I: pbuilder: network access will be disabled during build I: Current time: Wed Dec 24 08:10:10 +14 2025 I: pbuilder-time-stamp: 1766513410 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: using eatmydata during job I: Copying source file I: copying [biojava-live_1.9.7+dfsg-2.dsc] I: copying [./biojava-live_1.9.7+dfsg.orig.tar.xz] I: copying [./biojava-live_1.9.7+dfsg-2.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Oct 7 07:59:36 2024 gpgv: using RSA key B8CE4DE21080DCF903E16C40F513C419E4B9D0AC gpgv: issuer "ebourg@apache.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./biojava-live_1.9.7+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting biojava-live in biojava-live-1.9.7+dfsg dpkg-source: info: unpacking biojava-live_1.9.7+dfsg.orig.tar.xz dpkg-source: info: unpacking biojava-live_1.9.7+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying omit_tests_with_problematic_data.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/26036/tmp/hooks/D01_modify_environment starting debug: Running on infom08-i386. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Dec 23 18:10 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/26036/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/26036/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=5 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=0ba399d1a88741bca4c0e24129b717b0 LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=26036 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.agcYKqKA/pbuilderrc_UiWy --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.agcYKqKA/b2 --logfile b2/build.log biojava-live_1.9.7+dfsg-2.dsc' SUDO_GID=111 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' I: uname -a Linux i-capture-the-hostname 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/26036/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: i386 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 ... 19952 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} libdrm-radeon1{a} libdrm2{a} libedit2{a} libel-api-java{a} libelf1t64{a} libepoxy0{a} liberror-prone-java{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgbm1{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libgif7{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0t64{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgtk-3-0t64{a} libgtk-3-common{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{a} libhttpclient-java{a} libhttpcore-java{a} libicu72{a} libjansi-java{a} libjaxb-api-java{a} libjaxen-java{a} libjbig0{a} libjetty9-java{a} libjgraph-java{a} libjgrapht0.8-java{a} libjpeg62-turbo{a} libjsoup-java{a} libjsp-api-java{a} libjsr305-java{a} libjtidy-java{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} liblerc4{a} libllvm19{a} libmagic-mgc{a} libmagic1t64{a} libmaven-archiver-java{a} libmaven-clean-plugin-java{a} libmaven-common-artifact-filters-java{a} libmaven-compiler-plugin-java{a} libmaven-file-management-java{a} libmaven-filtering-java{a} libmaven-jar-plugin-java{a} libmaven-parent-java{a} libmaven-plugin-tools-java{a} libmaven-reporting-api-java{a} libmaven-reporting-exec-java{a} libmaven-resolver-1.6-java{a} libmaven-resolver-java{a} libmaven-resources-plugin-java{a} libmaven-shared-incremental-java{a} libmaven-shared-io-java{a} libmaven-shared-utils-java{a} libmaven-site-plugin-java{a} libmaven3-core-java{a} libnspr4{a} libnss3{a} libopentest4j-java{a} libopentest4j-reporting-java{a} liboro-java{a} libpam-systemd{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} 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} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libunivocity-parsers-java{a} libvelocity-tools-java{a} libvulkan1{a} libwagon-file-java{a} libwagon-http-shaded-java{a} libwagon-provider-api-java{a} libwayland-client0{a} libwayland-cursor0{a} libwayland-egl1{a} libwayland-server0{a} libwebp7{a} libwebsocket-api-java{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxbean-reflect-java{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxerces2-java{a} libxext6{a} libxfixes3{a} libxi6{a} libxinerama1{a} libxkbcommon0{a} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxml2-utils{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxtst6{a} libxxf86vm1{a} libxz-java{a} libz3-4{a} m4{a} man-db{a} maven{a} maven-debian-helper{a} maven-repo-helper{a} mesa-libgallium{a} openjdk-21-jdk{a} openjdk-21-jdk-headless{a} openjdk-21-jre{a} openjdk-21-jre-headless{a} openssl{a} po-debconf{a} procps{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} systemd{a} systemd-sysv{a} unzip{a} velocity{a} x11-common{a} xkb-data{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf ant-optional at-spi2-core chrony curl fonts-dejavu-extra krb5-locales libarchive-cpio-perl libatk-wrapper-java-jni libgdk-pixbuf2.0-bin libglib2.0-data libgtk-3-bin libkmod2 libltdl-dev libmail-sendmail-perl libnss-systemd librsvg2-common libxt-dev linux-sysctl-defaults lynx mesa-vulkan-drivers ntpsec openntpd psmisc systemd-cryptsetup systemd-timesyncd wget xdg-user-dirs 0 packages upgraded, 290 newly installed, 0 to remove and 0 not upgraded. Need to get 274 MB of archives. After unpacking 792 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 libapparmor1 i386 3.1.7-1+b3 [43.3 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 libsystemd-shared i386 257~rc2-3 [2200 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 systemd i386 257~rc2-3 [3608 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 systemd-sysv i386 257~rc2-3 [59.3 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 libdbus-1-3 i386 1.14.10-6 [217 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 dbus-bin i386 1.14.10-6 [107 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 dbus-session-bus-common all 1.14.10-6 [79.2 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.4-1 [107 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 dbus-daemon i386 1.14.10-6 [195 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 dbus-system-bus-common all 1.14.10-6 [80.2 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 dbus i386 1.14.10-6 [101 kB] Get: 12 http://deb.debian.org/debian unstable/main i386 sgml-base all 1.31 [15.4 kB] Get: 13 http://deb.debian.org/debian unstable/main i386 libproc2-0 i386 2:4.0.4-6 [65.7 kB] Get: 14 http://deb.debian.org/debian unstable/main i386 procps i386 2:4.0.4-6 [876 kB] Get: 15 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 16 http://deb.debian.org/debian unstable/main i386 openssl i386 3.3.2-2 [1387 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 ca-certificates all 20240203 [158 kB] Get: 18 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 19 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 21 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 22 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 23 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-5 [1196 kB] Get: 24 http://deb.debian.org/debian unstable/main i386 libpam-systemd i386 257~rc2-3 [305 kB] Get: 25 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.2-11 [95.6 kB] Get: 26 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 27 http://deb.debian.org/debian unstable/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 28 http://deb.debian.org/debian unstable/main i386 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [311 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 libglib2.0-0t64 i386 2.82.2-3 [1571 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-5+b1 [9583 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB] Get: 32 http://deb.debian.org/debian unstable/main i386 shared-mime-info i386 2.4-5+b1 [761 kB] Get: 33 http://deb.debian.org/debian unstable/main i386 libjpeg62-turbo i386 1:2.1.5-3+b1 [171 kB] Get: 34 http://deb.debian.org/debian unstable/main i386 libpng16-16t64 i386 1.6.44-2 [288 kB] Get: 35 http://deb.debian.org/debian unstable/main i386 libdeflate0 i386 1.22-1 [48.1 kB] Get: 36 http://deb.debian.org/debian unstable/main i386 libjbig0 i386 2.1-6.1+b2 [32.2 kB] Get: 37 http://deb.debian.org/debian unstable/main i386 liblerc4 i386 4.0.0+ds-5 [191 kB] Get: 38 http://deb.debian.org/debian unstable/main i386 libsharpyuv0 i386 1.4.0-0.1+b1 [113 kB] Get: 39 http://deb.debian.org/debian unstable/main i386 libwebp7 i386 1.4.0-0.1+b1 [322 kB] Get: 40 http://deb.debian.org/debian unstable/main i386 libtiff6 i386 4.5.1+git230720-5 [339 kB] Get: 41 http://deb.debian.org/debian unstable/main i386 libgdk-pixbuf-2.0-0 i386 2.42.12+dfsg-1+b1 [149 kB] Get: 42 http://deb.debian.org/debian unstable/main i386 gtk-update-icon-cache i386 4.16.5+ds-2 [50.6 kB] Get: 43 http://deb.debian.org/debian unstable/main i386 hicolor-icon-theme all 0.18-1 [12.0 kB] Get: 44 http://deb.debian.org/debian unstable/main i386 adwaita-icon-theme all 47.0-2 [463 kB] Get: 45 http://deb.debian.org/debian unstable/main i386 ca-certificates-java all 20240118 [11.6 kB] Get: 46 http://deb.debian.org/debian unstable/main i386 java-common all 0.76 [6776 B] Get: 47 http://deb.debian.org/debian unstable/main i386 liblcms2-2 i386 2.16-2 [171 kB] Get: 48 http://deb.debian.org/debian unstable/main i386 libnspr4 i386 2:4.36-1 [119 kB] Get: 49 http://deb.debian.org/debian unstable/main i386 libnss3 i386 2:3.106-1 [1504 kB] Get: 50 http://deb.debian.org/debian unstable/main i386 libpcsclite1 i386 2.3.0-3 [57.1 kB] Get: 51 http://deb.debian.org/debian unstable/main i386 openjdk-21-jre-headless i386 21.0.5+11-1 [43.2 MB] Get: 52 http://deb.debian.org/debian unstable/main i386 default-jre-headless i386 2:1.21-76 [3192 B] Get: 53 http://deb.debian.org/debian unstable/main i386 ant all 1.10.15-1 [2163 kB] Get: 54 http://deb.debian.org/debian unstable/main i386 at-spi2-common all 2.54.0-1 [170 kB] Get: 55 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB] Get: 56 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3 [493 kB] Get: 57 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 58 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 59 http://deb.debian.org/debian unstable/main i386 autopoint all 0.22.5-2 [723 kB] Get: 60 http://deb.debian.org/debian unstable/main i386 dbus-user-session i386 1.14.10-6 [79.0 kB] Get: 61 http://deb.debian.org/debian unstable/main i386 libdconf1 i386 0.40.0-4+b3 [43.8 kB] Get: 62 http://deb.debian.org/debian unstable/main i386 dconf-service i386 0.40.0-4+b3 [35.0 kB] Get: 63 http://deb.debian.org/debian unstable/main i386 dconf-gsettings-backend i386 0.40.0-4+b3 [30.6 kB] Get: 64 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 65 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-8 [517 kB] Get: 66 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 67 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 68 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 69 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 70 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 71 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 72 http://deb.debian.org/debian unstable/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 73 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 74 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 75 http://deb.debian.org/debian unstable/main i386 debhelper all 13.20 [915 kB] Get: 76 http://deb.debian.org/debian unstable/main i386 libatk1.0-0t64 i386 2.54.0-1 [51.0 kB] Get: 77 http://deb.debian.org/debian unstable/main i386 libxau6 i386 1:1.0.11-1 [20.7 kB] Get: 78 http://deb.debian.org/debian unstable/main i386 libxdmcp6 i386 1:1.1.5-1 [28.2 kB] Get: 79 http://deb.debian.org/debian unstable/main i386 libxcb1 i386 1.17.0-2+b1 [148 kB] Get: 80 http://deb.debian.org/debian unstable/main i386 libx11-data all 2:1.8.10-2 [337 kB] Get: 81 http://deb.debian.org/debian unstable/main i386 libx11-6 i386 2:1.8.10-2 [834 kB] Get: 82 http://deb.debian.org/debian unstable/main i386 libxext6 i386 2:1.3.4-1+b2 [52.6 kB] Get: 83 http://deb.debian.org/debian unstable/main i386 libxi6 i386 2:1.8.2-1 [81.2 kB] Get: 84 http://deb.debian.org/debian unstable/main i386 libatspi2.0-0t64 i386 2.54.0-1 [79.8 kB] Get: 85 http://deb.debian.org/debian unstable/main i386 libatk-bridge2.0-0t64 i386 2.54.0-1 [72.5 kB] Get: 86 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB] Get: 87 http://deb.debian.org/debian unstable/main i386 libfreetype6 i386 2.13.3+dfsg-1 [464 kB] Get: 88 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 89 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-core all 2.37-8 [840 kB] Get: 90 http://deb.debian.org/debian unstable/main i386 fontconfig-config i386 2.15.0-1.1+b1 [318 kB] Get: 91 http://deb.debian.org/debian unstable/main i386 libfontconfig1 i386 2.15.0-1.1+b1 [402 kB] Get: 92 http://deb.debian.org/debian unstable/main i386 libpixman-1-0 i386 0.44.0-3 [246 kB] Get: 93 http://deb.debian.org/debian unstable/main i386 libxcb-render0 i386 1.17.0-2+b1 [116 kB] Get: 94 http://deb.debian.org/debian unstable/main i386 libxcb-shm0 i386 1.17.0-2+b1 [105 kB] Get: 95 http://deb.debian.org/debian unstable/main i386 libxrender1 i386 1:0.9.10-1.1+b2 [28.9 kB] Get: 96 http://deb.debian.org/debian unstable/main i386 libcairo2 i386 1.18.2-2 [591 kB] Get: 97 http://deb.debian.org/debian unstable/main i386 libcairo-gobject2 i386 1.18.2-2 [129 kB] Get: 98 http://deb.debian.org/debian unstable/main i386 libcloudproviders0 i386 0.3.6-1+b1 [30.7 kB] Get: 99 http://deb.debian.org/debian unstable/main i386 libcolord2 i386 1.4.7-1+b2 [146 kB] Get: 100 http://deb.debian.org/debian unstable/main i386 libavahi-common-data i386 0.8-13+b3 [112 kB] Get: 101 http://deb.debian.org/debian unstable/main i386 libavahi-common3 i386 0.8-13+b3 [45.2 kB] Get: 102 http://deb.debian.org/debian unstable/main i386 libavahi-client3 i386 0.8-13+b3 [49.6 kB] Get: 103 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB] Get: 104 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.1-1+b1 [23.4 kB] Get: 105 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB] Get: 106 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-4 [9600 B] Get: 107 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.21.3-3 [350 kB] Get: 108 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB] Get: 109 http://deb.debian.org/debian unstable/main i386 libcups2t64 i386 2.4.10-2 [267 kB] Get: 110 http://deb.debian.org/debian unstable/main i386 libepoxy0 i386 1.5.10-2 [196 kB] Get: 111 http://deb.debian.org/debian unstable/main i386 libfribidi0 i386 1.0.15-1 [72.4 kB] Get: 112 http://deb.debian.org/debian unstable/main i386 libgraphite2-3 i386 1.3.14-2+b1 [77.8 kB] Get: 113 http://deb.debian.org/debian unstable/main i386 libharfbuzz0b i386 10.0.1-1 [503 kB] Get: 114 http://deb.debian.org/debian unstable/main i386 fontconfig i386 2.15.0-1.1+b1 [463 kB] Get: 115 http://deb.debian.org/debian unstable/main i386 libthai-data all 0.1.29-2 [168 kB] Get: 116 http://deb.debian.org/debian unstable/main i386 libdatrie1 i386 0.2.13-3+b1 [39.9 kB] Get: 117 http://deb.debian.org/debian unstable/main i386 libthai0 i386 0.1.29-2+b1 [50.3 kB] Get: 118 http://deb.debian.org/debian unstable/main i386 libpango-1.0-0 i386 1.54.0+ds-3 [230 kB] Get: 119 http://deb.debian.org/debian unstable/main i386 libpangoft2-1.0-0 i386 1.54.0+ds-3 [58.1 kB] Get: 120 http://deb.debian.org/debian unstable/main i386 libpangocairo-1.0-0 i386 1.54.0+ds-3 [36.1 kB] Get: 121 http://deb.debian.org/debian unstable/main i386 libwayland-client0 i386 1.23.0-1+b1 [27.2 kB] Get: 122 http://deb.debian.org/debian unstable/main i386 libwayland-cursor0 i386 1.23.0-1+b1 [12.4 kB] Get: 123 http://deb.debian.org/debian unstable/main i386 libwayland-egl1 i386 1.23.0-1+b1 [5752 B] Get: 124 http://deb.debian.org/debian unstable/main i386 libxcomposite1 i386 1:0.4.6-1 [16.6 kB] Get: 125 http://deb.debian.org/debian unstable/main i386 libxfixes3 i386 1:6.0.0-2+b2 [20.7 kB] Get: 126 http://deb.debian.org/debian unstable/main i386 libxcursor1 i386 1:1.2.2-1+b1 [38.9 kB] Get: 127 http://deb.debian.org/debian unstable/main i386 libxdamage1 i386 1:1.1.6-1+b2 [15.6 kB] Get: 128 http://deb.debian.org/debian unstable/main i386 libxinerama1 i386 2:1.1.4-3+b2 [16.3 kB] Get: 129 http://deb.debian.org/debian unstable/main i386 xkb-data all 2.42-1 [790 kB] Get: 130 http://deb.debian.org/debian unstable/main i386 libxkbcommon0 i386 1.7.0-1 [118 kB] Get: 131 http://deb.debian.org/debian unstable/main i386 libxrandr2 i386 2:1.5.4-1+b1 [37.9 kB] Get: 132 http://deb.debian.org/debian unstable/main i386 libgtk-3-common all 3.24.43-4 [4657 kB] Get: 133 http://deb.debian.org/debian unstable/main i386 libgtk-3-0t64 i386 3.24.43-4 [2920 kB] Get: 134 http://deb.debian.org/debian unstable/main i386 libglvnd0 i386 1.7.0-1+b2 [44.1 kB] Get: 135 http://deb.debian.org/debian unstable/main i386 libdrm-common all 2.4.123-1 [8084 B] Get: 136 http://deb.debian.org/debian unstable/main i386 libdrm2 i386 2.4.123-1 [41.8 kB] Get: 137 http://deb.debian.org/debian unstable/main i386 libglapi-mesa i386 24.2.7-1 [38.6 kB] Get: 138 http://deb.debian.org/debian unstable/main i386 libx11-xcb1 i386 2:1.8.10-2 [241 kB] Get: 139 http://deb.debian.org/debian unstable/main i386 libxcb-dri2-0 i386 1.17.0-2+b1 [107 kB] Get: 140 http://deb.debian.org/debian unstable/main i386 libxcb-dri3-0 i386 1.17.0-2+b1 [107 kB] Get: 141 http://deb.debian.org/debian unstable/main i386 libxcb-glx0 i386 1.17.0-2+b1 [124 kB] Get: 142 http://deb.debian.org/debian unstable/main i386 libxcb-present0 i386 1.17.0-2+b1 [106 kB] Get: 143 http://deb.debian.org/debian unstable/main i386 libxcb-randr0 i386 1.17.0-2+b1 [118 kB] Get: 144 http://deb.debian.org/debian unstable/main i386 libxcb-sync1 i386 1.17.0-2+b1 [109 kB] Get: 145 http://deb.debian.org/debian unstable/main i386 libxcb-xfixes0 i386 1.17.0-2+b1 [110 kB] Get: 146 http://deb.debian.org/debian unstable/main i386 libxshmfence1 i386 1.3-1+b2 [8992 B] Get: 147 http://deb.debian.org/debian unstable/main i386 libxxf86vm1 i386 1:1.1.4-1+b3 [20.1 kB] Get: 148 http://deb.debian.org/debian unstable/main i386 libdrm-amdgpu1 i386 2.4.123-1 [25.0 kB] Get: 149 http://deb.debian.org/debian unstable/main i386 libpciaccess0 i386 0.17-3+b2 [53.8 kB] Get: 150 http://deb.debian.org/debian unstable/main i386 libdrm-intel1 i386 2.4.123-1 [66.8 kB] Get: 151 http://deb.debian.org/debian unstable/main i386 libdrm-radeon1 i386 2.4.123-1 [23.0 kB] Get: 152 http://deb.debian.org/debian unstable/main i386 libedit2 i386 3.1-20240808-1 [98.0 kB] Get: 153 http://deb.debian.org/debian unstable/main i386 libz3-4 i386 4.13.3-1 [9211 kB] Get: 154 http://deb.debian.org/debian unstable/main i386 libllvm19 i386 1:19.1.3-2 [30.4 MB] Get: 155 http://deb.debian.org/debian unstable/main i386 libsensors-config all 1:3.6.0-10 [14.6 kB] Get: 156 http://deb.debian.org/debian unstable/main i386 libsensors5 i386 1:3.6.0-10+b1 [35.8 kB] Get: 157 http://deb.debian.org/debian unstable/main i386 mesa-libgallium i386 24.2.7-1 [9409 kB] Get: 158 http://deb.debian.org/debian unstable/main i386 libvulkan1 i386 1.3.296.0-1 [136 kB] Get: 159 http://deb.debian.org/debian unstable/main i386 libwayland-server0 i386 1.23.0-1+b1 [35.9 kB] Get: 160 http://deb.debian.org/debian unstable/main i386 libgbm1 i386 24.2.7-1 [43.9 kB] Get: 161 http://deb.debian.org/debian unstable/main i386 libgl1-mesa-dri i386 24.2.7-1 [42.5 kB] Get: 162 http://deb.debian.org/debian unstable/main i386 libglx-mesa0 i386 24.2.7-1 [160 kB] Get: 163 http://deb.debian.org/debian unstable/main i386 libglx0 i386 1.7.0-1+b2 [36.8 kB] Get: 164 http://deb.debian.org/debian unstable/main i386 libgl1 i386 1.7.0-1+b2 [82.7 kB] Get: 165 http://deb.debian.org/debian unstable/main i386 libasound2-data all 1.2.12-1 [21.0 kB] Get: 166 http://deb.debian.org/debian unstable/main i386 libasound2t64 i386 1.2.12-1+b1 [397 kB] Get: 167 http://deb.debian.org/debian unstable/main i386 libgif7 i386 5.2.2-1+b1 [45.6 kB] Get: 168 http://deb.debian.org/debian unstable/main i386 x11-common all 1:7.7+23.1 [216 kB] Get: 169 http://deb.debian.org/debian unstable/main i386 libxtst6 i386 2:1.2.3-1.1+b2 [26.5 kB] Get: 170 http://deb.debian.org/debian unstable/main i386 openjdk-21-jre i386 21.0.5+11-1 [203 kB] Get: 171 http://deb.debian.org/debian unstable/main i386 default-jre i386 2:1.21-76 [1068 B] Get: 172 http://deb.debian.org/debian unstable/main i386 openjdk-21-jdk-headless i386 21.0.5+11-1 [85.4 MB] Get: 173 http://deb.debian.org/debian unstable/main i386 default-jdk-headless i386 2:1.21-76 [1124 B] Get: 174 http://deb.debian.org/debian unstable/main i386 openjdk-21-jdk i386 21.0.5+11-1 [4309 kB] Get: 175 http://deb.debian.org/debian unstable/main i386 default-jdk i386 2:1.21-76 [1076 B] Get: 176 http://deb.debian.org/debian unstable/main i386 libhamcrest-java all 2.2-2 [121 kB] Get: 177 http://deb.debian.org/debian unstable/main i386 junit4 all 4.13.2-5 [350 kB] Get: 178 http://deb.debian.org/debian unstable/main i386 libapiguardian-java all 1.1.2-1 [4656 B] Get: 179 http://deb.debian.org/debian unstable/main i386 libopentest4j-java all 1.2.0-4 [9516 B] Get: 180 http://deb.debian.org/debian unstable/main i386 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 181 http://deb.debian.org/debian unstable/main i386 libpicocli-java all 4.6.2-2 [390 kB] Get: 182 http://deb.debian.org/debian unstable/main i386 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 183 http://deb.debian.org/debian unstable/main i386 junit5 all 5.10.3-1 [2459 kB] Get: 184 http://deb.debian.org/debian unstable/main i386 libactivation-java all 1.2.0-2 [84.7 kB] Get: 185 http://deb.debian.org/debian unstable/main i386 libaopalliance-java all 20070526-7 [8572 B] Get: 186 http://deb.debian.org/debian unstable/main i386 libapache-pom-java all 33-2 [5852 B] Get: 187 http://deb.debian.org/debian unstable/main i386 libasm-java all 9.7.1-1 [391 kB] Get: 188 http://deb.debian.org/debian unstable/main i386 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 189 http://deb.debian.org/debian unstable/main i386 libbsh-java all 2.0b4-20 [291 kB] Get: 190 http://deb.debian.org/debian unstable/main i386 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 191 http://deb.debian.org/debian unstable/main i386 libcdi-api-java all 1.2-4 [55.3 kB] Get: 192 http://deb.debian.org/debian unstable/main i386 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 193 http://deb.debian.org/debian unstable/main i386 libcommons-parent-java all 56-1 [10.8 kB] Get: 194 http://deb.debian.org/debian unstable/main i386 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 195 http://deb.debian.org/debian unstable/main i386 libcommons-beanutils-java all 1.9.4-2 [233 kB] Get: 196 http://deb.debian.org/debian unstable/main i386 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 197 http://deb.debian.org/debian unstable/main i386 libcommons-codec-java all 1.17.1-1 [303 kB] Get: 198 http://deb.debian.org/debian unstable/main i386 libcommons-io-java all 2.17.0-1 [488 kB] Get: 199 http://deb.debian.org/debian unstable/main i386 libcommons-compress-java all 1.27.1-2 [641 kB] Get: 200 http://deb.debian.org/debian unstable/main i386 libcommons-pool-java all 1.6-5 [109 kB] Get: 201 http://deb.debian.org/debian unstable/main i386 libcommons-dbcp-java all 1.4-8 [157 kB] Get: 202 http://deb.debian.org/debian unstable/main i386 libcommons-digester-java all 1.8.1-7 [138 kB] Get: 203 http://deb.debian.org/debian unstable/main i386 libcommons-lang-java all 2.6-10 [273 kB] Get: 204 http://deb.debian.org/debian unstable/main i386 libcommons-lang3-java all 3.17.0-1 [641 kB] Get: 205 http://deb.debian.org/debian unstable/main i386 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 206 http://deb.debian.org/debian unstable/main i386 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 207 http://deb.debian.org/debian unstable/main i386 libslf4j-java all 1.7.32-1 [144 kB] Get: 208 http://deb.debian.org/debian unstable/main i386 libsnappy1v5 i386 1.2.1-1+b1 [31.3 kB] Get: 209 http://deb.debian.org/debian unstable/main i386 libsnappy-jni i386 1.1.10.7-1 [6792 B] Get: 210 http://deb.debian.org/debian unstable/main i386 libsnappy-java all 1.1.10.7-1 [87.6 kB] Get: 211 http://deb.debian.org/debian unstable/main i386 libxz-java all 1.9-1 [143 kB] Get: 212 http://deb.debian.org/debian unstable/main i386 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 213 http://deb.debian.org/debian unstable/main i386 libplexus-interpolation-java all 1.27-1 [76.8 kB] Get: 214 http://deb.debian.org/debian unstable/main i386 libmaven-archiver-java all 3.6.2-1 [26.1 kB] Get: 215 http://deb.debian.org/debian unstable/main i386 libmaven-shared-utils-java all 3.4.2-1 [137 kB] Get: 216 http://deb.debian.org/debian unstable/main i386 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 217 http://deb.debian.org/debian unstable/main i386 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 218 http://deb.debian.org/debian unstable/main i386 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 219 http://deb.debian.org/debian unstable/main i386 libguava-java all 32.0.1-1 [2708 kB] Get: 220 http://deb.debian.org/debian unstable/main i386 libguice-java all 4.2.3-2 [1435 kB] Get: 221 http://deb.debian.org/debian unstable/main i386 libmaven-parent-java all 43-2 [6252 B] Get: 222 http://deb.debian.org/debian unstable/main i386 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 223 http://deb.debian.org/debian unstable/main i386 libmaven-resolver-1.6-java all 1.6.3-2 [558 kB] Get: 224 http://deb.debian.org/debian unstable/main i386 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 225 http://deb.debian.org/debian unstable/main i386 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 226 http://deb.debian.org/debian unstable/main i386 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 227 http://deb.debian.org/debian unstable/main i386 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 228 http://deb.debian.org/debian unstable/main i386 libsisu-inject-java all 0.3.4-2 [347 kB] Get: 229 http://deb.debian.org/debian unstable/main i386 libsisu-plexus-java all 0.3.4-3 [181 kB] Get: 230 http://deb.debian.org/debian unstable/main i386 libmaven3-core-java all 3.8.8-2 [1579 kB] Get: 231 http://deb.debian.org/debian unstable/main i386 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 232 http://deb.debian.org/debian unstable/main i386 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 233 http://deb.debian.org/debian unstable/main i386 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 234 http://deb.debian.org/debian unstable/main i386 libcommons-text-java all 1.12.0-1 [222 kB] Get: 235 http://deb.debian.org/debian unstable/main i386 libcommons-validator-java all 1:1.9.0-1 [191 kB] Get: 236 http://deb.debian.org/debian unstable/main i386 libjaxen-java all 1.1.6-5 [214 kB] Get: 237 http://deb.debian.org/debian unstable/main i386 libdom4j-java all 2.1.4-1 [312 kB] Get: 238 http://deb.debian.org/debian unstable/main i386 libdoxia-core-java all 2.0.0-1 [149 kB] Get: 239 http://deb.debian.org/debian unstable/main i386 libplexus-xml-java all 3.0.1-2 [93.7 kB] Get: 240 http://deb.debian.org/debian unstable/main i386 libdoxia-java all 2.0.0-1 [113 kB] Get: 241 http://deb.debian.org/debian unstable/main i386 libmaven-reporting-api-java all 4.0.0-1 [6724 B] Get: 242 http://deb.debian.org/debian unstable/main i386 libxbean-reflect-java all 4.5-9 [132 kB] Get: 243 http://deb.debian.org/debian unstable/main i386 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 244 http://deb.debian.org/debian unstable/main i386 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB] Get: 245 http://deb.debian.org/debian unstable/main i386 velocity all 1.7-7 [431 kB] Get: 246 http://deb.debian.org/debian unstable/main i386 libplexus-velocity-java all 1.2-4 [9676 B] Get: 247 http://deb.debian.org/debian unstable/main i386 liboro-java all 2.0.8a-14 [70.5 kB] Get: 248 http://deb.debian.org/debian unstable/main i386 libvelocity-tools-java all 2.0-9 [311 kB] Get: 249 http://deb.debian.org/debian unstable/main i386 libdoxia-sitetools-java all 2.0.0-1 [176 kB] Get: 250 http://deb.debian.org/debian unstable/main i386 libel-api-java all 3.0.0-3 [64.9 kB] Get: 251 http://deb.debian.org/debian unstable/main i386 libhttpcore-java all 4.4.16-1 [636 kB] Get: 252 http://deb.debian.org/debian unstable/main i386 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 253 http://deb.debian.org/debian unstable/main i386 libjansi-java all 2.4.1-2 [100 kB] Get: 254 http://deb.debian.org/debian unstable/main i386 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 255 http://deb.debian.org/debian unstable/main i386 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 256 http://deb.debian.org/debian unstable/main i386 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 257 http://deb.debian.org/debian unstable/main i386 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 258 http://deb.debian.org/debian unstable/main i386 libjetty9-java all 9.4.56-1 [2964 kB] Get: 259 http://deb.debian.org/debian unstable/main i386 libjgraph-java all 5.12.4.2+dfsg-7 [207 kB] Get: 260 http://deb.debian.org/debian unstable/main i386 libjgrapht0.8-java all 0.8.3-7 [216 kB] Get: 261 http://deb.debian.org/debian unstable/main i386 libjsoup-java all 1.15.3-1 [431 kB] Get: 262 http://deb.debian.org/debian unstable/main i386 libjtidy-java all 7+svn20110807-5 [250 kB] Get: 263 http://deb.debian.org/debian unstable/main i386 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB] Get: 264 http://deb.debian.org/debian unstable/main i386 libmaven-resolver-java all 1.6.3-1 [548 kB] Get: 265 http://deb.debian.org/debian unstable/main i386 libmaven-common-artifact-filters-java all 3.4.0-1 [47.7 kB] Get: 