I: pbuilder: network access will be disabled during build I: Current time: Wed Apr 3 11:14:11 +14 2024 I: pbuilder-time-stamp: 1712092451 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-1.dsc] I: copying [./biojava-live_1.9.7+dfsg.orig.tar.xz] I: copying [./biojava-live_1.9.7+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Nov 29 07:46:53 2023 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./biojava-live_1.9.7+dfsg-1.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-1.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/45107/tmp/hooks/D01_modify_environment starting debug: Running on ionos12-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 Apr 2 21:14 /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/45107/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/45107/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]="21" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.2.21(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=10 ' 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=38db3ca9b72d4dc49524c2e56db7b76d 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=45107 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.WfuD38P9/pbuilderrc_NmJB --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.WfuD38P9/b2 --logfile b2/build.log biojava-live_1.9.7+dfsg-1.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 30 20:35 /bin -> usr/bin I: user script /srv/workspace/pbuilder/45107/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, libjgrapht0.8-java-doc, libmaven-javadoc-plugin-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 ... 19703 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 libjgrapht0.8-java-doc; however: Package libjgrapht0.8-java-doc is not installed. pbuilder-satisfydepends-dummy depends on libmaven-javadoc-plugin-java; however: Package libmaven-javadoc-plugin-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} 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} java-wrappers{a} junit4{a} junit5{a} libactivation-java{a} libaopalliance-java{a} libapache-pom-java{a} libapiguardian-java{a} libarchive-zip-perl{a} libasm-java{a} libasound2-data{a} libasound2t64{a} libatinject-jsr330-api-java{a} libatk1.0-0t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbatik-java{a} libbrotli1{a} libbsd0{a} libbsh-java{a} libcairo2{a} libcdi-api-java{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-configuration-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} 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-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libel-api-java{a} libelf1t64{a} liberror-prone-java{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontbox2-java{a} libfontconfig1{a} libfop-java{a} libfreetype6{a} libfribidi0{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} libgtk2.0-0t64{a} libgtk2.0-common{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{a} libhttpclient-java{a} libhttpcore-java{a} libicu72{a} libitext1-java{a} libjansi-java{a} libjaxb-api-java{a} libjaxen-java{a} libjaxp1.3-java{a} libjbig0{a} libjetty9-java{a} libjgraph-java{a} libjgrapht0.8-java{a} libjgrapht0.8-java-doc{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} libllvm17t64{a} libmagic-mgc{a} libmagic1t64{a} libmaven-archiver-java{a} libmaven-artifact-transfer-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-invoker-java{a} libmaven-jar-plugin-java{a} libmaven-javadoc-plugin-java{a} libmaven-parent-java{a} libmaven-plugin-tools-java{a} libmaven-reporting-api-java{a} libmaven-reporting-exec-java{a} libmaven-reporting-impl-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} 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-interactivity-api-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} libpng16-16t64{a} libproc2-0{a} libqdox-java{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} libsub-override-perl{a} libsurefire-java{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} libwebp7{a} libwebsocket-api-java{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxalan2-java{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} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxml2-utils{a} libxmlgraphics-commons-java{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} openjdk-17-jdk{a} openjdk-17-jdk-headless{a} openjdk-17-jre{a} openjdk-17-jre-headless{a} openssl{a} po-debconf{a} procps{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} unzip{a} velocity{a} x11-common{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf ant-optional curl dbus fonts-dejavu-extra icc-profiles-free krb5-locales libarchive-cpio-perl libatk-wrapper-java-jni libgail-common libgdk-pixbuf2.0-bin libglib2.0-data libgtk2.0-bin libltdl-dev libmail-sendmail-perl librsvg2-common libsaxon-java libxt-dev lynx mesa-vulkan-drivers psmisc wget xdg-user-dirs 0 packages upgraded, 279 newly installed, 0 to remove and 0 not upgraded. Need to get 264 MB of archives. After unpacking 733 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 sgml-base all 1.31 [15.4 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 libproc2-0 i386 2:4.0.4-4 [65.4 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 procps i386 2:4.0.4-4 [876 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 openssl i386 3.1.5-1.1 [1246 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 ca-certificates all 20240203 [158 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3 [314 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3 [114 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3 [42.9 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 12 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-3+b1 [1195 kB] Get: 13 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.39.3-11 [93.7 kB] Get: 14 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.7-2 [39.7 kB] Get: 15 http://deb.debian.org/debian unstable/main i386 man-db i386 2.12.0-4 [1418 kB] Get: 16 http://deb.debian.org/debian unstable/main i386 libgdk-pixbuf2.0-common all 2.42.10+dfsg-3 [307 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 libglib2.0-0t64 i386 2.78.4-6 [1291 kB] Get: 18 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 19 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.9.14+dfsg-1.3+b2 [727 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 shared-mime-info i386 2.4-4 [760 kB] Get: 21 http://deb.debian.org/debian unstable/main i386 libjpeg62-turbo i386 1:2.1.5-2+b2 [169 kB] Get: 22 http://deb.debian.org/debian unstable/main i386 libpng16-16t64 i386 1.6.43-5 [286 kB] Get: 23 http://deb.debian.org/debian unstable/main i386 libdeflate0 i386 1.20-1 [46.9 kB] Get: 24 http://deb.debian.org/debian unstable/main i386 libjbig0 i386 2.1-6.1+b1 [31.8 kB] Get: 25 http://deb.debian.org/debian unstable/main i386 liblerc4 i386 4.0.0+ds-4+b1 [180 kB] Get: 26 http://deb.debian.org/debian unstable/main i386 libsharpyuv0 i386 1.3.2-0.4+b1 [107 kB] Get: 27 http://deb.debian.org/debian unstable/main i386 libwebp7 i386 1.3.2-0.4+b1 [314 kB] Get: 28 http://deb.debian.org/debian unstable/main i386 libtiff6 i386 4.5.1+git230720-4 [338 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 libgdk-pixbuf-2.0-0 i386 2.42.10+dfsg-3+b2 [147 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 gtk-update-icon-cache i386 3.24.41-4 [47.0 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 32 http://deb.debian.org/debian unstable/main i386 adwaita-icon-theme all 46.0-1 [614 kB] Get: 33 http://deb.debian.org/debian unstable/main i386 ca-certificates-java all 20240118 [11.6 kB] Get: 34 http://deb.debian.org/debian unstable/main i386 java-common all 0.75 [6640 B] Get: 35 http://deb.debian.org/debian unstable/main i386 liblcms2-2 i386 2.14-2+b1 [165 kB] Get: 36 http://deb.debian.org/debian unstable/main i386 libnspr4 i386 2:4.35-1.1+b1 [118 kB] Get: 37 http://deb.debian.org/debian unstable/main i386 libnss3 i386 2:3.99-1 [1523 kB] Get: 38 http://deb.debian.org/debian unstable/main i386 libpcsclite1 i386 2.0.3-1 [52.0 kB] Get: 39 http://deb.debian.org/debian unstable/main i386 openjdk-17-jre-headless i386 17.0.11~7ea-1 [42.7 MB] Get: 40 http://deb.debian.org/debian unstable/main i386 default-jre-headless i386 2:1.17-75 [3068 B] Get: 41 http://deb.debian.org/debian unstable/main i386 ant all 1.10.14-1 [2162 kB] Get: 42 http://deb.debian.org/debian unstable/main i386 at-spi2-common all 2.52.0-1 [166 kB] Get: 43 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB] Get: 44 http://deb.debian.org/debian unstable/main