.java:[1303,23] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.java:[1337,23] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/FeaturesSQL.java:[162,22] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/FeaturesSQL.java:[166,78] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/FeaturesSQL.java:[225,27] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/FeaturesSQL.java:[340,27] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/FeaturesSQL.java:[341,27] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/FeaturesSQL.java:[514,34] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/FeaturesSQL.java:[515,33] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/FeaturesSQL.java:[561,29] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/FeaturesSQL.java:[749,37] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/FeaturesSQL.java:[751,37] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/OntologySQL.java:[315,21] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/OntologySQL.java:[335,51] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/OntologySQL.java:[336,51] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/OntologySQL.java:[337,51] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/OntologySQL.java:[391,28] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/OntologySQL.java:[440,24] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/OntologySQL.java:[562,21] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/OntologySQL.java:[688,19] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/OntologySQL.java:[719,35] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLEntryChangeHub.java:[60,22] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLEntryChangeHub.java:[69,22] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLEntryChangeHub.java:[79,22] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLEntryChangeHub.java:[90,22] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLEntryAnnotationChangeHub.java:[63,31] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLEntryAnnotationChangeHub.java:[79,31] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLFeatureChangeHub.java:[63,31] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLFeatureChangeHub.java:[79,31] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLFeatureAnnotationChangeHub.java:[62,30] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLFeatureAnnotationChangeHub.java:[74,30] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLFeature.java:[376,68] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLFeature.java:[384,71] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/TaxonSQL.java:[318,38] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/TaxonSQL.java:[321,38] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/TaxonSQL.java:[324,38] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/TaxonSQL.java:[327,38] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/TaxonSQL.java:[343,38] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/TaxonSQL.java:[346,38] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/TaxonSQL.java:[349,38] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/TaxonSQL.java:[352,38] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/TaxonSQL.java:[608,15] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/TaxonSQL.java:[632,17] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLRichObjectBuilder.java:[129,94] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLRichObjectBuilder.java:[154,78] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/OracleDBHelper.java:[200,63] Long(long) in java.lang.Long has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLFeatureFilter.java:[602,64] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLFeatureFilter.java:[976,120] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLFeatureFilter.java:[978,114] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLFeatureFilter.java:[979,114] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLFeatureFilter.java:[1056,71] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLFeatureFilter.java:[1132,120] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLFeatureFilter.java:[1134,114] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLFeatureFilter.java:[1135,114] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLFeatureFilter.java:[1206,106] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLFeatureAnnotation.java:[232,59] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLFeatureAnnotation.java:[240,62] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceAnnotation.java:[81,61] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceAnnotation.java:[280,57] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceAnnotation.java:[288,60] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.java:[202,66] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.java:[229,70] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLRichSequenceHandler.java:[162,66] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLRichSequenceHandler.java:[163,66] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLRichSequenceHandler.java:[181,66] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLRichSequenceHandler.java:[181,82] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLRichSequenceHandler.java:[182,66] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLRichSequenceHandler.java:[182,82] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLRichSequenceHandler.java:[183,66] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLRichSequenceHandler.java:[184,66] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLCrossReferenceResolver.java:[101,66] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLCrossReferenceResolver.java:[102,66] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLCrossReferenceResolver.java:[103,66] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLCrossReferenceResolver.java:[103,82] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLBioEntryDB.java:[120,66] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLBioEntryDB.java:[147,70] Integer(int) in java.lang.Integer has been deprecated and marked for removal [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLSequence.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLSequence.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLSequence.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLSequence.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biosql --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biosql --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 2 source files with javac [debug target 1.8] to target/test-classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/test/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceDBTest.java: /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/test/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceDBTest.java uses or overrides a deprecated API. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/test/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceDBTest.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biosql --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biosql --- [INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/target/biosql-1.9.7.jar [INFO] [INFO] -------------------------< org.biojava:blast >-------------------------- [INFO] Building blast 1.9.7 [6/9] [INFO] from blast/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ blast --- [INFO] Copying 3 resources from src/main/resources to target/classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ blast --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 56 source files with javac [debug target 1.8] to target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/src/main/java/org/biojava/bio/program/sax/AbstractNativeAppSAXParser.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/src/main/java/org/biojava/bio/program/sax/AbstractNativeAppSAXParser.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/src/main/java/org/biojava/bio/program/sax/blastxml/StAXFeatureHandler.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/src/main/java/org/biojava/bio/program/sax/blastxml/StAXFeatureHandler.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ blast --- [INFO] Copying 22 resources from src/test/resources to target/test-classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ blast --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 19 source files with javac [debug target 1.8] to target/test-classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ blast --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ blast --- [INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/target/blast-1.9.7.jar [INFO] [INFO] -----------------------< org.biojava:sequencing >----------------------- [INFO] Building sequencing 1.9.7 [7/9] [INFO] from sequencing/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ sequencing --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ sequencing --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 33 source files with javac [debug target 1.8] to target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/program/scf/SCF.java:[372,32] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/program/scf/SCF.java:[373,32] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/program/scf/SCF.java:[374,32] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/program/scf/SCF.java:[375,32] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/program/scf/SCF.java:[377,30] Long(long) in java.lang.Long has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/program/scf/SCF.java:[378,30] Long(long) in java.lang.Long has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/program/scf/SCF.java:[380,34] Long(long) in java.lang.Long has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/program/scf/SCF.java:[383,34] Long(long) in java.lang.Long has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.java:[274,45] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.java:[276,47] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.java:[278,47] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.java:[1114,42] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.java:[1127,45] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.java:[1140,45] Integer(int) in java.lang.Integer has been deprecated and marked for removal [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/AbstractChromatogram.