266 http://deb.debian.org/debian unstable/main i386 libmaven-shared-incremental-java all 1.1-6 [9916 B] Get: 267 http://deb.debian.org/debian unstable/main i386 libplexus-compiler-java all 2.13.0-1 [99.5 kB] Get: 268 http://deb.debian.org/debian unstable/main i386 libqdox2-java all 2.0.3-1 [296 kB] Get: 269 http://deb.debian.org/debian unstable/main i386 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 270 http://deb.debian.org/debian unstable/main i386 libmaven-compiler-plugin-java all 3.13.0-1 [78.8 kB] Get: 271 http://deb.debian.org/debian unstable/main i386 libplexus-build-api-java all 0.0.7-4 [10.3 kB] Get: 272 http://deb.debian.org/debian unstable/main i386 libmaven-filtering-java all 3.4.0-1 [51.4 kB] Get: 273 http://deb.debian.org/debian unstable/main i386 libplexus-container-default1.5-java all 2.1.1-1 [4476 B] Get: 274 http://deb.debian.org/debian unstable/main i386 libplexus-ant-factory-java all 1.0~alpha2.1-4 [11.4 kB] Get: 275 http://deb.debian.org/debian unstable/main i386 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B] Get: 276 http://deb.debian.org/debian unstable/main i386 libmaven-plugin-tools-java all 3.10.2-1 [245 kB] Get: 277 http://deb.debian.org/debian unstable/main i386 libmaven-reporting-exec-java all 2.0.0-1 [23.9 kB] Get: 278 http://deb.debian.org/debian unstable/main i386 libmaven-resources-plugin-java all 3.3.1-1 [27.5 kB] Get: 279 http://deb.debian.org/debian unstable/main i386 libmaven-site-plugin-java all 3.21.0-1 [106 kB] Get: 280 http://deb.debian.org/debian unstable/main i386 libsurefire-java all 2.22.3-3 [1284 kB] Get: 281 http://deb.debian.org/debian unstable/main i386 libwagon-file-java all 3.5.3-1 [8388 B] Get: 282 http://deb.debian.org/debian unstable/main i386 libwagon-http-shaded-java all 3.5.3-1 [1341 kB] Get: 283 http://deb.debian.org/debian unstable/main i386 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 284 http://deb.debian.org/debian unstable/main i386 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 285 http://deb.debian.org/debian unstable/main i386 libxerces2-java all 2.12.2-1 [1440 kB] Get: 286 http://deb.debian.org/debian unstable/main i386 libxml2-utils i386 2.12.7+dfsg+really2.9.14-0.2+b1 [99.6 kB] Get: 287 http://deb.debian.org/debian unstable/main i386 maven all 3.8.8-2 [19.5 kB] Get: 288 http://deb.debian.org/debian unstable/main i386 maven-repo-helper all 1.11 [142 kB] Get: 289 http://deb.debian.org/debian unstable/main i386 unzip i386 6.0-28 [166 kB] Get: 290 http://deb.debian.org/debian unstable/main i386 maven-debian-helper all 2.6.5 [108 kB] Fetched 274 MB in 4s (61.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libapparmor1:i386. (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 ... 19952 files and directories currently installed.) Preparing to unpack .../libapparmor1_3.1.7-1+b3_i386.deb ... Unpacking libapparmor1:i386 (3.1.7-1+b3) ... Selecting previously unselected package libsystemd-shared:i386. Preparing to unpack .../libsystemd-shared_257~rc2-3_i386.deb ... Unpacking libsystemd-shared:i386 (257~rc2-3) ... Selecting previously unselected package systemd. Preparing to unpack .../systemd_257~rc2-3_i386.deb ... Unpacking systemd (257~rc2-3) ... Setting up libapparmor1:i386 (3.1.7-1+b3) ... Setting up libsystemd-shared:i386 (257~rc2-3) ... Setting up systemd (257~rc2-3) ... Created symlink '/etc/systemd/system/getty.target.wants/getty@tty1.service' -> '/usr/lib/systemd/system/getty@.service'. Created symlink '/etc/systemd/system/multi-user.target.wants/remote-fs.target' -> '/usr/lib/systemd/system/remote-fs.target'. Created symlink '/etc/systemd/system/sysinit.target.wants/systemd-pstore.service' -> '/usr/lib/systemd/system/systemd-pstore.service'. Initializing machine ID from random generator. Creating group 'systemd-journal' with GID 999. Creating group 'systemd-network' with GID 998. Creating user 'systemd-network' (systemd Network Management) with UID 998 and GID 998. /usr/lib/tmpfiles.d/legacy.conf:13: Duplicate line for path "/run/lock", ignoring. Selecting previously unselected package systemd-sysv. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20907 files and directories currently installed.) Preparing to unpack .../000-systemd-sysv_257~rc2-3_i386.deb ... Unpacking systemd-sysv (257~rc2-3) ... Selecting previously unselected package libdbus-1-3:i386. Preparing to unpack .../001-libdbus-1-3_1.14.10-6_i386.deb ... Unpacking libdbus-1-3:i386 (1.14.10-6) ... Selecting previously unselected package dbus-bin. Preparing to unpack .../002-dbus-bin_1.14.10-6_i386.deb ... Unpacking dbus-bin (1.14.10-6) ... Selecting previously unselected package dbus-session-bus-common. Preparing to unpack .../003-dbus-session-bus-common_1.14.10-6_all.deb ... Unpacking dbus-session-bus-common (1.14.10-6) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../004-libexpat1_2.6.4-1_i386.deb ... Unpacking libexpat1:i386 (2.6.4-1) ... Selecting previously unselected package dbus-daemon. Preparing to unpack .../005-dbus-daemon_1.14.10-6_i386.deb ... Unpacking dbus-daemon (1.14.10-6) ... Selecting previously unselected package dbus-system-bus-common. Preparing to unpack .../006-dbus-system-bus-common_1.14.10-6_all.deb ... Unpacking dbus-system-bus-common (1.14.10-6) ... Selecting previously unselected package dbus. Preparing to unpack .../007-dbus_1.14.10-6_i386.deb ... Unpacking dbus (1.14.10-6) ... Selecting previously unselected package sgml-base. Preparing to unpack .../008-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:i386. Preparing to unpack .../009-libproc2-0_2%3a4.0.4-6_i386.deb ... Unpacking libproc2-0:i386 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../010-procps_2%3a4.0.4-6_i386.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../011-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../012-openssl_3.3.2-2_i386.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../013-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../014-libmagic-mgc_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:i386. 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Preparing to unpack .../038-gtk-update-icon-cache_4.16.5+ds-2_i386.deb ... No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. No diversion 'diversion of /usr/share/man/man8/update-icon-caches.8.gz to /usr/share/man/man8/update-icon-caches.gtk2.8.gz by libgtk-3-bin', none removed. Unpacking gtk-update-icon-cache (4.16.5+ds-2) ... Selecting previously unselected package hicolor-icon-theme. Preparing to unpack .../039-hicolor-icon-theme_0.18-1_all.deb ... Unpacking hicolor-icon-theme (0.18-1) ... Selecting previously unselected package adwaita-icon-theme. Preparing to unpack .../040-adwaita-icon-theme_47.0-2_all.deb ... Unpacking adwaita-icon-theme (47.0-2) ... Selecting previously unselected package ca-certificates-java. Preparing to unpack .../041-ca-certificates-java_20240118_all.deb ... Unpacking ca-certificates-java (20240118) ... Selecting previously unselected package java-common. 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Preparing to unpack .../048-default-jre-headless_2%3a1.21-76_i386.deb ... Unpacking default-jre-headless (2:1.21-76) ... Selecting previously unselected package ant. Preparing to unpack .../049-ant_1.10.15-1_all.deb ... Unpacking ant (1.10.15-1) ... Selecting previously unselected package at-spi2-common. Preparing to unpack .../050-at-spi2-common_2.54.0-1_all.deb ... Unpacking at-spi2-common (2.54.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../051-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../052-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../053-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../054-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... 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Setting up libedit2:i386 (3.1-20240808-1) ... Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ... Setting up libmagic1t64:i386 (1:5.45-3+b1) ... Setting up libpicocli-java (4.6.2-2) ... Setting up libasm-java (9.7.1-1) ... Setting up x11-common (1:7.7+23.1) ... Running in chroot, ignoring request. Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libsensors-config (1:3.6.0-10) ... Setting up libdeflate0:i386 (1.22-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libel-api-java (3.0.0-3) ... Setting up xkb-data (2.42-1) ... Setting up libplexus-component-annotations-java (2.1.1-1) ... Setting up libxcb-shm0:i386 (1.17.0-2+b1) ... Setting up libcom-err2:i386 (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libunivocity-parsers-java (2.9.1-1) ... Setting up libjbig0:i386 (2.1-6.1+b2) ... Setting up libelf1t64:i386 (0.192-4) ... Setting up liboro-java (2.0.8a-14) ... Setting up libsnappy1v5:i386 (1.2.1-1+b1) ... Setting up libkrb5support0:i386 (1.21.3-3) ... Setting up libxcb-present0:i386 (1.17.0-2+b1) ... Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... Setting up libgeronimo-interceptor-3.0-spec-java (1.0.1-4) ... Setting up libcommons-collections3-java (3.2.2-3) ... Setting up libasound2-data (1.2.12-1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:i386 (4.13.3-1) ... Setting up libglib2.0-0t64:i386 (2.82.2-3) ... Setting up libasound2t64:i386 (1.2.12-1+b1) ... Setting up libjpeg62-turbo:i386 (1:2.1.5-3+b1) ... Setting up libjaxen-java (1.1.6-5) ... Setting up libapiguardian-java (1.1.2-1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libepoxy0:i386 (1.5.10-2) ... Setting up libnspr4:i386 (2:4.36-1) ... Setting up libxcb-sync1:i386 (1.17.0-2+b1) ... Setting up libjtidy-java (7+svn20110807-5) ... Setting up libjansi-java (2.4.1-2) ... Setting up libapache-pom-java (33-2) ... Setting up libavahi-common-data:i386 (0.8-13+b3) ... Setting up libatinject-jsr330-api-java (1.0+ds1-5) ... Setting up libdbus-1-3:i386 (1.14.10-6) ... Setting up libwebsocket-api-java (1.1-2) ... Setting up libfribidi0:i386 (1.0.15-1) ... Setting up libproc2-0:i386 (2:4.0.4-6) ... Setting up libplexus-interpolation-java (1.27-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:i386 (1.6.44-2) ... Setting up libxml-commons-resolver1.1-java (1.2-11) ... Setting up libxz-java (1.9-1) ... Setting up libcommons-pool-java (1.6-5) ... Setting up autopoint (0.22.5-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libpcsclite1:i386 (2.3.0-3) ... Setting up libsensors5:i386 (1:3.6.0-10+b1) ... Setting up libk5crypto3:i386 (1.21.3-3) ... Setting up libjgraph-java (5.12.4.2+dfsg-7) ... Setting up libactivation-java (1.2.0-2) ... Setting up libhamcrest-java (2.2-2) ... Setting up libglapi-mesa:i386 (24.2.7-1) ... Setting up libbsh-java (2.0b4-20) ... Setting up libjsp-api-java (2.3.4-3) ... Setting up libvulkan1:i386 (1.3.296.0-1) ... Setting up autoconf (2.72-3) ... Setting up libwebp7:i386 (1.4.0-0.1+b1) ... Setting up libxcb-dri2-0:i386 (1.17.0-2+b1) ... Setting up libgif7:i386 (5.2.2-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libxshmfence1:i386 (1.3-1+b2) ... Setting up libjsoup-java (1.15.3-1) ... Setting up at-spi2-common (2.54.0-1) ... Setting up libtiff6:i386 (4.5.1+git230720-5) ... Setting up libxcb-randr0:i386 (1.17.0-2+b1) ... Setting up dbus-session-bus-common (1.14.10-6) ... Setting up libuchardet0:i386 (0.0.8-1+b2) ... Setting up libxml-commons-external-java (1.4.01-6) ... Setting up procps (2:4.0.4-6) ... Setting up libxbean-reflect-java (4.5-9) ... Setting up libservlet-api-java (4.0.1-2) ... Setting up libplexus-xml-java (3.0.1-2) ... Setting up libopentest4j-java (1.2.0-4) ... Setting up libx11-6:i386 (2:1.8.10-2) ... Setting up libthai-data (0.1.29-2) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:i386 (1.21.3-3) ... Setting up libwagon-http-shaded-java (3.5.3-1) ... Setting up libwayland-egl1:i386 (1.23.0-1+b1) ... Setting up libhttpcore-java (4.4.16-1) ... Setting up libxerces2-java (2.12.2-1) ... Setting up dbus-system-bus-common (1.14.10-6) ... useradd: Warning: missing or non-executable shell '/usr/sbin/nologin' Setting up openssl (3.3.2-2) ... Setting up libdrm-common (2.4.123-1) ... Setting up libcdi-api-java (1.2-4) ... Setting up libsnappy-jni (1.1.10.7-1) ... Setting up libxcomposite1:i386 (1:0.4.6-1) ... Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up dbus-bin (1.14.10-6) ... Setting up libxkbcommon0:i386 (1.7.0-1) ... Setting up libwayland-client0:i386 (1.23.0-1+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libdom4j-java (2.1.4-1) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libxcb-dri3-0:i386 (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:i386 (1:19.1.3-2) ... Setting up libx11-xcb1:i386 (2:1.8.10-2) ... Setting up gettext (0.22.5-2) ... Setting up libjetty9-java (9.4.56-1) ... Setting up libxdamage1:i386 (1:1.1.6-1+b2) ... Setting up libatk1.0-0t64:i386 (2.54.0-1) ... Setting up libplexus-languages-java (1.1.1-2) ... Setting up libjgrapht0.8-java (0.8.3-7) ... Setting up libxrender1:i386 (1:0.9.10-1.1+b2) ... Setting up libtool (2.4.7-8) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libmaven-parent-java (43-2) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:i386 (0.8-13+b3) ... Setting up libcloudproviders0:i386 (0.3.6-1+b1) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxext6:i386 (2:1.3.4-1+b2) ... Setting up libsisu-inject-java (0.3.4-2) ... Setting up libnss3:i386 (2:3.106-1) ... Setting up dbus-daemon (1.14.10-6) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libcolord2:i386 (1.4.7-1+b2) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up libxxf86vm1:i386 (1:1.1.4-1+b3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libdconf1:i386 (0.40.0-4+b3) ... Setting up dh-autoreconf (20) ... Setting up libthai0:i386 (0.1.29-2+b1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.4-3) ... Setting up libfreetype6:i386 (2.13.3+dfsg-1) ... Setting up libxfixes3:i386 (1:6.0.0-2+b2) ... Setting up dbus (1.14.10-6) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up shared-mime-info (2.4-5+b1) ... Setting up libxinerama1:i386 (2:1.1.4-3+b2) ... Setting up libgssapi-krb5-2:i386 (1.21.3-3) ... Setting up libxrandr2:i386 (2:1.5.4-1+b1) ... Setting up libcommons-lang3-java (3.17.0-1) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libdrm2:i386 (2.4.123-1) ... Setting up groff-base (1.23.0-5) ... Setting up libwayland-cursor0:i386 (1.23.0-1+b1) ... Setting up libpam-systemd:i386 (257~rc2-3) ... Setting up libcommons-beanutils-java (1.9.4-2) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libharfbuzz0b:i386 (10.0.1-1) ... Setting up libgdk-pixbuf-2.0-0:i386 (2.42.12+dfsg-1+b1) ... Setting up libsnappy-java (1.1.10.7-1) ... Setting up libfontconfig1:i386 (2.15.0-1.1+b1) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libwagon-file-java (3.5.3-1) ... Setting up libxml2-utils (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libcommons-codec-java (1.17.1-1) ... Setting up libavahi-client3:i386 (0.8-13+b3) ... Setting up libdrm-amdgpu1:i386 (2.4.123-1) ... Setting up gtk-update-icon-cache (4.16.5+ds-2) ... Setting up velocity (1.7-7) ... Setting up fontconfig (2.15.0-1.1+b1) ... Regenerating fonts cache... done. Setting up openjdk-21-jre-headless:i386 (21.0.5+11-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libxi6:i386 (2:1.8.2-1) ... Setting up libcommons-io-java (2.17.0-1) ... Setting up libdrm-radeon1:i386 (2.4.123-1) ... Setting up libcommons-digester-java (1.8.1-7) ... Setting up libxtst6:i386 (2:1.2.3-1.1+b2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxcursor1:i386 (1:1.2.2-1+b1) ... Setting up libpango-1.0-0:i386 (1.54.0+ds-3) ... Setting up libdrm-intel1:i386 (2.4.123-1) ... 