I: pbuilder: network access will be disabled during build I: Current time: Thu Apr 16 22:07:15 -12 2026 I: pbuilder-time-stamp: 1776420435 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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 dpkg-source: warning: cannot verify inline signature for ./biojava-live_1.9.7+dfsg-2.dsc: unsupported subcommand 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/3247929/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='a3fe24e30e1b47ed9660b07b609a8ff9' 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='3247929' 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.jJGla0Ra/pbuilderrc_DY0s --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.jJGla0Ra/b1 --logfile b1/build.log biojava-live_1.9.7+dfsg-2.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3247929/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: amd64 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 ... 19785 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-intel1{a} libdrm2{a} libedit2{a} libel-api-java{a} libelf1t64{a} libepoxy0{a} liberror-prone-java{a} libexpat1{a} libffi8{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} libglib2.0-0t64{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgnutls30t64{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} libicu76{a} libidn2-0{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} libp11-kit0{a} libpam-systemd{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpciaccess0{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} libtasn1-6{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libunistring5{a} libunivocity-parsers-java{a} libvelocity-tools-java{a} libvulkan1{a} libwagon-file-java{a} libwagon-http-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-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, 292 newly installed, 0 to remove and 0 not upgraded. Need to get 263 MB of archives. After unpacking 783 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libsystemd-shared amd64 257.4-3 [2141 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libapparmor1 amd64 4.1.0~beta5-3 [43.5 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 systemd amd64 257.4-3 [3094 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 systemd-sysv amd64 257.4-3 [61.9 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.16.2-2 [178 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 dbus-bin amd64 1.16.2-2 [80.0 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 dbus-session-bus-common all 1.16.2-2 [52.3 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 dbus-daemon amd64 1.16.2-2 [159 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 dbus-system-bus-common all 1.16.2-2 [53.5 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 dbus amd64 1.16.2-2 [71.6 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-7 [878 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.4.1-1 [1427 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20241223 [164 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-2 [337 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-2 [109 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-2 [43.5 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libpam-systemd amd64 257.4-3 [294 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [311 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.84.0-2 [1513 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libicu76 amd64 76.1-3 [9721 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.3+b1 [699 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 shared-mime-info amd64 2.4-5+b2 [760 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3.1 [168 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.47-1.1 [282 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-2 [140 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 gtk-update-icon-cache amd64 4.17.5+ds-3 [51.5 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 hicolor-icon-theme all 0.18-2 [11.8 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 adwaita-icon-theme all 48.0-1 [504 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 java-common all 0.76 [6776 B] Get: 48 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libnspr4 amd64 2:4.36-1 [110 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libnss3 amd64 2:3.109-1 [1393 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libpcsclite1 amd64 2.3.1-1 [56.0 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 openjdk-21-jre-headless amd64 21.0.6+7-1 [41.7 MB] Get: 53 http://deb.debian.org/debian unstable/main amd64 default-jre-headless amd64 2:1.21-76 [3192 B] Get: 54 http://deb.debian.org/debian unstable/main amd64 ant all 1.10.15-1 [2163 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 at-spi2-common all 2.55.2-1 [170 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-7 [294 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 dbus-user-session amd64 1.16.2-2 [52.1 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libdconf1 amd64 0.40.0-5 [41.8 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 dconf-service amd64 0.40.0-5 [32.4 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 dconf-gsettings-backend amd64 0.40.0-5 [28.6 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 71 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libatk1.0-0t64 amd64 2.55.2-1 [51.4 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libatspi2.0-0t64 amd64 2.55.2-1 [77.0 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libatk-bridge2.0-0t64 amd64 2.55.2-1 [68.1 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2.1 [318 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2.1 [391 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b4 [27.8 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.4-1 [537 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libcairo-gobject2 amd64 1.18.4-1 [130 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libcloudproviders0 amd64 0.3.6-1+b1 [29.2 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libcolord2 amd64 1.4.7-3 [139 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-16 [112 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-16 [44.2 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-16 [48.4 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-1 [109 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 113 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.10-2+b1 [251 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libepoxy0 amd64 1.5.10-2 [193 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 10.2.0-1+b1 [479 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-2.1 [463 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.56.2-1 [226 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.56.2-1 [55.4 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.56.2-1 [35.8 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libwayland-client0 amd64 1.23.1-3 [26.8 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libwayland-cursor0 amd64 1.23.1-3 [11.9 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libwayland-egl1 amd64 1.23.1-3 [5860 B] Get: 130 http://deb.debian.org/debian unstable/main amd64 libxcomposite1 amd64 1:0.4.6-1 [16.3 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libxfixes3 amd64 1:6.0.0-2+b4 [20.2 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libxcursor1 amd64 1:1.2.3-1 [39.7 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libxdamage1 amd64 1:1.1.6-1+b2 [15.5 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libxinerama1 amd64 2:1.1.4-3+b3 [16.0 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 xkb-data all 2.42-1 [790 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libxkbcommon0 amd64 1.7.0-2 [113 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libxrandr2 amd64 2:1.5.4-1+b3 [36.3 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libgtk-3-common all 3.24.49-1 [4908 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libgtk-3-0t64 amd64 3.24.49-1 [2768 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.124-1 [8180 B] Get: 