i386 autoconf all 2.71-3 [332 kB] Get: 45 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 46 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 47 http://deb.debian.org/debian unstable/main i386 autopoint all 0.21-14 [496 kB] Get: 48 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 49 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-7 [517 kB] Get: 50 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 51 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 52 http://deb.debian.org/debian unstable/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 53 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 54 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 55 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.191-1 [194 kB] Get: 56 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 57 http://deb.debian.org/debian unstable/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 58 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 59 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 60 http://deb.debian.org/debian unstable/main i386 debhelper all 13.15.3 [901 kB] Get: 61 http://deb.debian.org/debian unstable/main i386 libgtk2.0-common all 2.24.33-4 [2661 kB] Get: 62 http://deb.debian.org/debian unstable/main i386 libatk1.0-0t64 i386 2.52.0-1 [50.9 kB] Get: 63 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.2-1 [107 kB] Get: 64 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b3 [314 kB] Get: 65 http://deb.debian.org/debian unstable/main i386 libfreetype6 i386 2.13.2+dfsg-1+b2 [449 kB] Get: 66 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 67 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-core all 2.37-8 [840 kB] Get: 68 http://deb.debian.org/debian unstable/main i386 fontconfig-config i386 2.15.0-1.1 [317 kB] Get: 69 http://deb.debian.org/debian unstable/main i386 libfontconfig1 i386 2.15.0-1.1 [401 kB] Get: 70 http://deb.debian.org/debian unstable/main i386 libpixman-1-0 i386 0.42.2-1+b1 [555 kB] Get: 71 http://deb.debian.org/debian unstable/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 72 http://deb.debian.org/debian unstable/main i386 libbsd0 i386 0.12.2-1 [134 kB] Get: 73 http://deb.debian.org/debian unstable/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 74 http://deb.debian.org/debian unstable/main i386 libxcb1 i386 1.15-1 [148 kB] Get: 75 http://deb.debian.org/debian unstable/main i386 libx11-data all 2:1.8.7-1 [328 kB] Get: 76 http://deb.debian.org/debian unstable/main i386 libx11-6 i386 2:1.8.7-1 [822 kB] Get: 77 http://deb.debian.org/debian unstable/main i386 libxcb-render0 i386 1.15-1 [116 kB] Get: 78 http://deb.debian.org/debian unstable/main i386 libxcb-shm0 i386 1.15-1 [106 kB] Get: 79 http://deb.debian.org/debian unstable/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 80 http://deb.debian.org/debian unstable/main i386 libxrender1 i386 1:0.9.10-1.1 [34.1 kB] Get: 81 http://deb.debian.org/debian unstable/main i386 libcairo2 i386 1.18.0-3 [587 kB] Get: 82 http://deb.debian.org/debian unstable/main i386 libavahi-common-data i386 0.8-13+b2 [112 kB] Get: 83 http://deb.debian.org/debian unstable/main i386 libavahi-common3 i386 0.8-13+b2 [45.3 kB] Get: 84 http://deb.debian.org/debian unstable/main i386 libdbus-1-3 i386 1.14.10-4+b1 [217 kB] Get: 85 http://deb.debian.org/debian unstable/main i386 libavahi-client3 i386 0.8-13+b2 [49.3 kB] Get: 86 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.20.1-6+b1 [36.1 kB] Get: 87 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.0-2.4 [20.6 kB] Get: 88 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.20.1-6+b1 [83.2 kB] Get: 89 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-3 [9432 B] Get: 90 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.20.1-6+b1 [360 kB] Get: 91 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.20.1-6+b1 [145 kB] Get: 92 http://deb.debian.org/debian unstable/main i386 libcups2t64 i386 2.4.7-1.2+b1 [264 kB] Get: 93 http://deb.debian.org/debian unstable/main i386 fontconfig i386 2.15.0-1.1 [462 kB] Get: 94 http://deb.debian.org/debian unstable/main i386 libfribidi0 i386 1.0.13-3+b1 [71.8 kB] Get: 95 http://deb.debian.org/debian unstable/main i386 libgraphite2-3 i386 1.3.14-2 [77.7 kB] Get: 