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:i386 (1.18.2-2) ... Setting up libmaven-resolver-1.6-java (1.6.3-2) ... Setting up libmaven-filtering-java (3.4.0-1) ... Setting up dbus-user-session (1.14.10-6) ... Setting up libmaven-resolver-java (1.6.3-1) ... Setting up adwaita-icon-theme (47.0-2) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up libatspi2.0-0t64:i386 (2.54.0-1) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up libmaven-common-artifact-filters-java (3.4.0-1) ... Setting up libcairo-gobject2:i386 (1.18.2-2) ... Setting up libmaven-shared-utils-java (3.4.2-1) ... Setting up libpangoft2-1.0-0:i386 (1.54.0+ds-3) ... Setting up libmaven-resources-plugin-java (3.3.1-1) ... Setting up libcups2t64:i386 (2.4.10-2) ... Setting up libpangocairo-1.0-0:i386 (1.54.0+ds-3) ... Setting up libatk-bridge2.0-0t64:i386 (2.54.0-1) ... Setting up mesa-libgallium:i386 (24.2.7-1) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up libcommons-compress-java (1.27.1-2) ... Setting up libcommons-validator-java (1:1.9.0-1) ... Setting up libgbm1:i386 (24.2.7-1) ... Setting up libgl1-mesa-dri:i386 (24.2.7-1) ... Setting up debhelper (13.20) ... Setting up dconf-service (0.40.0-4+b3) ... Setting up libmaven-clean-plugin-java (3.2.0-2) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libglx-mesa0:i386 (24.2.7-1) ... Setting up libglx0:i386 (1.7.0-1+b2) ... Setting up dconf-gsettings-backend:i386 (0.40.0-4+b3) ... Setting up libmaven-archiver-java (3.6.2-1) ... Setting up libgl1:i386 (1.7.0-1+b2) ... Setting up libgtk-3-common (3.24.43-4) ... Setting up libgtk-3-0t64:i386 (3.24.43-4) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libguava-java (32.0.1-1) ... Setting up libplexus-container-default-java (2.1.1-1) ... Setting up libguice-java (4.2.3-2) ... Setting up libplexus-i18n-java (1.0-beta-10-6) ... Setting up libplexus-container-default1.5-java (2.1.1-1) ... Setting up libplexus-velocity-java (1.2-4) ... Setting up libmaven3-core-java (3.8.8-2) ... Setting up libmaven-shared-incremental-java (1.1-6) ... Setting up libmaven-shared-io-java (3.0.0-4) ... Setting up libplexus-bsh-factory-java (1.0~alpha7-5) ... Setting up libplexus-compiler-java (2.13.0-1) ... Setting up libmaven-compiler-plugin-java (3.13.0-1) ... Setting up libmaven-file-management-java (3.0.0-1) ... Setting up libmaven-jar-plugin-java (3.3.0-2) ... Setting up libcommons-text-java (1.12.0-1) ... Setting up libdoxia-core-java (2.0.0-1) ... Setting up libdoxia-java (2.0.0-1) ... Setting up libmaven-reporting-api-java (4.0.0-1) ... Setting up libmaven-reporting-exec-java (2.0.0-1) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up maven-repo-helper (1.11) ... Setting up maven (3.8.8-2) ... update-alternatives: using /usr/share/maven/bin/mvn to provide /usr/bin/mvn (mvn) in auto mode Setting up openjdk-21-jre:i386 (21.0.5+11-1) ... Setting up ant (1.10.15-1) ... Setting up junit4 (4.13.2-5) ... Setting up openjdk-21-jdk-headless:i386 (21.0.5+11-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jwebserver to provide /usr/bin/jwebserver (jwebserver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jre-headless (2:1.21-76) ... Setting up default-jre (2:1.21-76) ... Setting up libplexus-ant-factory-java (1.0~alpha2.1-4) ... Setting up openjdk-21-jdk:i386 (21.0.5+11-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up default-jdk-headless (2:1.21-76) ... Setting up junit5 (5.10.3-1) ... Setting up libmaven-plugin-tools-java (3.10.2-1) ... Setting up default-jdk (2:1.21-76) ... Setting up libsurefire-java (2.22.3-3) ... Processing triggers for sgml-base (1.31) ... Setting up libvelocity-tools-java (2.0-9) ... Setting up libdoxia-sitetools-java (2.0.0-1) ... Setting up libmaven-site-plugin-java (3.21.0-1) ... Setting up maven-debian-helper (2.6.5) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/26036/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/26036/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/biojava-live-1.9.7+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-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 i386 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 Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release. [INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] biojava-legacy [pom] [INFO] bytecode [jar] [INFO] core [jar] [INFO] alignment [jar] [INFO] biosql [jar] [INFO] blast [jar] [INFO] sequencing [jar] [INFO] gui [jar] [INFO] phylo [jar] [INFO] [INFO] ---------------------< org.biojava:biojava-legacy >--------------------- [INFO] Building biojava-legacy 1.9.7 [1/9] [INFO] from pom.xml [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] ------------------------< org.biojava:bytecode >------------------------ [INFO] Building bytecode 1.9.7 [2/9] [INFO] from bytecode/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ bytecode --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ bytecode --- [INFO] Recompiling the module because of changed source code. [INFO] Compiling 44 source files with javac [debug target 1.8] to target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/MethodRootContext.java:[104,25] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/MethodRootContext.java:[117,28] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/ChildContext.java:[83,25] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/ChildContext.java:[140,28] Integer(int) in java.lang.Integer has been deprecated and marked for removal [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/IntrospectedCodeClass.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/IntrospectedCodeClass.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ bytecode --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ bytecode --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ bytecode --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ bytecode --- [INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/target/bytecode-1.9.7.jar [INFO] [INFO] --------------------------< org.biojava:core >-------------------------- [INFO] Building core 1.9.7 [3/9] [INFO] from core/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ core --- [INFO] Copying 29 resources from src/main/resources to target/classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ core --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 1063 source files with javac [debug target 1.8] to target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/SuffixTree.java:[147,22] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/SuffixTree.java:[150,18] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dist/DistributionTools.java:[237,24] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dist/DistributionTools.java:[240,24] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dist/DistributionTools.java:[269,25] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dist/AbstractDistribution.java:[124,28] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dist/AbstractDistribution.java:[125,28] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/db/emblcd/RecordParser.java:[156,30] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/db/emblcd/RecordParser.java:[184,30] Long(long) in java.lang.Long has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/db/emblcd/RecordParser.java:[185,30] Long(long) in java.lang.Long has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/db/emblcd/RecordParser.java:[186,30] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/db/emblcd/RecordParser.java:[211,25] Long(long) in java.lang.Long has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/db/emblcd/RecordParser.java:[212,25] Long(long) in java.lang.Long has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/db/emblcd/RecordParser.java:[230,24] Long(long) in java.lang.Long has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:[949,39] Boolean(java.lang.String) in java.lang.Boolean has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/SimpleRankedDocRef.java:[92,21] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/SimpleRankedDocRef.java:[93,21] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/SimpleRankedDocRef.java:[152,22] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/SimpleRankedDocRef.java:[153,20] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dp/twohead/DPCompiler.java:[1455,19] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dist/SimpleDistributionTrainer.java:[77,16] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dist/SimpleDistributionTrainer.java:[132,23] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dist/IndexedCount.java:[85,29] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dist/IndexedCount.java:[86,29] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dist/IndexedCount.java:[107,29] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dist/IndexedCount.java:[108,29] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/SimpleSymbolPropertyTable.java:[55,30] Double(java.lang.String) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/agave/AGAVESeqLocationPropHandler.java:[61,14] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/agave/AGAVESeqLocationPropHandler.java:[62,13] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/IntegerAlphabet.java:[157,19] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/RichSequence.java:[558,80] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/RichSequence.java:[585,89] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/proteomics/MassCalc.java:[150,25] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/proteomics/MassCalc.java:[190,38] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/proteomics/MassCalc.java:[224,26] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/proteomics/MassCalc.java:[459,33] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/proteomics/MassCalc.java:[466,37] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/ChunkedSymbolList.java:[52,18] finalize() in java.lang.Object has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/ChunkedSymbolList.java:[53,10] finalize() in java.lang.Object has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/SimpleRankedCrossRef.java:[74,21] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/SimpleRankedCrossRef.java:[75,21] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dp/BaumWelchTrainer.java:[145,29] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/UkkonenSuffixTree.java:[254,54] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/UkkonenSuffixTree.java:[345,54] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/UkkonenSuffixTree.java:[483,25] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/UkkonenSuffixTree.java:[495,17] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/UkkonenSuffixTree.java:[500,17] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/ThinRichSequence.java:[127,41] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/ThinRichSequence.java:[127,64] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/SimpleRichLocation.java:[261,21] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/SimpleRichLocation.java:[262,21] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/SimpleRichLocation.java:[302,21] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/SimpleRichLocation.java:[303,21] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.java:[429,108] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/agave/AGAVEMatchRegionPropHandler.java:[72,29] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/agave/AGAVEMatchRegionPropHandler.java:[73,27] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/taxa/io/SimpleNCBITaxonomyLoader.java:[71,52] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/taxa/io/SimpleNCBITaxonomyLoader.java:[73,36] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/taxa/io/SimpleNCBITaxonomyLoader.java:[74,33] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/ga/functions/AbstractCrossOverFunction.java:[59,40] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/ga/functions/AbstractCrossOverFunction.java:[60,40] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/ByLocationMinMaxComparator.java:[50,22] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/ByLocationMinMaxComparator.java:[51,22] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/ByLocationMinMaxComparator.java:[58,14] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/ByLocationMinMaxComparator.java:[59,14] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/EmblLikeLocationParser.java:[505,32] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/EmblLikeLocationParser.java:[516,36] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/EmblLikeLocationParser.java:[558,20] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/tagvalue/ChangeTable.java:[41,14] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/io/UniProtCommentParser.java:[208,85] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/NameTokenization.java:[64,20] finalize() in java.lang.Object has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/NameTokenization.java:[65,14] finalize() in java.lang.Object has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/process/ExternalProcess.java:[604,20] finalize() in java.lang.Object has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/indexdb/BioStoreFactory.java:[214,27] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/io/INSDseqFormat.java:[892,146] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/io/INSDseqFormat.java:[936,58] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/io/INSDseqFormat.java:[946,136] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/io/INSDseqFormat.java:[996,74] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/io/INSDseqFormat.java:[996,89] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/io/INSDseqFormat.java:[1034,143] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/SimpleRichFeatureRelationship.java:[82,21] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojavax/bio/seq/SimpleRichFeatureRelationship.java:[83,21] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:[76,33] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:[76,53] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:[77,33] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:[77,53] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:[78,33] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:[78,53] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:[79,33] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:[79,53] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:[80,33] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:[80,53] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:[81,33] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:[81,53] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:[82,33] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:[82,54] Character(char) in java.lang.Character has been deprecated and marked for removal [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dist/DistributionTools.