142 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.124-1 [38.9 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libx11-xcb1 amd64 2:1.8.10-2 [241 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b4 [19.3 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.124-1 [22.4 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libdrm-intel1 amd64 2.4.124-1 [63.8 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libllvm19 amd64 1:19.1.7-3 [26.0 MB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libsensors5 amd64 1:3.6.0-10+b1 [35.1 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libxshmfence1 amd64 1.3-1+b3 [8852 B] Get: 160 http://deb.debian.org/debian unstable/main amd64 mesa-libgallium amd64 25.0.1-2 [9619 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libwayland-server0 amd64 1.23.1-3 [34.4 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libgbm1 amd64 25.0.1-2 [44.0 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libvulkan1 amd64 1.4.304.0-1 [129 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libgl1-mesa-dri amd64 25.0.1-2 [45.5 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libglx-mesa0 amd64 25.0.1-2 [143 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libasound2-data all 1.2.13-1 [21.1 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 libasound2t64 amd64 1.2.13-1+b1 [373 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libgif7 amd64 5.2.2-1+b1 [44.2 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+24 [217 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libxtst6 amd64 2:1.2.5-1 [25.8 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 openjdk-21-jre amd64 21.0.6+7-1 [205 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 default-jre amd64 2:1.21-76 [1068 B] Get: 175 http://deb.debian.org/debian unstable/main amd64 openjdk-21-jdk-headless amd64 21.0.6+7-1 [82.8 MB] Get: 176 http://deb.debian.org/debian unstable/main amd64 default-jdk-headless amd64 2:1.21-76 [1124 B] Get: 177 http://deb.debian.org/debian unstable/main amd64 openjdk-21-jdk amd64 21.0.6+7-1 [3434 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 default-jdk amd64 2:1.21-76 [1076 B] Get: 179 http://deb.debian.org/debian unstable/main amd64 libhamcrest-java all 2.2-2 [121 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 junit4 all 4.13.2-5 [350 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 libapiguardian-java all 1.1.2-1 [4656 B] Get: 182 http://deb.debian.org/debian unstable/main amd64 libopentest4j-java all 1.2.0-4 [9516 B] Get: 183 http://deb.debian.org/debian unstable/main amd64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 libpicocli-java all 4.6.2-2 [390 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 junit5 all 5.10.3-1 [2459 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 libaopalliance-java all 20070526-7 [8572 B] Get: 189 http://deb.debian.org/debian unstable/main amd64 libapache-pom-java all 33-2 [5852 B] Get: 190 http://deb.debian.org/debian unstable/main amd64 libasm-java all 9.7.1-1 [391 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 libatinject-jsr330-api-java all 1.0+ds1-6 [5112 B] Get: 192 http://deb.debian.org/debian unstable/main amd64 libbsh-java all 2.0b4-20 [291 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-5 [8444 B] Get: 194 http://deb.debian.org/debian unstable/main amd64 libcdi-api-java all 1.2-4 [55.3 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 libcommons-beanutils-java all 1.9.4-2 [233 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 libcommons-codec-java all 1.18.0-1 [304 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 libcommons-io-java all 2.18.0-1 [509 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 libcommons-compress-java all 1.27.1-2 [641 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 libcommons-pool-java all 1.6-5 [109 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 libcommons-dbcp-java all 1.4-8 [157 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 libcommons-digester-java all 1.8.1-7 [138 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 libcommons-lang-java all 2.6-10 [273 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 libcommons-lang3-java all 3.17.0-1 [641 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 libslf4j-java all 1.7.32-1 [144 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 libsnappy1v5 amd64 1.2.1-1+b1 [29.6 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 libsnappy-jni amd64 1.1.10.7-1 [6492 B] Get: 213 http://deb.debian.org/debian unstable/main amd64 libsnappy-java all 1.1.10.7-1 [87.6 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 libxz-java all 1.9-1 [143 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 libplexus-interpolation-java all 1.27-1 [76.8 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 libmaven-archiver-java all 3.6.2-1 [26.1 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 libmaven-shared-utils-java all 3.4.2-1 [137 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 libjsr305-java all 0.1~+svn49-12 [26.6 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 libguava-java all 32.0.1-1 [2708 kB] Get: 223 http://deb.debian.org/debian unstable/main amd64 libguice-java all 5.1.0-1 [932 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 libmaven-parent-java all 43-2 [6252 B] Get: 225 http://deb.debian.org/debian unstable/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 libmaven-resolver-java all 1.9.22-1 [729 kB] Get: 227 http://deb.debian.org/debian unstable/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 230 http://deb.debian.org/debian unstable/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 libsisu-inject-java all 0.3.5-1 [352 kB] Get: 232 http://deb.debian.org/debian unstable/main amd64 libsisu-plexus-java all 0.3.5-1 [183 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 libmaven3-core-java all 3.9.9-1 [1661 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 libmaven-file-management-java all 3.0.0-2 [35.1 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 libcommons-text-java all 1.13.0-1 [228 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 libcommons-validator-java all 1:1.9.0-1 [191 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 libjaxen-java all 1.1.6-5 [214 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 libdom4j-java all 2.1.4-1 [312 kB] Get: 241 http://deb.debian.org/debian unstable/main amd64 libdoxia-core-java all 2.0.0-1 [149 kB] Get: 242 http://deb.debian.org/debian unstable/main amd64 libplexus-xml-java all 3.0.1-2 [93.7 kB] Get: 243 http://deb.debian.org/debian unstable/main amd64 libdoxia-java all 2.0.0-1 [113 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 libmaven-reporting-api-java all 4.0.0-1 [6724 B] Get: 245 http://deb.debian.org/debian unstable/main amd64 libxbean-reflect-java all 4.5-9 [132 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 247 http://deb.debian.org/debian unstable/main amd64 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 velocity all 1.7-7 [431 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 libplexus-velocity-java all 1.2-4 [9676 B] Get: 250 http://deb.debian.org/debian unstable/main amd64 liboro-java all 2.0.8a-14 [70.5 kB] Get: 251 http://deb.debian.org/debian unstable/main amd64 libvelocity-tools-java all 2.0-9 [311 kB] Get: 252 http://deb.debian.org/debian unstable/main amd64 libdoxia-sitetools-java all 2.0.0-1 [176 kB] Get: 253 http://deb.debian.org/debian unstable/main amd64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 254 http://deb.debian.org/debian unstable/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 255 http://deb.debian.org/debian unstable/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 256 http://deb.debian.org/debian unstable/main amd64 libjansi-java all 2.4.1-2 [100 kB] Get: 257 http://deb.debian.org/debian unstable/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 258 http://deb.debian.org/debian unstable/main amd64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 259 http://deb.debian.org/debian unstable/main amd64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 