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/AbstractChromatogram.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/program/abi/ABIFParser.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/program/abi/ABIFParser.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ sequencing --- [INFO] Copying 77 resources from src/test/resources to target/test-classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ sequencing --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 15 source files with javac [debug target 1.8] to target/test-classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/test/java/org/biojava/bio/program/fastq/AbstractFastqReaderTest.java: /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/test/java/org/biojava/bio/program/fastq/AbstractFastqReaderTest.java uses or overrides a deprecated API. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/test/java/org/biojava/bio/program/fastq/AbstractFastqReaderTest.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ sequencing --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ sequencing --- [INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/target/sequencing-1.9.7.jar [INFO] [INFO] --------------------------< org.biojava:gui >--------------------------- [INFO] Building gui 1.9.7 [8/9] [INFO] from gui/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ gui --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ gui --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 99 source files with javac [debug target 1.8] to target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/LineInfo.java:[51,28] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/AbiTraceRenderer.java:[157,53] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/AbiTraceRenderer.java:[157,72] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/FilteringRenderer.java:[119,26] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/FilteringRenderer.java:[119,48] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.java:[173,50] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.java:[174,50] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.java:[176,27] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.java:[206,27] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.java:[288,50] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.java:[289,50] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/AbstractBeadRenderer.java:[350,66] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/AbstractBeadRenderer.java:[351,66] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/AbstractBeadRenderer.java:[397,66] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/AbstractBeadRenderer.java:[398,66] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/TickFeatureRenderer.java:[132,26] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/TickFeatureRenderer.java:[132,50] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/RectangularBeadRenderer.java:[221,66] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/RectangularBeadRenderer.java:[222,66] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/BasicFeatureRenderer.java:[139,25] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/BasicFeatureRenderer.java:[139,53] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/BasicFeatureRenderer.java:[163,25] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/BasicFeatureRenderer.java:[163,53] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/BasicImapRenderer.java:[167,34] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/BasicImapRenderer.java:[168,34] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/BasicImapRenderer.java:[169,34] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/BasicImapRenderer.java:[170,34] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/PaddingRenderer.java:[107,24] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/PaddingRenderer.java:[107,50] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/PaddingRenderer.java:[118,26] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/PaddingRenderer.java:[118,52] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/RectangularImapRenderer.java:[201,30] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/RectangularImapRenderer.java:[202,30] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/RectangularImapRenderer.java:[203,30] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/RectangularImapRenderer.java:[204,30] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/EllipticalBeadRenderer.java:[195,66] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/EllipticalBeadRenderer.java:[196,66] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/ZiggyImapRenderer.java:[169,34] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/ZiggyImapRenderer.java:[170,34] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/ZiggyImapRenderer.java:[171,34] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/ZiggyImapRenderer.java:[172,34] Integer(int) in java.lang.Integer has been deprecated and marked for removal [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/SequenceRendererWrapper.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/SequenceRendererWrapper.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/LineInfo.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/LineInfo.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ gui --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ gui --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ gui --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ gui --- [INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/target/gui-1.9.7.jar [INFO] [INFO] -------------------------< org.biojava:phylo >-------------------------- [INFO] Building phylo 1.9.7 [9/9] [INFO] from phylo/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ phylo --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/phylo/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ phylo --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 37 source files with javac [debug target 1.8] to target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/phylo/src/main/java/org/biojavax/bio/phylo/io/nexus/DistancesBlock.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/phylo/src/main/java/org/biojavax/bio/phylo/io/nexus/DistancesBlock.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ phylo --- [INFO] Copying 3 resources from src/test/resources to target/test-classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ phylo --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 1 source file with javac [debug target 1.8] to target/test-classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ phylo --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ phylo --- [INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/phylo/target/phylo-1.9.7.jar [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava-legacy 1.9.7: [INFO] [INFO] biojava-legacy ..................................... SUCCESS [ 0.004 s] [INFO] bytecode ........................................... SUCCESS [ 3.241 s] [INFO] core ............................................... SUCCESS [ 9.684 s] [INFO] alignment .......................................... SUCCESS [ 0.461 s] [INFO] biosql ............................................. SUCCESS [ 0.489 s] [INFO] blast .............................................. SUCCESS [ 0.499 s] [INFO] sequencing ......................................... SUCCESS [ 0.580 s] [INFO] gui ................................................ SUCCESS [ 0.767 s] [INFO] phylo .............................................. SUCCESS [ 0.501 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 16.435 s [INFO] Finished at: 2025-12-16T06:04:24Z [INFO] ------------------------------------------------------------------------ dh_auto_test /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/biojava-live-1.9.7\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/biojava-live-1.9.7\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/biojava-live-1.9.7\+dfsg/debian/maven-repo --batch-mode test OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release. [INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] biojava-legacy [pom] [INFO] bytecode [jar] [INFO] core [jar] [INFO] alignment [jar] [INFO] biosql [jar] [INFO] blast [jar] [INFO] sequencing [jar] [INFO] gui [jar] [INFO] phylo [jar] [INFO] [INFO] ---------------------< org.biojava:biojava-legacy >--------------------- [INFO] Building biojava-legacy 1.9.7 [1/9] [INFO] from pom.xml [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] ------------------------< org.biojava:bytecode >------------------------ [INFO] Building bytecode 1.9.7 [2/9] [INFO] from bytecode/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ bytecode --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ bytecode --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ bytecode --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ bytecode --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ bytecode --- [INFO] No tests to run. [INFO] [INFO] --------------------------< org.biojava:core >-------------------------- [INFO] Building core 1.9.7 [3/9] [INFO] from core/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ core --- [INFO] Copying 29 resources from src/main/resources to target/classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ core --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ core --- [INFO] Copying 53 resources from src/test/resources to target/test-classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ core --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ core --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojavax.SimpleDocRefTest testGetTitle testToString testGetLocation testSetCrossref testGetCrossref testCompareTo testGetAuthors testGetAuthorList testHashCode testSetRemark testEquals testGetCRC testGetRemark [INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 s - in org.biojavax.SimpleDocRefTest [INFO] Running org.biojavax.SimpleNamespaceTest testGetAuthority testSetDescription testToString testGetAcronym testCompareTo testGetName testSetAuthority testGetDescription testHashCode testSetAcronym testEquals testGetURI testSetURI [INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojavax.SimpleNamespaceTest [INFO] Running org.biojavax.SimpleRankedCrossRefTest testToString testGetCrossRef testCompareTo testGetRank testHashCode testEquals testSetRank [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.SimpleRankedCrossRefTest [INFO] Running org.biojavax.SimpleNoteTest testGetValue testToString testCompareTo testGetRank testGetTerm testHashCode testEquals testSetRank testSetTerm testSetValue [INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojavax.SimpleNoteTest [INFO] Running org.biojavax.CrossReferenceResolutionExceptionTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.CrossReferenceResolutionExceptionTest [INFO] Running org.biojavax.DummyCrossReferenceResolverTest testGetRemoteBioEntry testGetRemoteSymbolList [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.183 s - in org.biojavax.DummyCrossReferenceResolverTest [INFO] Running org.biojavax.SimpleRankedDocRefTest testGetStart testSetLocation testToString testGetDocumentReference testCompareTo testGetRank testHashCode testEquals testGetEnd testSetRank [INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojavax.SimpleRankedDocRefTest [INFO] Running org.biojavax.SimpleDocRefAuthorTest testIsConsortium testToString testCompareTo testGetName testHashCode testEquals testGetExtendedName [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojavax.SimpleDocRefAuthorTest [INFO] Running org.biojavax.SimpleRichAnnotationTest testGetNoteSet testAddNote testAsMap testClear testKeys testToString testGetNote testSetNoteSet testContains testGetPropertys testSetProperty testRemoveNote testGetProperty testRemoveProperty testRemoveProperty2 testContainsProperty [INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojavax.SimpleRichAnnotationTest [INFO] Running org.biojavax.SimpleCommentTest testSetComment testToString testCompareTo testGetRank testHashCode testGetComment testEquals testSetRank [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojavax.SimpleCommentTest [INFO] Running org.biojavax.EmptyRichAnnotationTest testGetNoteSet testAddNote testAsMap testClear testKeys testGetNote testSetNoteSet testContains testSetProperty testRemoveNote testGetProperty testRemoveProperty testEquals testContainsProperty [INFO] Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojavax.EmptyRichAnnotationTest [INFO] Running org.biojavax.ontology.SimpleComparableOntologyTest testSetTripleSet testCreateTriple testContainsTriple testGetTerms testCreateVariable testContainsTerm testGetTermSet testSetDescription testToString testGetOrCreateTerm testCompareTo testGetTriples testGetName testGetTerm testGetOrImportTerm testGetTripleSet testCreateTerm testGetDescription testSetTermSet testHashCode testDeleteTerm testEquals testGetOps testImportTerm [INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojavax.ontology.SimpleComparableOntologyTest [INFO] Running org.biojavax.ontology.SimpleComparableTripleTest testGetSubject testSetDescriptors testToString testGetSynonyms testRemoveDescriptor testCompareTo testAddSynonym testGetName testGetOntology testGetPredicate testGetAnnotation testGetDescription testGetDescriptors testHashCode testAddDescriptor testEquals testGetObject testRemoveSynonym [INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojavax.ontology.SimpleComparableTripleTest [INFO] Running org.biojavax.ontology.SimpleComparableTermTest testSetDescription testGetRankedCrossRefs testToString testGetSynonyms testCompareTo testAddSynonym testGetName testGetOntology testSetRankedCrossRefs testGetIdentifier testGetAnnotation testRemoveRankedCrossRef testGetDescription testSetIdentifier testHashCode testEquals testAddRankedCrossRef testRemoveSynonym testSetObsolete testGetObsolete [INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojavax.ontology.SimpleComparableTermTest [INFO] Running org.biojavax.SimpleCrossRefTest testGetNoteSet testGetAccession testToString testCompareTo testGetAnnotation testSetNoteSet testGetVersion testHashCode testGetDbname testEquals [INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.SimpleCrossRefTest [INFO] Running org.biojavax.ga.util.GAToolsTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojavax.ga.util.GAToolsTest [INFO] Running org.biojavax.ga.util.WeightedSetTest [INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojavax.ga.util.WeightedSetTest [INFO] Running org.biojavax.ga.functions.SimpleCrossOverFunctionTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.ga.functions.SimpleCrossOverFunctionTest [INFO] Running org.biojavax.ga.functions.AbstractMutationFunctionTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojavax.ga.functions.AbstractMutationFunctionTest [INFO] Running org.biojavax.ga.functions.SimpleMutationFunctionTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.functions.SimpleMutationFunctionTest [INFO] Running org.biojavax.ga.functions.ProportionalSelectionTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.functions.ProportionalSelectionTest [INFO] Running org.biojavax.ga.functions.AbstractCrossOverFunctionTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.functions.AbstractCrossOverFunctionTest [INFO] Running org.biojavax.ga.impl.SimplePopulationTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.impl.SimplePopulationTest [INFO] Running org.biojavax.ga.impl.SimpleOrganismTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.impl.SimpleOrganismTest [INFO] Running org.biojavax.bio.SimpleBioEntryTest testGetNamespace testGetNoteSet testGetRankedDocRefs testGetRelationships testGetTaxon testSetDescription testGetAccession testGetRankedCrossRefs testToString testCompareTo testGetName testRemoveComment testSetRankedCrossRefs testGetIdentifier testGetAnnotation testSetNoteSet testRemoveRankedCrossRef testRemoveRankedDocRef testRemoveRelationship testGetVersion testGetDescription testSetIdentifier testGetComments testHashCode testEquals testAddRankedCrossRef testAddRankedDocRef testAddRelationship testSetDivision testGetDivision testSetTaxon testAddComment [INFO] Tests run: 32, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojavax.bio.SimpleBioEntryTest [INFO] Running org.biojavax.bio.seq.SimpleRichLocationTest testEquals [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.seq.SimpleRichLocationTest [INFO] Running org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest testEquals [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest [INFO] Running org.biojavax.bio.seq.RichLocationToolsTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.seq.RichLocationToolsTest [INFO] Running org.biojavax.bio.seq.SimpleRichFeatureTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojavax.bio.seq.SimpleRichFeatureTest [INFO] Running org.biojavax.bio.seq.io.GenbankFormatTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.169 s - in org.biojavax.bio.seq.io.GenbankFormatTest [INFO] Running org.biojavax.bio.seq.io.Bug2249_2248Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojavax.bio.seq.io.Bug2249_2248Test [INFO] Running org.biojavax.bio.seq.io.Bug2255Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojavax.bio.seq.io.Bug2255Test [INFO] Running org.biojavax.bio.seq.io.Bug2250_2256Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 s - in org.biojavax.bio.seq.io.Bug2250_2256Test [INFO] Running org.biojavax.bio.seq.io.INSDseqFormatTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 s - in org.biojavax.bio.seq.io.INSDseqFormatTest [INFO] Running org.biojavax.bio.seq.io.UniProtFormatTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojavax.bio.seq.io.UniProtFormatTest [INFO] Running org.biojavax.bio.seq.io.GenbankLocationParserTest Location 467: 467 Location 340..565: 340..565 Location <345..500: <345..500 Location <1..888: <1..888 Location (102.110): (102.110) Location (23.45)..600: (23.45)..600 Location (122.133)..(204.221): (122.133)..(204.221) Location 123^124: 123^124 Location 145^177: 145^177 Location join(12..78,134..202): join(12..78,134..202) Location complement(1..23): complement(1..23) Location complement(join(2691..4571,4918..5163): complement(join(2691..4571,4918..5163)) Location join(complement(4918..5163),complement(2691..4571)): complement(join(2691..4571,4918..5163)) Location complement(34..