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dist/DistributionTools.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java: Some input files additionally use or override a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/regex/Search.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/regex/Search.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ core --- [INFO] Copying 53 resources from src/test/resources to target/test-classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ core --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 148 source files with javac [debug target 1.8] to target/test-classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/ontology/SimpleComparableTermTest.java:[308,28] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojava/utils/walker/WalkerTest.java:[106,34] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojava/utils/walker/WalkerTest.java:[109,36] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojava/utils/walker/WalkerTest.java:[153,14] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/SimpleCommentTest.java:[82,26] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/SimpleCommentTest.java:[84,27] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojava/bio/symbol/UkkonenSuffixTreeTest.java:[88,40] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojava/bio/symbol/UkkonenSuffixTreeTest.java:[89,40] Character(char) in java.lang.Character has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/bio/SimpleBioEntryTest.java:[625,17] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/bio/SimpleBioEntryTest.java:[625,33] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/bio/SimpleBioEntryTest.java:[663,17] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/bio/SimpleBioEntryTest.java:[663,33] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/bio/SimpleBioEntryTest.java:[794,31] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/bio/SimpleBioEntryTest.java:[835,31] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/SimpleRankedDocRefTest.java:[40,17] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/SimpleRankedDocRefTest.java:[41,15] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/SimpleRankedDocRefTest.java:[76,26] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/SimpleRankedDocRefTest.java:[78,27] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/SimpleRankedDocRefTest.java:[174,43] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/SimpleRankedDocRefTest.java:[174,60] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/SimpleRankedDocRefTest.java:[203,43] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/SimpleRankedDocRefTest.java:[203,60] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/SimpleRankedDocRefTest.java:[227,43] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/SimpleRankedDocRefTest.java:[227,60] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/SimpleRankedCrossRefTest.java:[76,26] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/SimpleRankedCrossRefTest.java:[78,27] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/ga/util/WeightedSetTest.java:[89,29] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/ga/util/WeightedSetTest.java:[135,29] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/ga/util/WeightedSetTest.java:[139,27] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/ga/util/WeightedSetTest.java:[149,29] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/ga/util/WeightedSetTest.java:[150,27] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:[163,46] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:[164,22] Double(double) in java.lang.Double has been deprecated and marked for removal [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojava/bio/seq/io/SeqIOToolsTest.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojava/bio/seq/io/SeqIOToolsTest.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojava/bio/search/SimpleSeqSimilaritySearchHitTest.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojava/bio/search/SimpleSeqSimilaritySearchHitTest.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ core --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ core --- [INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/core/target/core-1.9.7.jar [INFO] [INFO] -----------------------< org.biojava:alignment >------------------------ [INFO] Building alignment 1.9.7 [4/9] [INFO] from alignment/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ alignment --- [INFO] Copying 89 resources from src/main/resources to target/classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ alignment --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 14 source files with javac [debug target 1.8] to target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/main/java/org/biojava/bio/alignment/SubstitutionMatrix.java:[180,48] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/main/java/org/biojava/bio/alignment/SubstitutionMatrix.java:[181,48] Integer(int) in java.lang.Integer has been deprecated and marked for removal [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ alignment --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ alignment --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 5 source files with javac [debug target 1.8] to target/test-classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/test/java/org/biojava/bio/alignment/FlexibleAlignmentTest.java: /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/test/java/org/biojava/bio/alignment/FlexibleAlignmentTest.java uses unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/test/java/org/biojava/bio/alignment/FlexibleAlignmentTest.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ alignment --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ alignment --- [INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/target/alignment-1.9.7.jar [INFO] [INFO] -------------------------< org.biojava:biosql >------------------------- [INFO] Building biosql 1.9.7 [5/9] [INFO] from biosql/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biosql --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biosql --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 35 source files with javac [debug target 1.8] to target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.java:[530,48] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.java:[618,35] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.java:[722,45] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.java:[1303,23] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.java:[1337,23] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/FeaturesSQL.java:[162,22] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/FeaturesSQL.java:[166,78] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/FeaturesSQL.java:[225,27] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/FeaturesSQL.java:[340,27] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/FeaturesSQL.java:[341,27] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/FeaturesSQL.java:[514,34] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/FeaturesSQL.java:[515,33] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/FeaturesSQL.java:[561,29] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/FeaturesSQL.java:[749,37] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/FeaturesSQL.java:[751,37] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/OntologySQL.java:[315,21] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/OntologySQL.java:[335,51] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/OntologySQL.java:[336,51] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/OntologySQL.java:[337,51] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/OntologySQL.java:[391,28] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/OntologySQL.java:[440,24] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/OntologySQL.java:[562,21] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/OntologySQL.java:[688,19] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/OntologySQL.java:[719,35] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLEntryChangeHub.java:[60,22] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLEntryChangeHub.java:[69,22] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLEntryChangeHub.java:[79,22] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLEntryChangeHub.java:[90,22] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLEntryAnnotationChangeHub.java:[63,31] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLEntryAnnotationChangeHub.java:[79,31] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLFeatureChangeHub.java:[63,31] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLFeatureChangeHub.java:[79,31] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLFeatureAnnotationChangeHub.java:[62,30] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLFeatureAnnotationChangeHub.java:[74,30] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLFeature.java:[376,68] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLFeature.java:[384,71] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/TaxonSQL.java:[318,38] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/TaxonSQL.java:[321,38] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/TaxonSQL.java:[324,38] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/TaxonSQL.java:[327,38] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/TaxonSQL.java:[343,38] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/TaxonSQL.java:[346,38] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/TaxonSQL.java:[349,38] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/TaxonSQL.java:[352,38] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/TaxonSQL.java:[608,15] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/TaxonSQL.java:[632,17] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/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] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biosql --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biosql --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 2 source files with javac [debug target 1.8] to target/test-classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/test/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceDBTest.java: /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/test/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceDBTest.java uses or overrides a deprecated API. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/test/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceDBTest.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biosql --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biosql --- [INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/target/biosql-1.9.7.jar [INFO] [INFO] -------------------------< org.biojava:blast >-------------------------- [INFO] Building blast 1.9.7 [6/9] [INFO] from blast/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ blast --- [INFO] Copying 3 resources from src/main/resources to target/classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ blast --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 56 source files with javac [debug target 1.8] to target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/src/main/java/org/biojava/bio/program/sax/AbstractNativeAppSAXParser.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/src/main/java/org/biojava/bio/program/sax/AbstractNativeAppSAXParser.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/src/main/java/org/biojava/bio/program/sax/blastxml/StAXFeatureHandler.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/src/main/java/org/biojava/bio/program/sax/blastxml/StAXFeatureHandler.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ blast --- [INFO] Copying 22 resources from src/test/resources to target/test-classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ blast --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 19 source files with javac [debug target 1.8] to target/test-classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ blast --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ blast --- [INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/target/blast-1.9.7.jar [INFO] [INFO] -----------------------< org.biojava:sequencing >----------------------- [INFO] Building sequencing 1.9.7 [7/9] [INFO] from sequencing/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ sequencing --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ sequencing --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 33 source files with javac [debug target 1.8] to target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/program/scf/SCF.java:[372,32] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/program/scf/SCF.java:[373,32] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/program/scf/SCF.java:[374,32] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/program/scf/SCF.java:[375,32] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/program/scf/SCF.java:[377,30] Long(long) in java.lang.Long has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/program/scf/SCF.java:[378,30] Long(long) in java.lang.Long has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/program/scf/SCF.java:[380,34] Long(long) in java.lang.Long has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/program/scf/SCF.java:[383,34] Long(long) in java.lang.Long has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.java:[274,45] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.java:[276,47] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.java:[278,47] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.java:[1114,42] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.java:[1127,45] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.java:[1140,45] Integer(int) in java.lang.Integer has been deprecated and marked for removal [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/AbstractChromatogram.