260 http://deb.debian.org/debian unstable/main amd64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 261 http://deb.debian.org/debian unstable/main amd64 libjetty9-java all 9.4.57-1 [2965 kB] Get: 262 http://deb.debian.org/debian unstable/main amd64 libjgraph-java all 5.12.4.2+dfsg-7 [207 kB] Get: 263 http://deb.debian.org/debian unstable/main amd64 libjgrapht0.8-java all 0.8.3-7 [216 kB] Get: 264 http://deb.debian.org/debian unstable/main amd64 libjsoup-java all 1.15.3-1 [431 kB] Get: 265 http://deb.debian.org/debian unstable/main amd64 libjtidy-java all 7+svn20110807-6 [251 kB] Get: 266 http://deb.debian.org/debian unstable/main amd64 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB] Get: 267 http://deb.debian.org/debian unstable/main amd64 libmaven-common-artifact-filters-java all 3.4.0-1 [47.7 kB] Get: 268 http://deb.debian.org/debian unstable/main amd64 libmaven-shared-incremental-java all 1.1-6 [9916 B] Get: 269 http://deb.debian.org/debian unstable/main amd64 libplexus-compiler-java all 2.13.0-1 [99.5 kB] Get: 270 http://deb.debian.org/debian unstable/main amd64 libqdox2-java all 2.0.3-1 [296 kB] Get: 271 http://deb.debian.org/debian unstable/main amd64 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 272 http://deb.debian.org/debian unstable/main amd64 libmaven-compiler-plugin-java all 3.13.0-1 [78.8 kB] Get: 273 http://deb.debian.org/debian unstable/main amd64 libplexus-build-api-java all 0.0.7-4 [10.3 kB] Get: 274 http://deb.debian.org/debian unstable/main amd64 libmaven-filtering-java all 3.4.0-1 [51.4 kB] Get: 275 http://deb.debian.org/debian unstable/main amd64 libplexus-ant-factory-java all 1.0~alpha2.1-5 [11.7 kB] Get: 276 http://deb.debian.org/debian unstable/main amd64 libplexus-container-default1.5-java all 2.1.1-1 [4476 B] Get: 277 http://deb.debian.org/debian unstable/main amd64 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B] Get: 278 http://deb.debian.org/debian unstable/main amd64 libmaven-plugin-tools-java all 3.10.2-1 [245 kB] Get: 279 http://deb.debian.org/debian unstable/main amd64 libmaven-reporting-exec-java all 2.0.0-1 [23.9 kB] Get: 280 http://deb.debian.org/debian unstable/main amd64 libmaven-resources-plugin-java all 3.3.1-1 [27.5 kB] Get: 281 http://deb.debian.org/debian unstable/main amd64 libmaven-site-plugin-java all 3.21.0-1 [106 kB] Get: 282 http://deb.debian.org/debian unstable/main amd64 libsurefire-java all 2.22.3-3 [1284 kB] Get: 283 http://deb.debian.org/debian unstable/main amd64 libwagon-file-java all 3.5.3-1 [8388 B] Get: 284 http://deb.debian.org/debian unstable/main amd64 libwagon-http-java all 3.5.3-1 [49.5 kB] Get: 285 http://deb.debian.org/debian unstable/main amd64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 286 http://deb.debian.org/debian unstable/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 287 http://deb.debian.org/debian unstable/main amd64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 288 http://deb.debian.org/debian unstable/main amd64 libxml2-utils amd64 2.12.7+dfsg+really2.9.14-0.3+b1 [99.4 kB] Get: 289 http://deb.debian.org/debian unstable/main amd64 maven all 3.9.9-1 [19.7 kB] Get: 290 http://deb.debian.org/debian unstable/main amd64 maven-repo-helper all 1.11 [142 kB] Get: 291 http://deb.debian.org/debian unstable/main amd64 unzip amd64 6.0-29 [173 kB] Get: 292 http://deb.debian.org/debian unstable/main amd64 maven-debian-helper all 2.6.7 [108 kB] Fetched 263 MB in 18s (14.4 MB/s) Preconfiguring packages ... Selecting previously unselected package libsystemd-shared:amd64. (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 ... 19785 files and directories currently installed.) Preparing to unpack .../libsystemd-shared_257.4-3_amd64.deb ... Unpacking libsystemd-shared:amd64 (257.4-3) ... Selecting previously unselected package libapparmor1:amd64. Preparing to unpack .../libapparmor1_4.1.0~beta5-3_amd64.deb ... Unpacking libapparmor1:amd64 (4.1.0~beta5-3) ... Setting up libsystemd-shared:amd64 (257.4-3) ... Selecting previously unselected package systemd. (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 ... 19798 files and directories currently installed.) Preparing to unpack .../systemd_257.4-3_amd64.deb ... Unpacking systemd (257.4-3) ... Setting up libapparmor1:amd64 (4.1.0~beta5-3) ... Setting up systemd (257.4-3) ... 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:14: 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 ... 20741 files and directories currently installed.) Preparing to unpack .../000-systemd-sysv_257.4-3_amd64.deb ... Unpacking systemd-sysv (257.4-3) ... Selecting previously unselected package libdbus-1-3:amd64. Preparing to unpack .../001-libdbus-1-3_1.16.2-2_amd64.deb ... Unpacking libdbus-1-3:amd64 (1.16.2-2) ... Selecting previously unselected package dbus-bin. Preparing to unpack .../002-dbus-bin_1.16.2-2_amd64.deb ... 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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 (1:5.46-2) ... Setting up libxcb-render0:amd64 (1.17.0-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglvnd0:amd64 (1.7.0-1+b2) ... Setting up libxcb-glx0:amd64 (1.17.0-2+b1) ... Setting up unzip (6.0-29) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libbrotli1:amd64 (1.1.0-2+b7) ... Setting up libedit2:amd64 (3.1-20250104-1) ... Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ... Setting up libmagic1t64:amd64 (1:5.46-2) ... Setting up libpicocli-java (4.6.2-2) ... Setting up libasm-java (9.7.1-1) ... Setting up x11-common (1:7.7+24) ... 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:amd64 (1.23-1+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-7) ... 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:amd64 (1.17.0-2+b1) ... Setting up libcom-err2:amd64 (1.47.2-1) ... Setting up file (1:5.46-2) ... Setting up libunivocity-parsers-java (2.9.1-1) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up liboro-java (2.0.8a-14) ... Setting up libsnappy1v5:amd64 (1.2.1-1+b1) ... Setting up libkrb5support0:amd64 (1.21.3-5) ... Setting up libxcb-present0:amd64 (1.17.0-2+b1) ... Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... Setting up libgeronimo-interceptor-3.0-spec-java (1.0.1-5) ... Setting up libcommons-collections3-java (3.2.2-3) ... Setting up libasound2-data (1.2.13-1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.13.3-1) ... Setting up libasound2t64:amd64 (1.2.13-1+b1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3.1) ... 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:amd64 (1.5.10-2) ... Setting up libnspr4:amd64 (2:4.36-1) ... Setting up libxcb-sync1:amd64 (1.17.0-2+b1) ... Setting up libjtidy-java (7+svn20110807-6) ... Setting up libjansi-java (2.4.1-2) ... Setting up libapache-pom-java (33-2) ... Setting up libavahi-common-data:amd64 (0.8-16) ... Setting up libatinject-jsr330-api-java (1.0+ds1-6) ... Setting up libdbus-1-3:amd64 (1.16.2-2) ... Setting up libwebsocket-api-java (1.1-2) ... Setting up libfribidi0:amd64 (1.0.16-1) ... Setting up libproc2-0:amd64 (2:4.0.4-7) ... Setting up libplexus-interpolation-java (1.27-1) ... Setting up libunistring5:amd64 (1.3-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.47-1.1) ... 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 (0.23.1-1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libpcsclite1:amd64 (2.3.1-1) ... Setting up libsensors5:amd64 (1:3.6.0-10+b1) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... 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 libbsh-java (2.0b4-20) ... Setting up libjsp-api-java (2.3.4-3) ... Setting up libvulkan1:amd64 (1.4.304.0-1) ... Setting up autoconf (2.72-3) ... Setting up libwebp7:amd64 (1.5.0-0.1) ... Setting up libgif7:amd64 (5.2.2-1+b1) ... Setting up libffi8:amd64 (3.4.7-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libxshmfence1:amd64 (1.3-1+b3) ... Setting up libjsoup-java (1.15.3-1) ... Setting up at-spi2-common (2.55.2-1) ... Setting up libtiff6:amd64 (4.5.1+git230720-5) ... Setting up libxcb-randr0:amd64 (1.17.0-2+b1) ... Setting up dbus-session-bus-common (1.16.2-2) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libxml-commons-external-java (1.4.01-6) ... Setting up procps (2:4.0.4-7) ... 