(122.126)): complement(34..(122.126)) Location complement((122.126)..34): complement((122.126)..34) Location J00194:100..202: J00194:100..202 Location (8298.8300)..10206: (8298.8300)..10206 Location join((8298.8300)..10206,1..855): join((8298.8300)..10206,1..855) [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.seq.io.GenbankLocationParserTest [INFO] Running org.biojavax.bio.seq.io.EMBLFormatTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojavax.bio.seq.io.EMBLFormatTest [INFO] Running org.biojavax.bio.seq.CompoundRichLocationTest testEquals [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.seq.CompoundRichLocationTest [INFO] Running org.biojavax.bio.taxa.SimpleNCBITaxonNameTest testGetNameClass testToString testCompareTo testSetNameClass testGetName testHashCode testEquals testSetName [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojavax.bio.taxa.SimpleNCBITaxonNameTest [INFO] Running org.biojava.naming.ObdaInitialContextFactoryTest Reached Attributes: No attributes Binding: urn -> org.biojava.naming.ObdaContext@7bc1a03d Reached urn Attributes: No attributes Binding: open-bio.org -> org.biojava.naming.ObdaContext@70b0b186 Reached urn:open-bio.org Attributes: {description=description: This is the root namespace for all OBDA URNs. All OBDA URNs should be prefixed by urn:open-bio.org as described in the file naming/open-bio_urns.txt in the module obda-specs in the cvs repository located at pub.open-bio.org:/home/repository/obf-common. } Binding: type -> org.biojava.naming.ObdaContext@5d20e46 Reached urn:open-bio.org:type Attributes: {description=description: The namespace for URNs that identify data types. It is expected that the types that are given IDs will be very general in nature, such as Sequence and File Format. All types are of type urn:open-bio.org:type:type. Any URN in the type namespace that is not of this type is not conforming to the OBDA specification for this namespace. } Binding: type -> org.biojava.naming.ObdaContext@709ba3fb Reached urn:open-bio.org:type:type Attributes: {description=description: The OBDA URN that identifies the concept of 'type'. In a given language, this may map to the types of data structures, or objects. Alternativel, it may map to a particular set of keys being present in a map, or a term in an ontology. This is not important. The important thing is that we have unique identifiers for common types that all projects use and interact with. } Binding: format -> org.biojava.naming.ObdaContext@3d36e4cd Reached urn:open-bio.org:type:format Attributes: {description=description: A file format. Many file formats are used in bioinformatics. Entities of this type identify a format. The format can be used to choose how to treat a file. The format is not expected to be resolvable to a formal deffinition of the file structure using OBDA-supplied functionality. Different applications may chose to process a stream with the same format URN in different ways. This type of URN is purely there to identify the format of the stream, not the manner in which it should be processed. } Binding: alphabet -> org.biojava.naming.ObdaContext@6a472554 Reached urn:open-bio.org:type:alphabet Attributes: {description=description: A biological sequence alphabet. Biological sequences are often represented as strings of characters. However, in differnt circumstances, the same characters can represent different things. For example, in DNA, the 't' character represents tyrosine. In Protein, this same character represents tryptophan. Associating alphabets with these sequences disambiguates their interpretation. Alphabets do not define a mapping to or from strings, but should be used wherever the type of the content of a sequence needs to be stated. } Binding: format -> org.biojava.naming.ObdaContext@7ff2a664 Reached urn:open-bio.org:format Attributes: {description=description: A namespace for OBDA URNs that define formats. All URNs within this namespace must be of the type urn:open-bio.org:type:format. Any URN in this namespace that is not of that type is not a valid OBDA URN. } Binding: enzyme -> org.biojava.naming.ObdaContext@525b461a Reached urn:open-bio.org:format:enzyme Attributes: {description=description: The Enzyme database entry format. The enzyme database can be downloaded from the ebi at: ftp://ftp.ebi.ac.uk/pub/databases/enzyme/ For an example of a file in this format, see: ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyme.dat The format is described more fully in ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyser.txt } Binding: genbank -> org.biojava.naming.ObdaContext@58c1c010 Reached urn:open-bio.org:format:genbank Attributes: {description=description: The GENBANK file format associated with the GENBANK sequence database. } Binding: swissprot -> org.biojava.naming.ObdaContext@b7f23d9 Reached urn:open-bio.org:format:swissprot Attributes: {description=description: The SWISSPROT file format as used in the SWISSPROT sequence database. } Binding: embl -> org.biojava.naming.ObdaContext@61d47554 Reached urn:open-bio.org:format:embl Attributes: {description=description: The EMBL file format associated with entries in the EMBL sequence database. } Binding: alphabet -> org.biojava.naming.ObdaContext@69b794e2 Reached urn:open-bio.org:alphabet Attributes: {description=description: A namespace within which to store alphabet identifiers. Alphabets should represent URNs that represent objects of the type identified by urn:open-bio.org:type:alphabet, and any useage outside of this is not supported. } Binding: rna -> org.biojava.naming.ObdaContext@3f200884 Reached urn:open-bio.org:alphabet:rna Attributes: {description=description: The RNA alphabet. RNA is composed from four nucleotides. Read a biochemistry or genetics introductory textbook to find out more. Commonly, the nucleotides are reprsented by the four letters a, g, c and u. However, this is not a formal requirement for a resource to declare this alphabet as its type. } Binding: protein -> org.biojava.naming.ObdaContext@4d339552 Reached urn:open-bio.org:alphabet:protein Attributes: {description=description: The protein alphabet. Proteins are composed from amino-acids. To find out more, read a biochemistry or genetics text book. It is common for protein sequences to be represented by characters, but this is not a formal requirement for a resource to publish an alphabet equal to this identifier. } Binding: dna -> org.biojava.naming.ObdaContext@f0f2775 Reached urn:open-bio.org:alphabet:dna Attributes: {description=description: The DNA alphabet. DNA is composed from four nucleotides. Read a biochemistry or genetics introductory textbook to find out more. Commonly, the nucleotides are reprsented by the four letters a, g, c and t. However, this is not a formal requirement for a resource to declare this alphabet as its type. } lookup: 'urn:open-bio.org:format:embl' for {urn=org.biojava.naming.ObdaContext@1dd92fe2} My component is urn:open-bio.org:format:embl lookup: 'open-bio.org:format:embl' for {open-bio.org=org.biojava.naming.ObdaContext@64d2d351} My component is open-bio.org:format:embl lookup: 'format:embl' for {type=org.biojava.naming.ObdaContext@1b68b9a4, format=org.biojava.naming.ObdaContext@4f9a3314, alphabet=org.biojava.naming.ObdaContext@3b2c72c2} My component is format:embl lookup: 'embl' for {enzyme=org.biojava.naming.ObdaContext@491666ad, genbank=org.biojava.naming.ObdaContext@176d53b2, swissprot=org.biojava.naming.ObdaContext@971d0d8, embl=org.biojava.naming.ObdaContext@51931956} My component is embl [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 s - in org.biojava.naming.ObdaInitialContextFactoryTest [INFO] Running org.biojava.naming.ObdaUriParserTest urn:obda.org:format:embl/ac :trail oneName lead: [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.naming.ObdaUriParserTest [INFO] Running org.biojava.utils.automata.NfaTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.utils.automata.NfaTest [INFO] Running org.biojava.utils.process.AllTests [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.094 s - in org.biojava.utils.process.AllTests [INFO] Running org.biojava.utils.process.ExternalProcessTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.053 s - in org.biojava.utils.process.ExternalProcessTest [INFO] Running org.biojava.utils.lsid.LifeScienceIdentifierTest [INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojava.utils.lsid.LifeScienceIdentifierTest [INFO] Running org.biojava.utils.RepeatedCharSequenceTest JAM [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.utils.RepeatedCharSequenceTest [INFO] Running org.biojava.utils.ListToolsTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.ListToolsTest [INFO] Running org.biojava.utils.SmallMapTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.utils.SmallMapTest [INFO] Running org.biojava.utils.regex.RegexTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.utils.regex.RegexTest [INFO] Running org.biojava.utils.regex.PatternCheckerTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.utils.regex.PatternCheckerTest [INFO] Running org.biojava.utils.walker.WalkerFactoryTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 s - in org.biojava.utils.walker.WalkerFactoryTest [INFO] Running org.biojava.utils.walker.WalkerTest Increasing counter: Overlaps([20,50]) Increasing counter: Overlaps([20,50]) Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature) Increasing counter: And(Overlaps([20,50]) , ByClass(org.biojava.bio.seq.StrandedFeature)) Increasing