96 http://deb.debian.org/debian unstable/main i386 libharfbuzz0b i386 8.3.0-2+b1 [2234 kB] Get: 97 http://deb.debian.org/debian unstable/main i386 libthai-data all 0.1.29-2 [168 kB] Get: 98 http://deb.debian.org/debian unstable/main i386 libdatrie1 i386 0.2.13-3 [39.5 kB] Get: 99 http://deb.debian.org/debian unstable/main i386 libthai0 i386 0.1.29-2 [50.1 kB] Get: 100 http://deb.debian.org/debian unstable/main i386 libpango-1.0-0 i386 1.52.1+ds-1 [224 kB] Get: 101 http://deb.debian.org/debian unstable/main i386 libpangoft2-1.0-0 i386 1.52.1+ds-1 [51.1 kB] Get: 102 http://deb.debian.org/debian unstable/main i386 libpangocairo-1.0-0 i386 1.52.1+ds-1 [36.0 kB] Get: 103 http://deb.debian.org/debian unstable/main i386 libxcomposite1 i386 1:0.4.5-1 [16.9 kB] Get: 104 http://deb.debian.org/debian unstable/main i386 libxfixes3 i386 1:6.0.0-2 [23.0 kB] Get: 105 http://deb.debian.org/debian unstable/main i386 libxcursor1 i386 1:1.2.1-1 [42.4 kB] Get: 106 http://deb.debian.org/debian unstable/main i386 libxdamage1 i386 1:1.1.6-1 [15.3 kB] Get: 107 http://deb.debian.org/debian unstable/main i386 libxi6 i386 2:1.8.1-1 [81.0 kB] Get: 108 http://deb.debian.org/debian unstable/main i386 libxinerama1 i386 2:1.1.4-3 [18.1 kB] Get: 109 http://deb.debian.org/debian unstable/main i386 libxrandr2 i386 2:1.5.4-1 [37.7 kB] Get: 110 http://deb.debian.org/debian unstable/main i386 libgtk2.0-0t64 i386 2.24.33-4 [1939 kB] Get: 111 http://deb.debian.org/debian unstable/main i386 libglvnd0 i386 1.7.0-1 [43.7 kB] Get: 112 http://deb.debian.org/debian unstable/main i386 libdrm-common all 2.4.120-2 [7688 B] Get: 113 http://deb.debian.org/debian unstable/main i386 libdrm2 i386 2.4.120-2 [41.4 kB] Get: 114 http://deb.debian.org/debian unstable/main i386 libglapi-mesa i386 24.0.4-1 [36.0 kB] Get: 115 http://deb.debian.org/debian unstable/main i386 libx11-xcb1 i386 2:1.8.7-1 [232 kB] Get: 116 http://deb.debian.org/debian unstable/main i386 libxcb-dri2-0 i386 1.15-1 [107 kB] Get: 117 http://deb.debian.org/debian unstable/main i386 libxcb-dri3-0 i386 1.15-1 [107 kB] Get: 118 http://deb.debian.org/debian unstable/main i386 libxcb-glx0 i386 1.15-1 [124 kB] Get: 119 http://deb.debian.org/debian unstable/main i386 libxcb-present0 i386 1.15-1 [106 kB] Get: 120 http://deb.debian.org/debian unstable/main i386 libxcb-randr0 i386 1.15-1 [118 kB] Get: 121 http://deb.debian.org/debian unstable/main i386 libxcb-sync1 i386 1.15-1 [109 kB] Get: 122 http://deb.debian.org/debian unstable/main i386 libxcb-xfixes0 i386 1.15-1 [110 kB] Get: 123 http://deb.debian.org/debian unstable/main i386 libxshmfence1 i386 1.3-1 [8976 B] Get: 124 http://deb.debian.org/debian unstable/main i386 libxxf86vm1 i386 1:1.1.4-1+b2 [21.7 kB] Get: 125 http://deb.debian.org/debian unstable/main i386 libvulkan1 i386 1.3.275.0-1 [141 kB] Get: 126 http://deb.debian.org/debian unstable/main i386 libdrm-amdgpu1 i386 2.4.120-2 [24.4 kB] Get: 127 http://deb.debian.org/debian unstable/main i386 libpciaccess0 i386 0.17-3 [53.6 kB] Get: 128 http://deb.debian.org/debian unstable/main i386 libdrm-intel1 i386 2.4.120-2 [66.5 kB] Get: 129 http://deb.debian.org/debian unstable/main i386 libdrm-nouveau2 i386 2.4.120-2 [20.8 kB] Get: 130 http://deb.debian.org/debian unstable/main i386 libdrm-radeon1 i386 2.4.120-2 [23.0 kB] Get: 131 http://deb.debian.org/debian unstable/main i386 libedit2 i386 3.1-20230828-1 [97.5 kB] Get: 132 http://deb.debian.org/debian unstable/main i386 libz3-4 i386 4.8.12-3.1+b2 [7989 kB] Get: 133 http://deb.debian.org/debian unstable/main i386 libllvm17t64 i386 1:17.0.6-9+b1 [27.7 MB] Get: 134 http://deb.debian.org/debian unstable/main i386 libsensors-config all 1:3.6.0-9 [14.6 kB] Get: 135 http://deb.debian.org/debian unstable/main i386 libsensors5 i386 1:3.6.0-9 [35.4 kB] Get: 136 http://deb.debian.org/debian unstable/main i386 libgl1-mesa-dri i386 24.0.4-1 [8454 kB] Get: 137 http://deb.debian.org/debian unstable/main i386 libglx-mesa0 i386 24.0.4-1 [158 kB] Get: 138 http://deb.debian.org/debian unstable/main i386 libglx0 i386 1.7.0-1 [37.8 kB] Get: 139 http://deb.debian.org/debian unstable/main i386 libgl1 i386 1.7.0-1 [82.0 kB] Get: 140 http://deb.debian.org/debian unstable/main i386 libasound2-data all 1.2.11-1 [20.9 kB] Get: 141 