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/AbstractChromatogram.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/program/abi/ABIFParser.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/program/abi/ABIFParser.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ sequencing --- [INFO] Copying 77 resources from src/test/resources to target/test-classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ sequencing --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 15 source files with javac [debug target 1.8] to target/test-classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/test/java/org/biojava/bio/program/fastq/AbstractFastqReaderTest.java: /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/test/java/org/biojava/bio/program/fastq/AbstractFastqReaderTest.java uses or overrides a deprecated API. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/test/java/org/biojava/bio/program/fastq/AbstractFastqReaderTest.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ sequencing --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ sequencing --- [INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/target/sequencing-1.9.7.jar [INFO] [INFO] --------------------------< org.biojava:gui >--------------------------- [INFO] Building gui 1.9.7 [8/9] [INFO] from gui/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ gui --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ gui --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 99 source files with javac [debug target 1.8] to target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/LineInfo.java:[51,28] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/AbiTraceRenderer.java:[157,53] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/AbiTraceRenderer.java:[157,72] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/FilteringRenderer.java:[119,26] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/FilteringRenderer.java:[119,48] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.java:[173,50] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.java:[174,50] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.java:[176,27] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.java:[206,27] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.java:[288,50] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.java:[289,50] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/AbstractBeadRenderer.java:[350,66] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/AbstractBeadRenderer.java:[351,66] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/AbstractBeadRenderer.java:[397,66] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/AbstractBeadRenderer.java:[398,66] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/TickFeatureRenderer.java:[132,26] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/TickFeatureRenderer.java:[132,50] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/RectangularBeadRenderer.java:[221,66] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/RectangularBeadRenderer.java:[222,66] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/BasicFeatureRenderer.java:[139,25] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/BasicFeatureRenderer.java:[139,53] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/BasicFeatureRenderer.java:[163,25] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/BasicFeatureRenderer.java:[163,53] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/BasicImapRenderer.java:[167,34] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/BasicImapRenderer.java:[168,34] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/BasicImapRenderer.java:[169,34] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/BasicImapRenderer.java:[170,34] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/PaddingRenderer.java:[107,24] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/PaddingRenderer.java:[107,50] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/PaddingRenderer.java:[118,26] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/PaddingRenderer.java:[118,52] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/RectangularImapRenderer.java:[201,30] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/RectangularImapRenderer.java:[202,30] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/RectangularImapRenderer.java:[203,30] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/RectangularImapRenderer.java:[204,30] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/EllipticalBeadRenderer.java:[195,66] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/EllipticalBeadRenderer.java:[196,66] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/ZiggyImapRenderer.java:[169,34] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/ZiggyImapRenderer.java:[170,34] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/ZiggyImapRenderer.java:[171,34] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/ZiggyImapRenderer.java:[172,34] Integer(int) in java.lang.Integer has been deprecated and marked for removal [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/SequenceRendererWrapper.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/SequenceRendererWrapper.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/LineInfo.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/LineInfo.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ gui --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ gui --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ gui --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ gui --- [INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/target/gui-1.9.7.jar [INFO] [INFO] -------------------------< org.biojava:phylo >-------------------------- [INFO] Building phylo 1.9.7 [9/9] [INFO] from phylo/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ phylo --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/phylo/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ phylo --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 37 source files with javac [debug target 1.8] to target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/phylo/src/main/java/org/biojavax/bio/phylo/io/nexus/DistancesBlock.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/phylo/src/main/java/org/biojavax/bio/phylo/io/nexus/DistancesBlock.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ phylo --- [INFO] Copying 3 resources from src/test/resources to target/test-classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ phylo --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 1 source file with javac [debug target 1.8] to target/test-classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ phylo --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ phylo --- [INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/phylo/target/phylo-1.9.7.jar [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava-legacy 1.9.7: [INFO] [INFO] biojava-legacy ..................................... SUCCESS [ 0.002 s] [INFO] bytecode ........................................... SUCCESS [ 2.425 s] [INFO] core ............................................... SUCCESS [ 9.472 s] [INFO] alignment .......................................... SUCCESS [ 0.403 s] [INFO] biosql ............................................. SUCCESS [ 0.468 s] [INFO] blast .............................................. SUCCESS [ 0.524 s] [INFO] sequencing ......................................... SUCCESS [ 0.534 s] [INFO] gui ................................................ SUCCESS [ 0.469 s] [INFO] phylo .............................................. SUCCESS [ 0.323 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 14.845 s [INFO] Finished at: 2025-12-23T18:11:26Z [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 Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release. [INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] biojava-legacy [pom] [INFO] bytecode [jar] [INFO] core [jar] [INFO] alignment [jar] [INFO] biosql [jar] [INFO] blast [jar] [INFO] sequencing [jar] [INFO] gui [jar] [INFO] phylo [jar] [INFO] [INFO] ---------------------< org.biojava:biojava-legacy >--------------------- [INFO] Building biojava-legacy 1.9.7 [1/9] [INFO] from pom.xml [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] ------------------------< org.biojava:bytecode >------------------------ [INFO] Building bytecode 1.9.7 [2/9] [INFO] from bytecode/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ bytecode --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ bytecode --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ bytecode --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ bytecode --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ bytecode --- [INFO] No tests to run. [INFO] [INFO] --------------------------< org.biojava:core >-------------------------- [INFO] Building core 1.9.7 [3/9] [INFO] from core/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ core --- [INFO] Copying 29 resources from src/main/resources to target/classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ core --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ core --- [INFO] Copying 53 resources from src/test/resources to target/test-classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ core --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ core --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.bio.molbio.RestrictionEnzymeTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.288 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: 0.02 s - in org.biojava.bio.molbio.RestrictionEnzymeManagerTest [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.TestSoftMaskedAlphabet [INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 s - in org.biojava.bio.symbol.TestSoftMaskedAlphabet [INFO] Running org.biojava.bio.symbol.CompoundLocationTest [INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.biojava.bio.symbol.CompoundLocationTest [INFO] Running org.biojava.bio.symbol.CrossProductTokenizationTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.symbol.CrossProductTokenizationTest [INFO] Running org.biojava.bio.symbol.SimpleSymbolListTest [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.SimpleSymbolListTest [INFO] Running org.biojava.bio.symbol.DoubleAlphabetTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 s - in org.biojava.bio.symbol.DoubleAlphabetTest [INFO] Running org.biojava.bio.symbol.SymbolListTest [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.77 s - in org.biojava.bio.symbol.SymbolListTest [INFO] Running org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest [INFO] Running org.biojava.bio.symbol.TranslationTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.bio.symbol.TranslationTest [INFO] Running org.biojava.bio.symbol.MergeLocationTest [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.MergeLocationTest [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.LinearAlphabetIndexTest symbolForIndex getAlphabet indexForSymbol [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.LinearAlphabetIndexTest [INFO] Running org.biojava.bio.symbol.PointLocationTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.symbol.PointLocationTest [INFO] Running org.biojava.bio.symbol.CrossProductAlphabetIndexTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.963 s - in org.biojava.bio.symbol.CrossProductAlphabetIndexTest [INFO] Running org.biojava.bio.symbol.IndexedNoAmbPackTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.symbol.IndexedNoAmbPackTest [INFO] Running org.biojava.bio.symbol.BetweenLocationTest [INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojava.bio.symbol.BetweenLocationTest [INFO] Running org.biojava.bio.symbol.CodonPrefToolsTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.062 s - in org.biojava.bio.symbol.CodonPrefToolsTest [INFO] Running org.biojava.bio.symbol.AlphabetSerializationTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.124 s - in org.biojava.bio.symbol.AlphabetSerializationTest [INFO] Running org.biojava.bio.symbol.MotifToolsTest [INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.symbol.MotifToolsTest [INFO] Running org.biojava.bio.symbol.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.SimpleWobbleDistributionTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.symbol.SimpleWobbleDistributionTest [INFO] Running org.biojava.bio.symbol.AlphabetManagerTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.symbol.AlphabetManagerTest [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: 0.034 s - in org.biojava.bio.symbol.UkkonenSuffixTreeTest [INFO] Running org.biojava.bio.symbol.NameTokenizationTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.NameTokenizationTest [INFO] Running org.biojava.bio.symbol.RangeLocationTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.RangeLocationTest [INFO] Running org.biojava.bio.symbol.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.SymbolSerializationTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.bio.symbol.SymbolSerializationTest [INFO] Running org.biojava.bio.symbol.CircularLocationTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.symbol.CircularLocationTest [INFO] Running org.biojava.bio.symbol.GappedSymbolListTest [INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.bio.symbol.GappedSymbolListTest [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.program.phred.PhredToolsTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.program.phred.PhredToolsTest [INFO] Running org.biojava.bio.program.indexdb.IndexToolsTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.059 s - in org.biojava.bio.program.indexdb.IndexToolsTest [INFO] Running org.biojava.bio.seq.db.HashSequenceDBTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.seq.db.HashSequenceDBTest [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.emblcd.EntryNamIdxReaderTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 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: 0.006 s - in org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest [INFO] Running org.biojava.bio.seq.db.TestHashSequenceDB [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 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: 0.005 s - in org.biojava.bio.seq.db.EmblCDROMIndexStoreTest [INFO] Running org.biojava.bio.seq.filter.FilterTransformerTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojava.bio.seq.filter.FilterTransformerTest [INFO] Running org.biojava.bio.seq.DNAToolsTest [INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.DNAToolsTest [INFO] Running org.biojava.bio.seq.