counter: Overlaps([20,50]) Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature) Increasing counter: ByClass(org.biojava.bio.seq.ComponentFeature) Increasing counter: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)) Increasing counter: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))) OverlapsLocation: Overlaps([20,50]) Feature: ByClass(org.biojava.bio.seq.StrandedFeature) OverlapsLocation: Overlaps([20,50]) Feature: ByClass(org.biojava.bio.seq.StrandedFeature) Feature: ByClass(org.biojava.bio.seq.ComponentFeature) Feature: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)) Feature: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))) [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.utils.walker.WalkerTest [INFO] Running org.biojava.ontology.TripleImplTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.ontology.TripleImplTest [INFO] Running org.biojava.ontology.OntologyTest [INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.ontology.OntologyTest [INFO] Running org.biojava.ontology.ParseOBOFileTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.117 s - in org.biojava.ontology.ParseOBOFileTest [INFO] Running org.biojava.ontology.TermImplTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.ontology.TermImplTest [INFO] Running org.biojava.bio.MergeAnnotationTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.MergeAnnotationTest [INFO] Running org.biojava.bio.dp.MarkovModelEventTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.dp.MarkovModelEventTest [INFO] Running org.biojava.bio.dp.DPSerializationTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 s - in org.biojava.bio.dp.DPSerializationTest [INFO] Running org.biojava.bio.dp.EmissionStateEventTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.dp.EmissionStateEventTest [INFO] Running org.biojava.bio.dist.DistributionTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.dist.DistributionTest [INFO] Running org.biojava.bio.dist.TranslatedDistributionTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.dist.TranslatedDistributionTest [INFO] Running org.biojava.bio.dist.DistSerTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 s - in org.biojava.bio.dist.DistSerTest [INFO] Running org.biojava.bio.dist.DistributionToolsTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 s - in org.biojava.bio.dist.DistributionToolsTest [INFO] Running org.biojava.bio.AnnotationTypeTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojava.bio.AnnotationTypeTest [INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest [INFO] Running org.biojava.bio.search.MaxMismatchPatternTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.search.MaxMismatchPatternTest [INFO] Running org.biojava.bio.search.SeqContentPatternTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.search.SeqContentPatternTest [INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest [INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest [INFO] Running org.biojava.bio.symbol.CrossProductAlphabetIndexTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.692 s - in org.biojava.bio.symbol.CrossProductAlphabetIndexTest [INFO] Running org.biojava.bio.symbol.TranslationTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.TranslationTest [INFO] Running org.biojava.bio.symbol.SimpleBasisSymbolEventTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.SimpleBasisSymbolEventTest [INFO] Running org.biojava.bio.symbol.SymbolSerializationTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.symbol.SymbolSerializationTest [INFO] Running org.biojava.bio.symbol.MotifToolsTest [INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.symbol.MotifToolsTest [INFO] Running org.biojava.bio.symbol.BetweenLocationTest [INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.bio.symbol.BetweenLocationTest [INFO] Running org.biojava.bio.symbol.PointLocationTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.symbol.PointLocationTest [INFO] Running org.biojava.bio.symbol.CrossProductTokenizationTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.symbol.CrossProductTokenizationTest [INFO] Running org.biojava.bio.symbol.AlphabetSerializationTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 s - in org.biojava.bio.symbol.AlphabetSerializationTest [INFO] Running org.biojava.bio.symbol.SimpleSymbolListTest [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.symbol.SimpleSymbolListTest [INFO] Running org.biojava.bio.symbol.IndexedNoAmbPackTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.IndexedNoAmbPackTest [INFO] Running org.biojava.bio.symbol.SymbolListTest [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.504 s - in org.biojava.bio.symbol.SymbolListTest [INFO] Running org.biojava.bio.symbol.MergeLocationTest [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.symbol.MergeLocationTest [INFO] Running org.biojava.bio.symbol.LinearAlphabetIndexTest symbolForIndex getAlphabet indexForSymbol [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.LinearAlphabetIndexTest [INFO] Running org.biojava.bio.symbol.CodonPrefToolsTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 s - in org.biojava.bio.symbol.CodonPrefToolsTest [INFO] Running org.biojava.bio.symbol.UkkonenSuffixTreeTest Adding symbol list taccaccagga$ Adding symbol list taccaccagga$ [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 s - in org.biojava.bio.symbol.UkkonenSuffixTreeTest [INFO] Running org.biojava.bio.symbol.SimpleCodonPrefTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.SimpleCodonPrefTest [INFO] Running org.biojava.bio.symbol.IntegerAlphabetTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.symbol.IntegerAlphabetTest [INFO] Running org.biojava.bio.symbol.SimpleWobbleDistributionTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.SimpleWobbleDistributionTest [INFO] Running org.biojava.bio.symbol.SimpleAtomicSymbolEventTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.SimpleAtomicSymbolEventTest [INFO] Running org.biojava.bio.symbol.RangeLocationTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.RangeLocationTest [INFO] Running org.biojava.bio.symbol.CompoundLocationTest [INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s - in org.biojava.bio.symbol.CompoundLocationTest [INFO] Running org.biojava.bio.symbol.CircularLocationTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.symbol.CircularLocationTest [INFO] Running org.biojava.bio.symbol.TestSoftMaskedAlphabet [INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.TestSoftMaskedAlphabet [INFO] Running org.biojava.bio.symbol.GappedSymbolListTest [INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.symbol.GappedSymbolListTest [INFO] Running org.biojava.bio.symbol.AlphabetManagerTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.AlphabetManagerTest [INFO] Running org.biojava.bio.symbol.NameTokenizationTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.symbol.NameTokenizationTest [INFO] Running org.biojava.bio.symbol.DoubleAlphabetTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.DoubleAlphabetTest [INFO] Running org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest [INFO] Running org.biojava.bio.symbol.SimpleSymbolEventTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.SimpleSymbolEventTest [INFO] Running org.biojava.bio.molbio.RestrictionEnzymeManagerTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojava.bio.molbio.RestrictionEnzymeManagerTest [INFO] Running org.biojava.bio.molbio.RestrictionEnzymeTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.molbio.RestrictionEnzymeTest [INFO] Running org.biojava.bio.program.phred.PhredToolsTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.program.phred.PhredToolsTest [INFO] Running org.biojava.bio.program.indexdb.IndexToolsTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.104 s - in org.biojava.bio.program.indexdb.IndexToolsTest [INFO] Running org.biojava.bio.proteomics.MassCalcTest [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.proteomics.MassCalcTest [INFO] Running org.biojava.bio.proteomics.IsoelectricPointCalcTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.bio.proteomics.IsoelectricPointCalcTest [INFO] Running org.biojava.bio.proteomics.aaindex.AAindexTest org.biojava.bio.symbol.IllegalSymbolException: Symbol adenine not found in alphabet PROTEIN at org.biojava.bio.symbol.AbstractAlphabet.validate(AbstractAlphabet.java:327) at org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper.validate(AlphabetManager.java:1601) at org.biojava.bio.symbol.SimpleSymbolPropertyTable.getDoubleValue(SimpleSymbolPropertyTable.java:67) at org.biojava.bio.proteomics.aaindex.AAindexTest.testDoubleValue(AAindexTest.java:189) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at junit.framework.TestCase.runTest(TestCase.java:177) at junit.framework.TestCase.runBare(TestCase.java:142) at junit.framework.TestResult$1.protect(TestResult.java:122) at junit.framework.TestResult.runProtected(TestResult.java:142) at junit.framework.TestResult.run(TestResult.java:125) at junit.framework.TestCase.run(TestCase.java:130) at junit.framework.TestSuite.runTest(TestSuite.java:241) at junit.framework.TestSuite.run(TestSuite.java:236) at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90) at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365) at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273) at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238) at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159) at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384) at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345) at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126) at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418) [INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.bio.proteomics.aaindex.AAindexTest [INFO] Running org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest java.lang.NullPointerException: name is null. at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.table(SimpleSymbolPropertyTableDB.java:172) at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testTable(SimpleSymbolPropertyTableDBTest.java:126) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at junit.framework.TestCase.runTest(TestCase.java:177) at junit.framework.TestCase.runBare(TestCase.java:142) at junit.framework.TestResult$1.protect(TestResult.java:122) at junit.framework.TestResult.runProtected(TestResult.java:142) at junit.framework.TestResult.run(TestResult.java:125) at junit.framework.TestCase.run(TestCase.java:130) at junit.framework.TestSuite.runTest(TestSuite.java:241) at junit.framework.TestSuite.run(TestSuite.java:236) at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90) at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365) at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273) at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238) at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159) at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384) at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345) at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126) at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418) org.biojava.bio.seq.db.IllegalIDException: No table found with name test. at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.table(SimpleSymbolPropertyTableDB.java:175) at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testTable(SimpleSymbolPropertyTableDBTest.java:134) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at junit.framework.TestCase.runTest(TestCase.java:177) at junit.framework.TestCase.runBare(TestCase.java:142) at junit.framework.TestResult$1.protect(TestResult.java:122) at junit.framework.TestResult.runProtected(TestResult.java:142) at junit.framework.TestResult.run(TestResult.java:125) at junit.framework.TestCase.run(TestCase.java:130) at junit.framework.TestSuite.runTest(TestSuite.java:241) at junit.framework.TestSuite.run(TestSuite.java:236) at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90) at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365) at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273) at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238) at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159) at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384) at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345) at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126) at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418) java.lang.NullPointerException: table is null. at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.addTable(SimpleSymbolPropertyTableDB.java:145) at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testAddTable(SimpleSymbolPropertyTableDBTest.java:113) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at junit.framework.TestCase.runTest(TestCase.java:177) at junit.framework.TestCase.runBare(TestCase.java:142) at junit.framework.TestResult$1.protect(TestResult.java:122) at junit.framework.TestResult.runProtected(TestResult.java:142) at junit.framework.TestResult.run(TestResult.java:125) at junit.framework.TestCase.run(TestCase.java:130) at junit.framework.TestSuite.runTest(TestSuite.java:241) at junit.framework.TestSuite.run(TestSuite.java:236) at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90) at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365) at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273) at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238) at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159) at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384) at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345) at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126) at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418) [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest [INFO] Running org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 s - in org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest [INFO] Running org.biojava.bio.seq.MergeFeatureHolderTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.seq.MergeFeatureHolderTest [INFO] Running org.biojava.bio.seq.DNAToolsTest [INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.DNAToolsTest [INFO] Running org.biojava.bio.seq.SimpleAssemblyTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojava.bio.seq.SimpleAssemblyTest [INFO] Running org.biojava.bio.seq.NewSimpleAssemblyTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.seq.NewSimpleAssemblyTest [INFO] Running org.biojava.bio.seq.filter.FilterTransformerTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.seq.filter.FilterTransformerTest [INFO] Running org.biojava.bio.seq.FeatureFilterTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.FeatureFilterTest [INFO] Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.seq.project.ProjectedFeatureHolderTest [INFO] Running org.biojava.bio.seq.RNAToolsTest [INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.bio.seq.RNAToolsTest [INFO] Running org.biojava.bio.seq.ProteinToolsTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.ProteinToolsTest [INFO] Running org.biojava.bio.seq.FilterUtilsTest [INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.seq.FilterUtilsTest [INFO] Running org.biojava.bio.seq.impl.GappedSequenceTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.seq.impl.GappedSequenceTest [INFO] Running org.biojava.bio.seq.impl.SubSequenceTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.biojava.bio.seq.impl.SubSequenceTest [INFO] Running org.biojava.bio.seq.impl.ViewSequenceTest template: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} orignal: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} copy: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} template: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} orignal: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} copy: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.seq.impl.ViewSequenceTest [INFO] Running org.biojava.bio.seq.impl.ViewSeqSerializationTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.043 s - in org.biojava.bio.seq.impl.ViewSeqSerializationTest [INFO] Running org.biojava.bio.seq.FeatureHolderUtilsTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.seq.FeatureHolderUtilsTest [INFO] Running org.biojava.bio.seq.SeqSerializationTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojava.bio.seq.SeqSerializationTest [INFO] Running org.biojava.bio.seq.io.LocationFormatterTest [INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 s - in org.biojava.bio.seq.io.LocationFormatterTest [INFO] Running org.biojava.bio.seq.io.SmartSequenceBuilderTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.412 s - in org.biojava.bio.seq.io.SmartSequenceBuilderTest [INFO] Running org.biojava.bio.seq.io.MSFAlignmentFormatTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.seq.io.MSFAlignmentFormatTest [INFO] Running org.biojava.bio.seq.io.SymbolListCharSequenceTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.io.SymbolListCharSequenceTest [INFO] Running org.biojava.bio.seq.io.SeqIOToolsTest idb length: 79 [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.292 s - in org.biojava.bio.seq.io.SeqIOToolsTest [INFO] Running org.biojava.bio.seq.io.filterxml.FilterXMLTest [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s - in org.biojava.bio.seq.io.filterxml.FilterXMLTest [INFO] Running org.biojava.bio.seq.CircularSequenceTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.CircularSequenceTest [INFO] Running org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest [INFO] Running org.biojava.bio.seq.db.HashSequenceDBTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.db.HashSequenceDBTest [INFO] Running org.biojava.bio.seq.db.TestHashSequenceDB [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.seq.db.TestHashSequenceDB [INFO] Running org.biojava.bio.seq.db.EmblCDROMIndexStoreTest [INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojava.bio.seq.db.EmblCDROMIndexStoreTest [INFO] Running org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest [INFO] Running org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest [INFO] Running org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest [INFO] Running org.biojava.directory.RegistryConfigurationTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.directory.RegistryConfigurationTest [INFO] Running org.biojava.directory.SystemRegistryTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojava.directory.SystemRegistryTest [INFO] Running org.biojava.directory.OBDARegistryParserTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.directory.OBDARegistryParserTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 890, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] -----------------------< org.biojava:alignment >------------------------ [INFO] Building alignment 1.9.7 [4/9] [INFO] from alignment/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ alignment --- [INFO] Copying 89 resources from src/main/resources to target/classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ alignment --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ alignment --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ alignment --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ alignment --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.bio.alignment.SubstitutionMatrixTest [INFO] Tests run: 96, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.868 s - in org.biojava.bio.alignment.SubstitutionMatrixTest [INFO] Running org.biojava.bio.alignment.AlignmentPairTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 s - in org.biojava.bio.alignment.AlignmentPairTest [INFO] Running org.biojava.bio.alignment.FlexibleAlignmentTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 s - in org.biojava.bio.alignment.FlexibleAlignmentTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 102, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] -------------------------< org.biojava:biosql >------------------------- [INFO] Building biosql 1.9.7 [5/9] [INFO] from biosql/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biosql --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biosql --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biosql --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biosql --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biosql --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest No hsqldb driver found. [INFO] Tests run: 0, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 s - in org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 0, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] -------------------------< org.biojava:blast >-------------------------- [INFO] Building blast 1.9.7 [6/9] [INFO] from blast/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ blast --- [INFO] Copying 3 resources from src/main/resources to target/classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ blast --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ blast --- [INFO] Copying 22 resources from src/test/resources to target/test-classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ blast --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ blast --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.bio.program.sax.BlastTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.246 s - in org.biojava.bio.program.sax.BlastTest [INFO] Running org.biojava.bio.program.sax.blastxml.BlastXMLTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.141 s - in org.biojava.bio.program.sax.blastxml.BlastXMLTest [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.362 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 s - in org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.613 s - in org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.197 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.179 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 s - in org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.241 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.207 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.154 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.062 s - in org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.07 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.595 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.827 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test [INFO] [INFO] Results: [INFO] [INFO] Tests run: 118, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] -----------------------< org.biojava:sequencing >----------------------- [INFO] Building sequencing 1.9.7 [7/9] [INFO] from sequencing/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ sequencing --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ sequencing --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ sequencing --- [INFO] Copying 77 resources from src/test/resources to target/test-classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ sequencing --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ sequencing --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.bio.program.fastq.IlluminaFastqWriterTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 s - in org.biojava.bio.program.fastq.IlluminaFastqWriterTest [INFO] Running org.biojava.bio.program.fastq.StreamingFastqParserTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.program.fastq.StreamingFastqParserTest [INFO] Running org.biojava.bio.program.fastq.FastqVariantTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.program.fastq.FastqVariantTest [INFO] Running org.biojava.bio.program.fastq.SolexaFastqReaderTest [INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.113 s - in org.biojava.bio.program.fastq.SolexaFastqReaderTest [INFO] Running org.biojava.bio.program.fastq.SangerFastqWriterTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s - in org.biojava.bio.program.fastq.SangerFastqWriterTest [INFO] Running org.biojava.bio.program.fastq.FastqTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.bio.program.fastq.FastqTest [INFO] Running org.biojava.bio.program.fastq.FastqToolsTest [INFO] Tests run: 38, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.208 s - in org.biojava.bio.program.fastq.FastqToolsTest [INFO] Running org.biojava.bio.program.fastq.IlluminaFastqReaderTest [INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojava.bio.program.fastq.IlluminaFastqReaderTest [INFO] Running org.biojava.bio.program.fastq.SolexaFastqWriterTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.program.fastq.SolexaFastqWriterTest [INFO] Running org.biojava.bio.program.fastq.FastqBuilderTest [INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.program.fastq.FastqBuilderTest [INFO] Running org.biojava.bio.program.fastq.SangerFastqReaderTest [INFO] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 s - in org.biojava.bio.program.fastq.SangerFastqReaderTest [INFO] Running org.biojava.bio.program.fastq.ConvertTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.program.fastq.ConvertTest [INFO] Running org.biojava.bio.program.scf.SCFTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 s - in org.biojava.bio.program.scf.SCFTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 192, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] --------------------------< org.biojava:gui >--------------------------- [INFO] Building gui 1.9.7 [8/9] [INFO] from gui/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ gui --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ gui --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ gui --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ gui --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ gui --- [INFO] No tests to run. [INFO] [INFO] -------------------------< org.biojava:phylo >-------------------------- [INFO] Building phylo 1.9.7 [9/9] [INFO] from phylo/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ phylo --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/phylo/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ phylo --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ phylo --- [INFO] Copying 3 resources from src/test/resources to target/test-classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ phylo --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ phylo --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojavax.bio.phylo.io.nexus.TreesBlockTest [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.14 s - in org.biojavax.bio.phylo.io.nexus.TreesBlockTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava-legacy 1.9.7: [INFO] [INFO] biojava-legacy ..................................... SUCCESS [ 0.004 s] [INFO] bytecode ........................................... SUCCESS [ 0.620 s] [INFO] core ............................................... SUCCESS [ 35.536 s] [INFO] alignment .......................................... SUCCESS [ 32.477 s] [INFO] biosql ............................................. SUCCESS [ 31.301 s] [INFO] blast .............................................. SUCCESS [ 34.943 s] [INFO] sequencing ......................................... SUCCESS [ 31.397 s] [INFO] gui ................................................ SUCCESS [ 0.090 s] [INFO] phylo .............................................. SUCCESS [ 30.915 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 03:17 min [INFO] Finished at: 2025-12-16T06:07:43Z [INFO] ------------------------------------------------------------------------ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/biojava-live-1.9.7\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/biojava-live-1.9.7\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/biojava-live-1.9.7\+dfsg/debian/maven-repo --batch-mode -Ddebian.dir=/build/reproducible-path/biojava-live-1.9.7\+dfsg/debian -Ddebian.package=libbiojava1.9-java -Dmaven.repo.local=/build/reproducible-path/biojava-live-1.9.7\+dfsg/debian/maven-repo -Dinstall.to.usj=true org.debian.maven:debian-maven-plugin:2.6:install OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release. [INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] biojava-legacy [pom] [INFO] bytecode [jar] [INFO] core [jar] [INFO] alignment [jar] [INFO] biosql [jar] [INFO] blast [jar] [INFO] sequencing [jar] [INFO] gui [jar] [INFO] phylo [jar] [INFO] [INFO] ---------------------< org.biojava:biojava-legacy >--------------------- [INFO] Building biojava-legacy 1.9.7 [1/9] [INFO] from pom.xml [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-legacy --- [INFO] Cleaning pom file: /build/reproducible-path/biojava-live-1.9.7+dfsg/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava1.9-java [INFO] --rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.publishedRules [INFO] --no-parent [INFO] [INFO] ------------------------< org.biojava:bytecode >------------------------ [INFO] Building bytecode 1.9.7 [2/9] [INFO] from bytecode/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ bytecode --- [INFO] Cleaning pom file: /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava1.9-java [INFO] --rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.publishedRules [INFO] Install jar for bytecode into /usr/share/java [INFO] [INFO] --------------------------< org.biojava:core >-------------------------- [INFO] Building core 1.9.7 [3/9] [INFO] from core/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ core --- [INFO] Cleaning pom file: /build/reproducible-path/biojava-live-1.9.7+dfsg/core/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava1.9-java [INFO] --rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.publishedRules [INFO] Install jar for core into /usr/share/java [INFO] [INFO] -----------------------< org.biojava:alignment >------------------------ [INFO] Building alignment 1.9.7 [4/9] [INFO] from alignment/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ alignment --- [INFO] Cleaning pom file: /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava1.9-java [INFO] --rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.publishedRules [INFO] Install jar for alignment into /usr/share/java [INFO] [INFO] -------------------------< org.biojava:biosql >------------------------- [INFO] Building biosql 1.9.7 [5/9] [INFO] from biosql/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biosql --- [INFO] Cleaning pom file: /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava1.9-java [INFO] --rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.publishedRules [INFO] Install jar for biosql into /usr/share/java [INFO] [INFO] -------------------------< org.biojava:blast >-------------------------- [INFO] Building blast 1.9.7 [6/9] [INFO] from blast/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ blast --- [INFO] Cleaning pom file: /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava1.9-java [INFO] --rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.publishedRules [INFO] Install jar for blast into /usr/share/java [INFO] [INFO] -----------------------< org.biojava:sequencing >----------------------- [INFO] Building sequencing 1.9.7 [7/9] [INFO] from sequencing/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ sequencing --- [INFO] Cleaning pom file: /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava1.9-java [INFO] --rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.publishedRules [INFO] Install jar for sequencing into /usr/share/java [INFO] [INFO] --------------------------< org.biojava:gui >--------------------------- [INFO] Building gui 1.9.7 [8/9] [INFO] from gui/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ gui --- [INFO] Cleaning pom file: /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava1.9-java [INFO] --rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.publishedRules [INFO] Install jar for gui into /usr/share/java [INFO] [INFO] -------------------------< org.biojava:phylo >-------------------------- [INFO] Building phylo 1.9.7 [9/9] [INFO] from phylo/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ phylo --- [INFO] Cleaning pom file: /build/reproducible-path/biojava-live-1.9.7+dfsg/phylo/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava1.9-java [INFO] --rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.publishedRules [INFO] Install jar for phylo into /usr/share/java [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava-legacy 1.9.7: [INFO] [INFO] biojava-legacy ..................................... SUCCESS [ 0.358 s] [INFO] bytecode ........................................... SUCCESS [ 0.037 s] [INFO] core ............................................... SUCCESS [ 0.026 s] [INFO] alignment .......................................... SUCCESS [ 0.030 s] [INFO] biosql ............................................. SUCCESS [ 0.024 s] [INFO] blast .............................................. SUCCESS [ 0.024 s] [INFO] sequencing ......................................... SUCCESS [ 0.030 s] [INFO] gui ................................................ SUCCESS [ 0.022 s] [INFO] phylo .............................................. SUCCESS [ 0.023 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.797 s [INFO] Finished at: 2025-12-16T06:07:46Z [INFO] ------------------------------------------------------------------------ mh_resolve_dependencies --non-interactive --offline --build -plibbiojava1.9-java --base-directory=/build/reproducible-path/biojava-live-1.9.7\+dfsg --non-explore Analysing pom.xml... Analysing alignment/pom.xml... Checking the parent dependency in the sub project alignment/pom.xml Analysing biosql/pom.xml... Checking the parent dependency in the sub project biosql/pom.xml Analysing blast/pom.xml... Checking the parent dependency in the sub project blast/pom.xml Analysing bytecode/pom.xml... Checking the parent dependency in the sub project bytecode/pom.xml Analysing core/pom.xml... Checking the parent dependency in the sub project core/pom.xml Analysing gui/pom.xml... Checking the parent dependency in the sub project gui/pom.xml Analysing phylo/pom.xml... Checking the parent dependency in the sub project phylo/pom.xml Analysing sequencing/pom.xml... Checking the parent dependency in the sub project sequencing/pom.xml mh_unpatchpoms -plibbiojava1.9-java debian/rules override_dh_installdocs make[1]: Entering directory '/build/reproducible-path/biojava-live-1.9.7+dfsg' dh_installdocs # Deleting calls to urchinTracker to enhance privacy. for F in $(find . -name "*.html"); do \ sed -i 's/^$//' $F; \ done make[1]: Leaving directory '/build/reproducible-path/biojava-live-1.9.7+dfsg' dh_installchangelogs dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libbiojava1.9-java' in '../libbiojava1.9-java_1.9.7+dfsg-2_all.deb'. dpkg-deb: building package 'libbiojava-java' in '../libbiojava-java_1.9.7+dfsg-2_all.deb'. dpkg-genbuildinfo --build=binary -O../biojava-live_1.9.7+dfsg-2_arm64.buildinfo dpkg-genchanges --build=binary -O../biojava-live_1.9.7+dfsg-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3325553 and its subdirectories I: Current time: Mon Dec 15 18:07:54 -12 2025 I: pbuilder-time-stamp: 1765865274 Tue Nov 12 23:44:56 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Tue Nov 12 23:44:56 UTC 2024 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Tue Nov 12 23:49:40 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Tue Nov 12 23:49:41 UTC 2024 I: biojava-live_1.9.7+dfsg-2_arm64.changes: Format: 1.8 Date: Mon, 07 Oct 2024 09:59:24 +0200 Source: biojava-live Binary: libbiojava-java libbiojava1.9-java Architecture: all Version: 1:1.9.7+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Emmanuel Bourg Description: libbiojava-java - Java API to biological data and applications (default version) libbiojava1.9-java - Java API to biological data and applications (version 1.9) Changes: biojava-live (1:1.9.7+dfsg-2) unstable; urgency=medium . * Team upload. * Removed the -java-doc package * Standards-Version updated to 4.7.0 Checksums-Sha1: 302057d5208063aafa23df70fbd8c0e4e29f1c63 13914 biojava-live_1.9.7+dfsg-2_arm64.buildinfo 1c135db37b4e03de237b91520425a55e5e0cbb5f 5552 libbiojava-java_1.9.7+dfsg-2_all.deb 2eceafa3ea1c4703a066e73d80dd32c206979078 3164480 libbiojava1.9-java_1.9.7+dfsg-2_all.deb Checksums-Sha256: fbfa7116e82326c85893d1543aef16ccd97e3695ef3587ce7beb46262a35d1c7 13914 biojava-live_1.9.7+dfsg-2_arm64.buildinfo bd9afd161cd82b63e08c2c737f3f3528c74d68c59ebeb779b96aba708b0216ef 5552 libbiojava-java_1.9.7+dfsg-2_all.deb dd2f187b2d555c03fd158594a706462b52d350b35be9fd226669c870b2e2774a 3164480 libbiojava1.9-java_1.9.7+dfsg-2_all.deb Files: 3701c020a0bfa10edd877c9cdfed492e 13914 java optional biojava-live_1.9.7+dfsg-2_arm64.buildinfo 704c8314d95b835199800c4def80c727 5552 java optional libbiojava-java_1.9.7+dfsg-2_all.deb 612ff7f7f33dca47360a370977079197 3164480 java optional libbiojava1.9-java_1.9.7+dfsg-2_all.deb Tue Nov 12 23:49:42 UTC 2024 I: diffoscope 283 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_23-65917.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.HGIaNXaC/biojava-live_1.9.7+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.HGIaNXaC/biojava-live_1.9.7+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.HGIaNXaC/biojava-live_1.9.7+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.HGIaNXaC/b1/biojava-live_1.9.7+dfsg-2_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.HGIaNXaC/b2/biojava-live_1.9.7+dfsg-2_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.429s) 0.429s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.051s) 0.051s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 762ms CPU time consumed: 763ms Tue Nov 12 23:49:43 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Tue Nov 12 23:49:43 UTC 2024 I: biojava-live from trixie built successfully and reproducibly on arm64. Tue Nov 12 23:49:44 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Nov 12 23:49:44 UTC 2024 I: Submitting 16K b1/biojava-live_1.9.7+dfsg-2_arm64.buildinfo.asc Tue Nov 12 23:49:45 UTC 2024 I: Submitting 16K b2/biojava-live_1.9.7+dfsg-2_arm64.buildinfo.asc Tue Nov 12 23:49:46 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Nov 12 23:49:46 UTC 2024 I: Done submitting .buildinfo files. Tue Nov 12 23:49:46 UTC 2024 I: Removing signed biojava-live_1.9.7+dfsg-2_arm64.buildinfo.asc files: removed './b1/biojava-live_1.9.7+dfsg-2_arm64.buildinfo.asc' removed './b2/biojava-live_1.9.7+dfsg-2_arm64.buildinfo.asc'