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 libtasn1-6:amd64 (4.20.0-2) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up libthai-data (0.1.29-2) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libwayland-egl1:amd64 (1.23.1-3) ... Setting up libicu76:amd64 (76.1-3) ... Setting up libhttpcore-java (4.4.16-1) ... Setting up libxerces2-java (2.12.2-1) ... Setting up dbus-system-bus-common (1.16.2-2) ... Creating group 'messagebus' with GID 997. Creating user 'messagebus' (System Message Bus) with UID 997 and GID 997. Setting up openssl (3.4.1-1) ... Setting up libdrm-common (2.4.124-1) ... Setting up libcdi-api-java (1.2-4) ... Setting up libsnappy-jni (1.1.10.7-1) ... Setting up libxcomposite1:amd64 (1:0.4.6-1) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.3+b1) ... Setting up dbus-bin (1.16.2-2) ... Setting up libxkbcommon0:amd64 (1.7.0-2) ... Setting up libwayland-client0:amd64 (1.23.1-3) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 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 (1.14.1-2) ... Setting up libxcb-dri3-0:amd64 (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:amd64 (1:19.1.7-3) ... Setting up libwayland-server0:amd64 (1.23.1-3) ... Setting up libx11-xcb1:amd64 (2:1.8.10-2) ... Setting up gettext (0.23.1-1) ... Setting up libjetty9-java (9.4.57-1) ... Setting up libxdamage1:amd64 (1:1.1.6-1+b2) ... Setting up libplexus-languages-java (1.1.1-2) ... Setting up libjgrapht0.8-java (0.8.3-7) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b4) ... Setting up libtool (2.5.4-4) ... Setting up fontconfig-config (2.15.0-2.1) ... Setting up libmaven-parent-java (43-2) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-16) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up libsisu-inject-java (0.3.5-1) ... Setting up libidn2-0:amd64 (2.3.8-1) ... Setting up libnss3:amd64 (2:3.109-1) ... Setting up dbus-daemon (1.16.2-2) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libthai0:amd64 (0.1.29-2+b1) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.5-1) ... Setting up libglib2.0-0t64:amd64 (2.84.0-2) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libxfixes3:amd64 (1:6.0.0-2+b4) ... Setting up dbus (1.16.2-2) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up shared-mime-info (2.4-5+b2) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libxinerama1:amd64 (2:1.1.4-3+b3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libxrandr2:amd64 (2:1.5.4-1+b3) ... Setting up libcommons-lang3-java (3.17.0-1) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up libdrm2:amd64 (2.4.124-1) ... Setting up groff-base (1.23.0-7) ... Setting up libwayland-cursor0:amd64 (1.23.1-3) ... Setting up libpam-systemd:amd64 (257.4-3) ... Setting up libcommons-beanutils-java (1.9.4-2) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libharfbuzz0b:amd64 (10.2.0-1+b1) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-2) ... Setting up libsnappy-java (1.1.10.7-1) ... Setting up libfontconfig1:amd64 (2.15.0-2.1) ... 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+really2.9.14-0.3+b1) ... Setting up libcommons-codec-java (1.18.0-1) ... Setting up libavahi-client3:amd64 (0.8-16) ... Setting up libdrm-amdgpu1:amd64 (2.4.124-1) ... Setting up libgnutls30t64:amd64 (3.8.9-2) ... Setting up gtk-update-icon-cache (4.17.5+ds-3) ... Setting up velocity (1.7-7) ... Setting up fontconfig (2.15.0-2.1) ... Regenerating fonts cache... done. Setting up libatk1.0-0t64:amd64 (2.55.2-1) ... Setting up openjdk-21-jre-headless:amd64 (21.0.6+7-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libxi6:amd64 (2:1.8.2-1) ... Setting up libcommons-io-java (2.18.0-1) ... Setting up libcommons-digester-java (1.8.1-7) ... Setting up libxtst6:amd64 (2:1.2.5-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxcursor1:amd64 (1:1.2.3-1) ... Setting up libpango-1.0-0:amd64 (1.56.2-1) ... Setting up libdrm-intel1:amd64 (2.4.124-1) ... Setting up libcloudproviders0:amd64 (0.3.6-1+b1) ... 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:amd64 (1.18.4-1) ... Setting up libcolord2:amd64 (1.4.7-3) ... Setting up libdconf1:amd64 (0.40.0-5) ... Setting up libmaven-filtering-java (3.4.0-1) ... Setting up dbus-user-session (1.16.2-2) ... Setting up libmaven-resolver-java (1.9.22-1) ... Setting up adwaita-icon-theme (48.0-1) ... 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:amd64 (2.55.2-1) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up libmaven-common-artifact-filters-java (3.4.0-1) ... Setting up libwagon-http-java (3.5.3-1) ... Setting up libcairo-gobject2:amd64 (1.18.4-1) ... Setting up libmaven-shared-utils-java (3.4.2-1) ... Setting up libpangoft2-1.0-0:amd64 (1.56.2-1) ... Setting up libmaven-resources-plugin-java (3.3.1-1) ... Setting up libcups2t64:amd64 (2.4.10-2+b1) ... Setting up libpangocairo-1.0-0:amd64 (1.56.2-1) ... Setting up libatk-bridge2.0-0t64:amd64 (2.55.2-1) ... Setting up mesa-libgallium:amd64 (25.0.1-2) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up libcommons-compress-java (1.27.1-2) ... Setting up libcommons-validator-java (1:1.9.0-1) ... Setting up libgbm1:amd64 (25.0.1-2) ... Setting up libgl1-mesa-dri:amd64 (25.0.1-2) ... Setting up debhelper (13.24.1) ... Setting up dconf-service (0.40.0-5) ... Setting up libmaven-clean-plugin-java (3.2.0-2) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libglx-mesa0:amd64 (25.0.1-2) ... Setting up libglx0:amd64 (1.7.0-1+b2) ... Setting up dconf-gsettings-backend:amd64 (0.40.0-5) ... Setting up libmaven-archiver-java (3.6.2-1) ... Setting up libgl1:amd64 (1.7.0-1+b2) ... Setting up libgtk-3-common (3.24.49-1) ... Setting up libgtk-3-0t64:amd64 (3.24.49-1) ... 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 (5.1.0-1) ... 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 (3.9.9-1) ... 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 (3.0.0-2) ... Setting up libmaven-jar-plugin-java (3.3.0-2) ... Setting up libcommons-text-java (1.13.0-1) ... 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 (2.41-4) ... 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:FIRMAPROFESIONAL_CA_ROOT-A_WEB.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:SecureSign_Root_CA12.pem Adding debian:SecureSign_Root_CA14.pem Adding debian:SecureSign_Root_CA15.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: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_CYBER_Root_CA.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem Adding debian:Telekom_Security_TLS_RSA_Root_2023.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 (3.9.9-1) ... update-alternatives: using /usr/share/maven/bin/mvn to provide /usr/bin/mvn (mvn) in auto mode Setting up openjdk-21-jre:amd64 (21.0.6+7-1) ... Setting up ant (1.10.15-1) ... Setting up junit4 (4.13.2-5) ... Setting up openjdk-21-jdk-headless:amd64 (21.0.6+7-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jwebserver to provide /usr/bin/jwebserver (jwebserver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/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~alpha2.1-5) ... Setting up openjdk-21-jdk:amd64 (21.0.6+7-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/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 (2.6.7) ... Processing triggers for ca-certificates (20241223) ... 