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.FeatureHolderUtilsTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.FeatureHolderUtilsTest [INFO] Running org.biojava.bio.seq.SeqSerializationTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 s - in org.biojava.bio.seq.SeqSerializationTest [INFO] Running org.biojava.bio.seq.MergeFeatureHolderTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.MergeFeatureHolderTest [INFO] Running org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest [INFO] Running org.biojava.bio.seq.NewSimpleAssemblyTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.bio.seq.NewSimpleAssemblyTest [INFO] Running org.biojava.bio.seq.FilterUtilsTest [INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.seq.FilterUtilsTest [INFO] Running org.biojava.bio.seq.SimpleAssemblyTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.SimpleAssemblyTest [INFO] Running org.biojava.bio.seq.RNAToolsTest [INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.seq.RNAToolsTest [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: 0.008 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: 0.008 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: 0.01 s - in org.biojava.bio.seq.impl.ViewSeqSerializationTest [INFO] Running org.biojava.bio.seq.ProteinToolsTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.ProteinToolsTest [INFO] Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.seq.project.ProjectedFeatureHolderTest [INFO] Running org.biojava.bio.seq.io.SmartSequenceBuilderTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.666 s - in org.biojava.bio.seq.io.SmartSequenceBuilderTest [INFO] Running org.biojava.bio.seq.io.MSFAlignmentFormatTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.seq.io.MSFAlignmentFormatTest [INFO] Running org.biojava.bio.seq.io.SeqIOToolsTest idb length: 79 [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.373 s - in org.biojava.bio.seq.io.SeqIOToolsTest [INFO] Running org.biojava.bio.seq.io.SymbolListCharSequenceTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.io.SymbolListCharSequenceTest [INFO] Running org.biojava.bio.seq.io.filterxml.FilterXMLTest [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 s - in org.biojava.bio.seq.io.filterxml.FilterXMLTest [INFO] Running org.biojava.bio.seq.io.LocationFormatterTest [INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 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: 0.003 s - in org.biojava.bio.seq.FeatureFilterTest [INFO] Running org.biojava.bio.search.SeqContentPatternTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 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: 0.04 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: 0.001 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest [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.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.dist.DistSerTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 s - in org.biojava.bio.dist.DistSerTest [INFO] Running org.biojava.bio.dist.DistributionToolsTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojava.bio.dist.DistributionToolsTest [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.AnnotationTypeTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.AnnotationTypeTest [INFO] Running org.biojava.bio.dp.MarkovModelEventTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 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: 0.012 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.bio.proteomics.IsoelectricPointCalcTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.proteomics.IsoelectricPointCalcTest [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$1.protect(TestResult.java:122) at junit.framework.TestResult.runProtected(TestResult.java:142) at junit.framework.TestResult.run(TestResult.java:125) at junit.framework.TestCase.run(TestCase.java:130) at junit.framework.TestSuite.runTest(TestSuite.java:241) at junit.framework.TestSuite.run(TestSuite.java:236) at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90) at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365) at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273) at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238) at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159) at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384) at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345) at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126) at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418) [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest [INFO] Running org.biojava.bio.proteomics.aaindex.AAindexTest org.biojava.bio.symbol.IllegalSymbolException: Symbol adenine not found in alphabet PROTEIN at org.biojava.bio.symbol.AbstractAlphabet.validate(AbstractAlphabet.java:327) at org.biojava.bio.symbol.AlphabetManager$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: 0.004 s - in org.biojava.bio.proteomics.aaindex.AAindexTest [INFO] Running org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 s - in org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest [INFO] Running org.biojava.bio.proteomics.MassCalcTest [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.proteomics.MassCalcTest [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.naming.ObdaUriParserTest urn:obda.org:format:embl/ac :trail oneName lead: [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.naming.ObdaUriParserTest [INFO] Running org.biojava.naming.ObdaInitialContextFactoryTest Reached Attributes: No attributes Binding: urn -> org.biojava.naming.ObdaContext@5d7d2f Reached urn Attributes: No attributes Binding: open-bio.org -> org.biojava.naming.ObdaContext@ea99e7 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@1d38fed 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@17dfb8d 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@a0786f 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@17523ba 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@3e705e 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@c74647 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@1652a30 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@163a655 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@c8067 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@bb0bdf 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@1f9d92 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@84d80a 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@eb6c45 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@3b6963} My component is urn:open-bio.org:format:embl lookup: 'open-bio.org:format:embl' for {open-bio.org=org.biojava.naming.ObdaContext@1a0f011} My component is open-bio.org:format:embl lookup: 'format:embl' for {type=org.biojava.naming.ObdaContext@a42c82, format=org.biojava.naming.ObdaContext@1133244, alphabet=org.biojava.naming.ObdaContext@eb7701} My component is format:embl lookup: 'embl' for {enzyme=org.biojava.naming.ObdaContext@193ef5, genbank=org.biojava.naming.ObdaContext@106c988, swissprot=org.biojava.naming.ObdaContext@1274afe, embl=org.biojava.naming.ObdaContext@a362a4} My component is embl [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 s - in org.biojava.naming.ObdaInitialContextFactoryTest [INFO] Running org.biojava.ontology.OntologyTest [INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.ontology.OntologyTest [INFO] Running org.biojava.ontology.TripleImplTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.ontology.TripleImplTest [INFO] Running org.biojava.ontology.TermImplTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.ontology.TermImplTest [INFO] Running org.biojava.ontology.ParseOBOFileTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.144 s - in org.biojava.ontology.ParseOBOFileTest [INFO] Running org.biojava.utils.RepeatedCharSequenceTest JAM [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.utils.RepeatedCharSequenceTest [INFO] Running org.biojava.utils.SmallMapTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.SmallMapTest [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.process.AllTests [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.113 s - in org.biojava.utils.process.AllTests [INFO] Running org.biojava.utils.process.ExternalProcessTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.043 s - in org.biojava.utils.process.ExternalProcessTest [INFO] Running org.biojava.utils.walker.WalkerFactoryTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 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: 0.026 s - in org.biojava.utils.walker.WalkerTest [INFO] Running org.biojava.utils.automata.NfaTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.automata.NfaTest [INFO] Running org.biojava.utils.regex.PatternCheckerTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojava.utils.regex.PatternCheckerTest [INFO] Running org.biojava.utils.regex.RegexTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.regex.RegexTest [INFO] Running org.biojava.utils.lsid.LifeScienceIdentifierTest [INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.lsid.LifeScienceIdentifierTest [INFO] Running org.biojava.directory.RegistryConfigurationTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.directory.RegistryConfigurationTest [INFO] Running org.biojava.directory.SystemRegistryTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 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.biojavax.SimpleCommentTest testSetComment testToString testCompareTo testGetRank testHashCode testGetComment testEquals testSetRank [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 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: 0.004 s - in org.biojavax.SimpleNamespaceTest [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: 0.012 s - in org.biojavax.SimpleDocRefTest [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.SimpleDocRefAuthorTest testIsConsortium testToString testCompareTo testGetName testHashCode testEquals testGetExtendedName [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.SimpleDocRefAuthorTest [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.SimpleRichLocationTest testEquals [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.bio.seq.SimpleRichLocationTest [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.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.RichLocationToolsTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.seq.RichLocationToolsTest [INFO] Running org.biojavax.bio.seq.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.io.Bug2255Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojavax.bio.seq.io.Bug2255Test [INFO] Running org.biojavax.bio.seq.io.EMBLFormatTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.seq.io.EMBLFormatTest [INFO] Running org.biojavax.bio.seq.io.Bug2249_2248Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojavax.bio.seq.io.Bug2249_2248Test [INFO] Running org.biojavax.bio.seq.io.INSDseqFormatTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 s - in org.biojavax.bio.seq.io.INSDseqFormatTest [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: 0.001 s - in org.biojavax.bio.seq.io.GenbankLocationParserTest [INFO] Running org.biojavax.bio.seq.io.Bug2250_2256Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 s - in org.biojavax.bio.seq.io.Bug2250_2256Test [INFO] Running org.biojavax.bio.seq.io.UniProtFormatTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojavax.bio.seq.io.UniProtFormatTest [INFO] Running org.biojavax.bio.seq.io.GenbankFormatTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.biojavax.bio.seq.io.GenbankFormatTest [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: 0.008 s - in org.biojavax.bio.SimpleBioEntryTest [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.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.SimpleNoteTest testGetValue testToString testCompareTo testGetRank testGetTerm testHashCode testEquals testSetRank testSetTerm testSetValue [INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.SimpleNoteTest [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 s - in org.biojavax.SimpleRankedDocRefTest [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] 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.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.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: 0.009 s - in org.biojavax.ontology.SimpleComparableOntologyTest [INFO] Running org.biojavax.ontology.SimpleComparableTripleTest testGetSubject testSetDescriptors testToString testGetSynonyms testRemoveDescriptor testCompareTo testAddSynonym testGetName testGetOntology testGetPredicate testGetAnnotation testGetDescription testGetDescriptors testHashCode testAddDescriptor testEquals testGetObject testRemoveSynonym [INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.ontology.SimpleComparableTripleTest [INFO] Running org.biojavax.ga.functions.ProportionalSelectionTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.functions.ProportionalSelectionTest [INFO] Running org.biojavax.ga.functions.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.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.