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 amd64 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] --- resources: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] --- compiler: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] --- resources: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] --- compiler:3.13.0:testCompile (default-testCompile) @ bytecode --- [INFO] No sources to compile [INFO] [INFO] --- surefire:2.22.3:test (default-test) @ bytecode --- [INFO] Tests are skipped. [INFO] [INFO] --- jar: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] --- resources:3.3.1:resources (default-resources) @ core --- [INFO] Copying 29 resources from src/main/resources to target/classes [INFO] [INFO] --- compiler: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] --- resources:3.3.1:testResources (default-testResources) @ core --- [INFO] Copying 53 resources from src/test/resources to target/test-classes [INFO] [INFO] --- compiler: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] --- surefire:2.22.3:test (default-test) @ core --- [INFO] Tests are skipped. [INFO] [INFO] --- jar: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] --- resources:3.3.1:resources (default-resources) @ alignment --- [INFO] Copying 89 resources from src/main/resources to target/classes [INFO] [INFO] --- compiler: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] --- resources:3.3.1:testResources (default-testResources) @ alignment --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler: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] --- surefire:2.22.3:test (default-test) @ alignment --- [INFO] Tests are skipped. [INFO] [INFO] --- jar: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] --- resources: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] --- compiler: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/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/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/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] --- resources: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] --- compiler: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] --- surefire:2.22.3:test (default-test) @ biosql --- [INFO] Tests are skipped. [INFO] [INFO] --- jar: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] --- resources:3.3.1:resources (default-resources) @ blast --- [INFO] Copying 3 resources from src/main/resources to target/classes [INFO] [INFO] --- compiler: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] --- resources:3.3.1:testResources (default-testResources) @ blast --- [INFO] Copying 22 resources from src/test/resources to target/test-classes [INFO] [INFO] --- compiler: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] --- surefire:2.22.3:test (default-test) @ blast --- [INFO] Tests are skipped. [INFO] [INFO] --- jar: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] --- resources: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] --- compiler: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] --- resources:3.3.1:testResources (default-testResources) @ sequencing --- [INFO] Copying 77 resources from src/test/resources to target/test-classes [INFO] [INFO] --- compiler: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] --- surefire:2.22.3:test (default-test) @ sequencing --- [INFO] Tests are skipped. [INFO] [INFO] --- jar: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] --- resources: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] --- compiler: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/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/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/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] --- resources: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] --- compiler:3.13.0:testCompile (default-testCompile) @ gui --- [INFO] No sources to compile [INFO] [INFO] --- surefire:2.22.3:test (default-test) @ gui --- [INFO] Tests are skipped. [INFO] [INFO] --- jar: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] --- resources: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] --- compiler: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] --- resources:3.3.1:testResources (default-testResources) @ phylo --- [INFO] Copying 3 resources from src/test/resources to target/test-classes [INFO] [INFO] --- compiler: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] --- surefire:2.22.3:test (default-test) @ phylo --- [INFO] Tests are skipped. [INFO] [INFO] --- jar: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 [ 0.014 s] [INFO] bytecode ........................................... SUCCESS [ 7.481 s] [INFO] core ............................................... SUCCESS [ 23.577 s] [INFO] alignment .......................................... SUCCESS [ 1.409 s] [INFO] biosql ............................................. SUCCESS [ 0.956 s] [INFO] blast .............................................. SUCCESS [ 0.981 s] [INFO] sequencing ......................................... SUCCESS [ 1.282 s] [INFO] gui ................................................ SUCCESS [ 1.095 s] [INFO] phylo .............................................. SUCCESS [ 3.193 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 40.445 s [INFO] Finished at: 2026-04-17T10:12:17Z [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] --- resources: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] --- compiler:3.13.0:compile (default-compile) @ bytecode --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- resources: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] --- compiler:3.13.0:testCompile (default-testCompile) @ bytecode --- [INFO] No sources to compile [INFO] [INFO] --- surefire: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] --- resources:3.3.1:resources (default-resources) @ core --- [INFO] Copying 29 resources from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.13.0:compile (default-compile) @ core --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ core --- [INFO] Copying 53 resources from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ core --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- surefire:2.22.3:test (default-test) @ core --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.utils.SmallMapTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 s - in org.biojava.utils.SmallMapTest [INFO] Running org.biojava.utils.process.ExternalProcessTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.utils.process.ExternalProcessTest [INFO] Running org.biojava.utils.process.AllTests [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.process.AllTests [INFO] Running org.biojava.utils.lsid.LifeScienceIdentifierTest [INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.utils.lsid.LifeScienceIdentifierTest [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.walker.WalkerFactoryTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 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: 0.018 s - in org.biojava.utils.walker.WalkerTest [INFO] Running org.biojava.utils.RepeatedCharSequenceTest JAM [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.utils.RepeatedCharSequenceTest [INFO] Running org.biojava.utils.automata.NfaTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.253 s - in org.biojava.utils.automata.NfaTest [INFO] Running org.biojava.utils.regex.RegexTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 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: 0.002 s - in org.biojava.utils.regex.PatternCheckerTest [INFO] Running org.biojava.directory.RegistryConfigurationTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.directory.RegistryConfigurationTest [INFO] Running org.biojava.directory.SystemRegistryTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 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] Running org.biojava.bio.proteomics.MassCalcTest [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.proteomics.MassCalcTest [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$1.protect(TestResult.java:122) at junit.framework.TestResult.runProtected(TestResult.java:142) at junit.framework.TestResult.run(TestResult.java:125) at junit.framework.TestCase.run(TestCase.java:130) at junit.framework.TestSuite.runTest(TestSuite.java:241) at junit.framework.TestSuite.run(TestSuite.java:236) at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90) at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365) at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273) at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238) at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159) at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384) at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345) at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126) at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418) [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest [INFO] Running org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 s - in org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest [INFO] Running org.biojava.bio.proteomics.aaindex.AAindexTest org.biojava.bio.symbol.IllegalSymbolException: Symbol adenine not found in alphabet PROTEIN at org.biojava.bio.symbol.AbstractAlphabet.validate(AbstractAlphabet.java:327) at org.biojava.bio.symbol.AlphabetManager$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: 0.01 s - in org.biojava.bio.proteomics.aaindex.AAindexTest [INFO] Running org.biojava.bio.proteomics.IsoelectricPointCalcTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.proteomics.IsoelectricPointCalcTest [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.dist.DistributionTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 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 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: 0.071 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 s - in org.biojava.bio.dist.DistributionToolsTest [INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest [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.SimpleSeqSimilaritySearchSubHitTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest [INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest [INFO] Running org.biojava.bio.search.MaxMismatchPatternTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.search.MaxMismatchPatternTest [INFO] Running org.biojava.bio.seq.FilterUtilsTest [INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.FilterUtilsTest [INFO] Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.bio.seq.project.ProjectedFeatureHolderTest [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.MergeFeatureHolderTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.MergeFeatureHolderTest [INFO] Running org.biojava.bio.seq.NewSimpleAssemblyTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.NewSimpleAssemblyTest [INFO] Running org.biojava.bio.seq.SimpleAssemblyTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.SimpleAssemblyTest [INFO] Running org.biojava.bio.seq.SeqSerializationTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.SeqSerializationTest [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.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: 0.001 s - in org.biojava.bio.seq.impl.ViewSequenceTest [INFO] Running org.biojava.bio.seq.impl.GappedSequenceTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 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 s - in org.biojava.bio.seq.impl.SubSequenceTest [INFO] Running org.biojava.bio.seq.impl.ViewSeqSerializationTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.impl.ViewSeqSerializationTest [INFO] Running org.biojava.bio.seq.DNAToolsTest [INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.DNAToolsTest [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.emblcd.EntryNamIdxReaderTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 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.bio.seq.db.emblcd.DivisionLkpReaderTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest [INFO] Running org.biojava.bio.seq.db.TestHashSequenceDB [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 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 s - in org.biojava.bio.seq.db.EmblCDROMIndexStoreTest [INFO] Running org.biojava.bio.seq.io.MSFAlignmentFormatTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.io.MSFAlignmentFormatTest [INFO] Running org.biojava.bio.seq.io.filterxml.FilterXMLTest [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.io.filterxml.FilterXMLTest [INFO] Running org.biojava.bio.seq.io.SmartSequenceBuilderTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.337 s - in org.biojava.bio.seq.io.SmartSequenceBuilderTest [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: 0.355 s - in org.biojava.bio.seq.io.SeqIOToolsTest [INFO] Running org.biojava.bio.seq.io.LocationFormatterTest [INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.io.LocationFormatterTest [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.homol.SimpleSimilarityPairFeatureTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest [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.RNAToolsTest [INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.RNAToolsTest [INFO] Running org.biojava.bio.seq.FeatureHolderUtilsTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.FeatureHolderUtilsTest [INFO] Running org.biojava.bio.MergeAnnotationTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.MergeAnnotationTest [INFO] Running org.biojava.bio.program.indexdb.IndexToolsTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.biojava.bio.program.indexdb.IndexToolsTest [INFO] Running org.biojava.bio.program.phred.PhredToolsTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.program.phred.PhredToolsTest [INFO] Running org.biojava.bio.molbio.RestrictionEnzymeTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.bio.molbio.RestrictionEnzymeTest [INFO] Running org.biojava.bio.molbio.RestrictionEnzymeManagerTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.bio.molbio.RestrictionEnzymeManagerTest [INFO] Running org.biojava.bio.symbol.CodonPrefToolsTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.CodonPrefToolsTest [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.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.SimpleSymbolListTest [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.SimpleSymbolListTest [INFO] Running org.biojava.bio.symbol.MotifToolsTest [INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.MotifToolsTest [INFO] Running org.biojava.bio.symbol.TranslationTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.TranslationTest [INFO] Running org.biojava.bio.symbol.AlphabetSerializationTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.AlphabetSerializationTest [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.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.symbol.PointLocationTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.PointLocationTest [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.CrossProductAlphabetIndexTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.991 s - in org.biojava.bio.symbol.CrossProductAlphabetIndexTest [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: 0.007 s - in org.biojava.bio.symbol.UkkonenSuffixTreeTest [INFO] Running org.biojava.bio.symbol.CompoundLocationTest [INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojava.bio.symbol.CompoundLocationTest [INFO] Running org.biojava.bio.symbol.IntegerAlphabetTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.IntegerAlphabetTest [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.SymbolListTest [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.625 s - in org.biojava.bio.symbol.SymbolListTest [INFO] Running org.biojava.bio.symbol.SymbolSerializationTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.symbol.SymbolSerializationTest [INFO] Running org.biojava.bio.symbol.BetweenLocationTest [INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 s - in org.biojava.bio.symbol.BetweenLocationTest [INFO] Running org.biojava.bio.symbol.CircularLocationTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.CircularLocationTest [INFO] Running org.biojava.bio.symbol.CrossProductTokenizationTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.CrossProductTokenizationTest [INFO] Running org.biojava.bio.symbol.MergeLocationTest [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.MergeLocationTest [INFO] Running org.biojava.bio.symbol.RangeLocationTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.RangeLocationTest [INFO] Running org.biojava.bio.symbol.IndexedNoAmbPackTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.IndexedNoAmbPackTest [INFO] Running org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest [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.GappedSymbolListTest [INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.GappedSymbolListTest [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.NameTokenizationTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.NameTokenizationTest [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.dp.MarkovModelEventTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 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 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 s - in org.biojava.bio.dp.EmissionStateEventTest [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: 0.001 s - in org.biojava.naming.ObdaUriParserTest [INFO] Running org.biojava.naming.ObdaInitialContextFactoryTest Reached Attributes: No attributes Binding: urn -> org.biojava.naming.ObdaContext@6206b4a7 Reached urn Attributes: No attributes Binding: open-bio.org -> org.biojava.naming.ObdaContext@77896335 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@5c1b89ac 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@40a1b6d4 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@175581eb 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@2b79c8ff 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@2baf72d5 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@66756662 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@5d14e99e 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@38cfecf3 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@682618e5 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@25ad25f5 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@5f0f70c7 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@1860a7a1 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@40d96578 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@50122012} My component is urn:open-bio.org:format:embl lookup: 'open-bio.org:format:embl' for {open-bio.org=org.biojava.naming.ObdaContext@7db5b890} My component is open-bio.org:format:embl lookup: 'format:embl' for {type=org.biojava.naming.ObdaContext@407b8435, format=org.biojava.naming.ObdaContext@1282e98, alphabet=org.biojava.naming.ObdaContext@4db0ba1c} My component is format:embl lookup: 'embl' for {enzyme=org.biojava.naming.ObdaContext@1d91fa02, genbank=org.biojava.naming.ObdaContext@1578fa9, swissprot=org.biojava.naming.ObdaContext@414b2df5, embl=org.biojava.naming.ObdaContext@9e30f9a} My component is embl [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.naming.ObdaInitialContextFactoryTest [INFO] Running org.biojava.ontology.TripleImplTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.ontology.TripleImplTest [INFO] Running org.biojava.ontology.OntologyTest [INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.ontology.OntologyTest [INFO] Running org.biojava.ontology.ParseOBOFileTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 s - in org.biojava.ontology.ParseOBOFileTest [INFO] Running org.biojava.ontology.TermImplTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.ontology.TermImplTest [INFO] Running org.biojavax.ga.util.WeightedSetTest [INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.ga.util.WeightedSetTest [INFO] Running org.biojavax.ga.util.GAToolsTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.ga.util.GAToolsTest [INFO] Running org.biojavax.ga.functions.ProportionalSelectionTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 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.functions.SimpleCrossOverFunctionTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 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 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.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.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.SimpleDocRefAuthorTest testIsConsortium testToString testCompareTo testGetName testHashCode testEquals testGetExtendedName [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.SimpleDocRefAuthorTest [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: 0.001 s - in org.biojavax.SimpleDocRefTest [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: 0.007 s - in org.biojavax.SimpleNoteTest [INFO] Running org.biojavax.CrossReferenceResolutionExceptionTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.CrossReferenceResolutionExceptionTest [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: 0.003 s - in org.biojavax.SimpleRankedDocRefTest [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: 0.001 s - in org.biojavax.SimpleCommentTest [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: 0.003 s - in org.biojavax.SimpleNamespaceTest [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.bio.taxa.SimpleNCBITaxonNameTest testGetNameClass testToString testCompareTo testSetNameClass testGetName testHashCode testEquals testSetName [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.taxa.SimpleNCBITaxonNameTest [INFO] Running org.biojavax.bio.seq.RichLocationToolsTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.bio.seq.RichLocationToolsTest [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.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.seq.MultiSourceCompoundRichLocationTest testEquals [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest [INFO] Running org.biojavax.bio.seq.io.Bug2255Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojavax.bio.seq.io.Bug2255Test [INFO] Running org.biojavax.bio.seq.io.Bug2249_2248Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojavax.bio.seq.io.Bug2249_2248Test [INFO] Running org.biojavax.bio.seq.io.GenbankFormatTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 s - in org.biojavax.bio.seq.io.GenbankFormatTest [INFO] Running org.biojavax.bio.seq.io.INSDseqFormatTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojavax.bio.seq.io.INSDseqFormatTest [INFO] Running org.biojavax.bio.seq.io.EMBLFormatTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.bio.seq.io.EMBLFormatTest [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.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.Bug2250_2256Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.033 s - in org.biojavax.bio.seq.io.Bug2250_2256Test [INFO] Running org.biojavax.bio.seq.SimpleRichFeatureTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.seq.SimpleRichFeatureTest [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: 0.004 s - in org.biojavax.bio.SimpleBioEntryTest [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: 0.005 s - in org.biojavax.ontology.SimpleComparableTripleTest [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: 0.001 s - in org.biojavax.ontology.SimpleComparableOntologyTest [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 s - in org.biojavax.ontology.SimpleComparableTermTest [INFO] Running org.biojavax.DummyCrossReferenceResolverTest testGetRemoteBioEntry testGetRemoteSymbolList [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.DummyCrossReferenceResolverTest [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: 0.001 s - in org.biojavax.EmptyRichAnnotationTest [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 s - in org.biojavax.SimpleRankedCrossRefTest [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: 0.001 s - in org.biojavax.SimpleRichAnnotationTest [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] --- resources:3.3.1:resources (default-resources) @ alignment --- [INFO] Copying 89 resources from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.13.0:compile (default-compile) @ alignment --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ alignment --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ alignment --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- surefire: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: 0.323 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: 0.015 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: 0.008 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] --- resources: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] --- compiler:3.13.0:compile (default-compile) @ biosql --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- resources: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] --- compiler:3.13.0:testCompile (default-testCompile) @ biosql --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- surefire: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: 0.021 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] --- resources:3.3.1:resources (default-resources) @ blast --- [INFO] Copying 3 resources from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.13.0:compile (default-compile) @ blast --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ blast --- [INFO] Copying 22 resources from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ blast --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- surefire:2.22.3:test (default-test) @ blast --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.bio.program.sax.blastxml.BlastXMLTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.506 s - in org.biojava.bio.program.sax.blastxml.BlastXMLTest [INFO] Running org.biojava.bio.program.sax.BlastTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.724 s - in org.biojava.bio.program.sax.BlastTest [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.409 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.082 s - in org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.647 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.54 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 s - in org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.491 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.305 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.07 s - in org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.064 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: 0.509 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.339 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 s - in org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.359 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.35 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 s - in org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.315 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test [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] --- resources: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] --- compiler:3.13.0:compile (default-compile) @ sequencing --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ sequencing --- [INFO] Copying 77 resources from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ sequencing --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- surefire:2.22.3:test (default-test) @ sequencing --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.bio.program.fastq.FastqTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.093 s - in org.biojava.bio.program.fastq.FastqTest [INFO] Running org.biojava.bio.program.fastq.SolexaFastqWriterTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 s - in org.biojava.bio.program.fastq.SolexaFastqWriterTest [INFO] Running org.biojava.bio.program.fastq.ConvertTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.112 s - in org.biojava.bio.program.fastq.ConvertTest [INFO] Running org.biojava.bio.program.fastq.IlluminaFastqWriterTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojava.bio.program.fastq.IlluminaFastqWriterTest [INFO] Running org.biojava.bio.program.fastq.FastqToolsTest [INFO] Tests run: 38, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.357 s - in org.biojava.bio.program.fastq.FastqToolsTest [INFO] Running org.biojava.bio.program.fastq.SangerFastqWriterTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.program.fastq.SangerFastqWriterTest [INFO] Running org.biojava.bio.program.fastq.FastqVariantTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.program.fastq.FastqVariantTest [INFO] Running org.biojava.bio.program.fastq.SangerFastqReaderTest [INFO] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 s - in org.biojava.bio.program.fastq.SangerFastqReaderTest [INFO] Running org.biojava.bio.program.fastq.FastqBuilderTest [INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.program.fastq.FastqBuilderTest [INFO] Running org.biojava.bio.program.fastq.SolexaFastqReaderTest [INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.bio.program.fastq.SolexaFastqReaderTest [INFO] Running org.biojava.bio.program.fastq.StreamingFastqParserTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.program.fastq.StreamingFastqParserTest [INFO] Running org.biojava.bio.program.fastq.IlluminaFastqReaderTest [INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.biojava.bio.program.fastq.IlluminaFastqReaderTest [INFO] Running org.biojava.bio.program.scf.SCFTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.1 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] --- resources: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] --- compiler:3.13.0:compile (default-compile) @ gui --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- resources: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] --- compiler:3.13.0:testCompile (default-testCompile) @ gui --- [INFO] No sources to compile [INFO] [INFO] --- surefire: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] --- resources: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] --- compiler:3.13.0:compile (default-compile) @ phylo --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ phylo --- [INFO] Copying 3 resources from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ phylo --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- surefire: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: 0.372 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 [ 0.005 s] [INFO] bytecode ........................................... SUCCESS [ 0.996 s] [INFO] core ............................................... SUCCESS [ 37.071 s] [INFO] alignment .......................................... SUCCESS [ 30.991 s] [INFO] biosql ............................................. SUCCESS [ 31.010 s] [INFO] blast .............................................. SUCCESS [ 44.992 s] [INFO] sequencing ......................................... SUCCESS [ 32.932 s] [INFO] gui ................................................ SUCCESS [ 0.112 s] [INFO] phylo .............................................. SUCCESS [ 31.325 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 03:29 min [INFO] Finished at: 2026-04-17T10:15:49Z [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: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: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: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: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: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: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: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: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: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 [ 0.314 s] [INFO] bytecode ........................................... SUCCESS [ 0.034 s] [INFO] core ............................................... SUCCESS [ 0.023 s] [INFO] alignment .......................................... SUCCESS [ 0.020 s] [INFO] biosql ............................................. SUCCESS [ 0.020 s] [INFO] blast .............................................. SUCCESS [ 0.019 s] [INFO] sequencing ......................................... SUCCESS [ 0.021 s] [INFO] gui ................................................ SUCCESS [ 0.020 s] [INFO] phylo .............................................. SUCCESS [ 0.021 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.653 s [INFO] Finished at: 2026-04-17T10:15:51Z [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 'libbiojava-java' in '../libbiojava-java_1.9.7+dfsg-2_all.deb'. dpkg-deb: building package 'libbiojava1.9-java' in '../libbiojava1.9-java_1.9.7+dfsg-2_all.deb'. dpkg-genbuildinfo --build=binary -O../biojava-live_1.9.7+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../biojava-live_1.9.7+dfsg-2_amd64.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/3247929 and its subdirectories I: Current time: Thu Apr 16 22:15:59 -12 2026 I: pbuilder-time-stamp: 1776420959