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.SimpleMutationFunctionTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.ga.functions.SimpleMutationFunctionTest [INFO] Running org.biojavax.ga.util.GAToolsTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.util.GAToolsTest [INFO] Running org.biojavax.ga.util.WeightedSetTest [INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.ga.util.WeightedSetTest [INFO] Running org.biojavax.ga.impl.SimplePopulationTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.impl.SimplePopulationTest [INFO] Running org.biojavax.ga.impl.SimpleOrganismTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.impl.SimpleOrganismTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 890, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] -----------------------< org.biojava:alignment >------------------------ [INFO] Building alignment 1.9.7 [4/9] [INFO] from alignment/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ alignment --- [INFO] Copying 89 resources from src/main/resources to target/classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ alignment --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ alignment --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ alignment --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ alignment --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.bio.alignment.SubstitutionMatrixTest [INFO] Tests run: 96, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.555 s - in org.biojava.bio.alignment.SubstitutionMatrixTest [INFO] Running org.biojava.bio.alignment.FlexibleAlignmentTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.033 s - in org.biojava.bio.alignment.FlexibleAlignmentTest [INFO] Running org.biojava.bio.alignment.AlignmentPairTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.alignment.AlignmentPairTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 102, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] -------------------------< org.biojava:biosql >------------------------- [INFO] Building biosql 1.9.7 [5/9] [INFO] from biosql/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biosql --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biosql --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biosql --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biosql --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biosql --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest No hsqldb driver found. [INFO] Tests run: 0, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 s - in org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 0, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] -------------------------< org.biojava:blast >-------------------------- [INFO] Building blast 1.9.7 [6/9] [INFO] from blast/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ blast --- [INFO] Copying 3 resources from src/main/resources to target/classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ blast --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ blast --- [INFO] Copying 22 resources from src/test/resources to target/test-classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ blast --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ blast --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.545 s - in org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.67 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.803 s - in org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.173 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: 0.327 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.159 s - in org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.23 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.805 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.298 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.119 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.124 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.283 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 s - in org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.823 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.22 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 s - in org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test [INFO] Running org.biojava.bio.program.sax.blastxml.BlastXMLTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.078 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: 0.041 s - in org.biojava.bio.program.sax.BlastTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 118, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] -----------------------< org.biojava:sequencing >----------------------- [INFO] Building sequencing 1.9.7 [7/9] [INFO] from sequencing/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ sequencing --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ sequencing --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ sequencing --- [INFO] Copying 77 resources from src/test/resources to target/test-classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ sequencing --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ sequencing --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.bio.program.fastq.SolexaFastqReaderTest [INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.129 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: 0.014 s - in org.biojava.bio.program.fastq.StreamingFastqParserTest [INFO] Running org.biojava.bio.program.fastq.FastqVariantTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 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: 0.027 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: 0.012 s - in org.biojava.bio.program.fastq.FastqBuilderTest [INFO] Running org.biojava.bio.program.fastq.FastqToolsTest [INFO] Tests run: 38, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.241 s - in org.biojava.bio.program.fastq.FastqToolsTest [INFO] Running org.biojava.bio.program.fastq.ConvertTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 s - in org.biojava.bio.program.fastq.ConvertTest [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.IlluminaFastqWriterTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.program.fastq.IlluminaFastqWriterTest [INFO] Running org.biojava.bio.program.fastq.IlluminaFastqReaderTest [INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojava.bio.program.fastq.IlluminaFastqReaderTest [INFO] Running org.biojava.bio.program.fastq.FastqTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 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: 0.006 s - in org.biojava.bio.program.fastq.SolexaFastqWriterTest [INFO] Running org.biojava.bio.program.scf.SCFTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.082 s - in org.biojava.bio.program.scf.SCFTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 192, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] --------------------------< org.biojava:gui >--------------------------- [INFO] Building gui 1.9.7 [8/9] [INFO] from gui/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ gui --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ gui --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ gui --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ gui --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ gui --- [INFO] No tests to run. [INFO] [INFO] -------------------------< org.biojava:phylo >-------------------------- [INFO] Building phylo 1.9.7 [9/9] [INFO] from phylo/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ phylo --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/phylo/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ phylo --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ phylo --- [INFO] Copying 3 resources from src/test/resources to target/test-classes [INFO] [INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ phylo --- [INFO] Nothing to compile - all classes are up to date. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ phylo --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojavax.bio.phylo.io.nexus.TreesBlockTest [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.146 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 [ 0.001 s] [INFO] bytecode ........................................... SUCCESS [ 0.500 s] [INFO] core ............................................... SUCCESS [ 36.109 s] [INFO] alignment .......................................... SUCCESS [ 31.424 s] [INFO] biosql ............................................. SUCCESS [ 30.811 s] [INFO] blast .............................................. SUCCESS [ 37.874 s] [INFO] sequencing ......................................... SUCCESS [ 31.448 s] [INFO] gui ................................................ SUCCESS [ 0.049 s] [INFO] phylo .............................................. SUCCESS [ 30.831 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 03:19 min [INFO] Finished at: 2025-12-23T18:14:47Z [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 Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release. [INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] biojava-legacy [pom] [INFO] bytecode [jar] [INFO] core [jar] [INFO] alignment [jar] [INFO] biosql [jar] [INFO] blast [jar] [INFO] sequencing [jar] [INFO] gui [jar] [INFO] phylo [jar] [INFO] [INFO] ---------------------< org.biojava:biojava-legacy >--------------------- [INFO] Building biojava-legacy 1.9.7 [1/9] [INFO] from pom.xml [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-legacy --- [INFO] Cleaning pom file: /build/reproducible-path/biojava-live-1.9.7+dfsg/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava1.9-java [INFO] --rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.publishedRules [INFO] --no-parent [INFO] [INFO] ------------------------< org.biojava:bytecode >------------------------ [INFO] Building bytecode 1.9.7 [2/9] [INFO] from bytecode/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ bytecode --- [INFO] Cleaning pom file: /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava1.9-java [INFO] --rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.publishedRules [INFO] Install jar for bytecode into /usr/share/java [INFO] [INFO] --------------------------< org.biojava:core >-------------------------- [INFO] Building core 1.9.7 [3/9] [INFO] from core/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ core --- [INFO] Cleaning pom file: /build/reproducible-path/biojava-live-1.9.7+dfsg/core/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava1.9-java [INFO] --rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.publishedRules [INFO] Install jar for core into /usr/share/java [INFO] [INFO] -----------------------< org.biojava:alignment >------------------------ [INFO] Building alignment 1.9.7 [4/9] [INFO] from alignment/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ alignment --- [INFO] Cleaning pom file: /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava1.9-java [INFO] --rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.publishedRules [INFO] Install jar for alignment into /usr/share/java [INFO] [INFO] -------------------------< org.biojava:biosql >------------------------- [INFO] Building biosql 1.9.7 [5/9] [INFO] from biosql/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biosql --- [INFO] Cleaning pom file: /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava1.9-java [INFO] --rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.publishedRules [INFO] Install jar for biosql into /usr/share/java [INFO] [INFO] -------------------------< org.biojava:blast >-------------------------- [INFO] Building blast 1.9.7 [6/9] [INFO] from blast/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ blast --- [INFO] Cleaning pom file: /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava1.9-java [INFO] --rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.publishedRules [INFO] Install jar for blast into /usr/share/java [INFO] [INFO] -----------------------< org.biojava:sequencing >----------------------- [INFO] Building sequencing 1.9.7 [7/9] [INFO] from sequencing/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ sequencing --- [INFO] Cleaning pom file: /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava1.9-java [INFO] --rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.publishedRules [INFO] Install jar for sequencing into /usr/share/java [INFO] [INFO] --------------------------< org.biojava:gui >--------------------------- [INFO] Building gui 1.9.7 [8/9] [INFO] from gui/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ gui --- [INFO] Cleaning pom file: /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava1.9-java [INFO] --rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.publishedRules [INFO] Install jar for gui into /usr/share/java [INFO] [INFO] -------------------------< org.biojava:phylo >-------------------------- [INFO] Building phylo 1.9.7 [9/9] [INFO] from phylo/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ phylo --- [INFO] Cleaning pom file: /build/reproducible-path/biojava-live-1.9.7+dfsg/phylo/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava1.9-java [INFO] --rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.publishedRules [INFO] Install jar for phylo into /usr/share/java [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava-legacy 1.9.7: [INFO] [INFO] biojava-legacy ..................................... SUCCESS [ 0.288 s] [INFO] bytecode ........................................... SUCCESS [ 0.051 s] [INFO] core ............................................... SUCCESS [ 0.040 s] [INFO] alignment .......................................... SUCCESS [ 0.025 s] [INFO] biosql ............................................. SUCCESS [ 0.027 s] [INFO] blast .............................................. SUCCESS [ 0.025 s] [INFO] sequencing ......................................... SUCCESS [ 0.030 s] [INFO] gui ................................................ SUCCESS [ 0.043 s] [INFO] phylo .............................................. SUCCESS [ 0.034 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.727 s [INFO] Finished at: 2025-12-23T18:14:49Z [INFO] ------------------------------------------------------------------------ mh_resolve_dependencies --non-interactive --offline --build -plibbiojava1.9-java --base-directory=/build/reproducible-path/biojava-live-1.9.7\+dfsg --non-explore Analysing pom.xml... Analysing alignment/pom.xml... Checking the parent dependency in the sub project alignment/pom.xml Analysing biosql/pom.xml... Checking the parent dependency in the sub project biosql/pom.xml Analysing blast/pom.xml... Checking the parent dependency in the sub project blast/pom.xml Analysing bytecode/pom.xml... Checking the parent dependency in the sub project bytecode/pom.xml Analysing core/pom.xml... Checking the parent dependency in the sub project core/pom.xml Analysing gui/pom.xml... Checking the parent dependency in the sub project gui/pom.xml Analysing phylo/pom.xml... Checking the parent dependency in the sub project phylo/pom.xml Analysing sequencing/pom.xml... Checking the parent dependency in the sub project sequencing/pom.xml mh_unpatchpoms -plibbiojava1.9-java debian/rules override_dh_installdocs make[1]: Entering directory '/build/reproducible-path/biojava-live-1.9.7+dfsg' dh_installdocs # Deleting calls to urchinTracker to enhance privacy. for F in $(find . -name "*.html"); do \ sed -i 's/^$//' $F; \ done make[1]: Leaving directory '/build/reproducible-path/biojava-live-1.9.7+dfsg' dh_installchangelogs dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libbiojava1.9-java' in '../libbiojava1.9-java_1.9.7+dfsg-2_all.deb'. dpkg-deb: building package 'libbiojava-java' in '../libbiojava-java_1.9.7+dfsg-2_all.deb'. dpkg-genbuildinfo --build=binary -O../biojava-live_1.9.7+dfsg-2_i386.buildinfo dpkg-genchanges --build=binary -O../biojava-live_1.9.7+dfsg-2_i386.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: user script /srv/workspace/pbuilder/26036/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/26036/tmp/hooks/B01_cleanup finished 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/26036 and its subdirectories I: Current time: Wed Dec 24 08:14:57 +14 2025 I: pbuilder-time-stamp: 1766513697