http://deb.debian.org/debian unstable/main i386 libasound2t64 i386 1.2.11-1+b1 [395 kB] Get: 142 http://deb.debian.org/debian unstable/main i386 libgif7 i386 5.2.2-1 [45.3 kB] Get: 143 http://deb.debian.org/debian unstable/main i386 x11-common all 1:7.7+23 [252 kB] Get: 144 http://deb.debian.org/debian unstable/main i386 libxtst6 i386 2:1.2.3-1.1 [28.6 kB] Get: 145 http://deb.debian.org/debian unstable/main i386 openjdk-17-jre i386 17.0.11~7ea-1 [184 kB] Get: 146 http://deb.debian.org/debian unstable/main i386 default-jre i386 2:1.17-75 [1056 B] Get: 147 http://deb.debian.org/debian unstable/main i386 openjdk-17-jdk-headless i386 17.0.11~7ea-1 [74.0 MB] Get: 148 http://deb.debian.org/debian unstable/main i386 default-jdk-headless i386 2:1.17-75 [1108 B] Get: 149 http://deb.debian.org/debian unstable/main i386 openjdk-17-jdk i386 17.0.11~7ea-1 [10.4 kB] Get: 150 http://deb.debian.org/debian unstable/main i386 default-jdk i386 2:1.17-75 [1068 B] Get: 151 http://deb.debian.org/debian unstable/main i386 unzip i386 6.0-28 [166 kB] Get: 152 http://deb.debian.org/debian unstable/main i386 java-wrappers all 0.4 [8916 B] Get: 153 http://deb.debian.org/debian unstable/main i386 libhamcrest-java all 2.2-2 [121 kB] Get: 154 http://deb.debian.org/debian unstable/main i386 junit4 all 4.13.2-4 [349 kB] Get: 155 http://deb.debian.org/debian unstable/main i386 libapiguardian-java all 1.1.2-1 [4656 B] Get: 156 http://deb.debian.org/debian unstable/main i386 libopentest4j-java all 1.2.0-4 [9516 B] Get: 157 http://deb.debian.org/debian unstable/main i386 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 158 http://deb.debian.org/debian unstable/main i386 libpicocli-java all 4.6.2-2 [390 kB] Get: 159 http://deb.debian.org/debian unstable/main i386 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 160 http://deb.debian.org/debian unstable/main i386 junit5 all 5.10.1-1 [2458 kB] Get: 161 http://deb.debian.org/debian unstable/main i386 libactivation-java all 1.2.0-2 [84.7 kB] Get: 162 http://deb.debian.org/debian unstable/main i386 libaopalliance-java all 20070526-7 [8572 B] Get: 163 http://deb.debian.org/debian unstable/main i386 libapache-pom-java all 29-2 [5276 B] Get: 164 http://deb.debian.org/debian unstable/main i386 libasm-java all 9.5-1 [387 kB] Get: 165 http://deb.debian.org/debian unstable/main i386 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 166 http://deb.debian.org/debian unstable/main i386 libjaxp1.3-java all 1.3.05-6 [227 kB] Get: 167 http://deb.debian.org/debian unstable/main i386 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 168 http://deb.debian.org/debian unstable/main i386 libcommons-parent-java all 56-1 [10.8 kB] Get: 169 http://deb.debian.org/debian unstable/main i386 libcommons-io-java all 2.11.0-2 [319 kB] Get: 170 http://deb.debian.org/debian unstable/main i386 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 171 http://deb.debian.org/debian unstable/main i386 libxmlgraphics-commons-java all 2.8-2 [623 kB] Get: 172 http://deb.debian.org/debian unstable/main i386 libbatik-java all 1.17+dfsg-1 [3923 kB] Get: 173 http://deb.debian.org/debian unstable/main i386 libbsh-java all 2.0b4-20 [291 kB] Get: 174 http://deb.debian.org/debian unstable/main i386 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 175 http://deb.debian.org/debian unstable/main i386 libcdi-api-java all 1.2-3 [54.3 kB] Get: 176 http://deb.debian.org/debian unstable/main i386 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 177 http://deb.debian.org/debian unstable/main i386 libcommons-beanutils-java all 1.9.4-2 [233 kB] Get: 178 http://deb.debian.org/debian unstable/main i386 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 179 http://deb.debian.org/debian unstable/main i386 libcommons-codec-java all 1.16.0-1 [297 kB] Get: 180 http://deb.debian.org/debian unstable/main i386 libcommons-compress-java all 1.25.0-1 [635 kB] Get: 181 http://deb.debian.org/debian unstable/main i386 libcommons-lang-java all 2.6-10 [273 kB] Get: 182 http://deb.debian.org/debian unstable/main i386 libcommons-configuration-java all 1.10-6 [347 kB] Get: 183 http://deb.debian.org/debian unstable/main i386 libcommons-pool-java all 1.6-5 [109 kB] Get: 184 http://deb.debian.org/debian unstable/main i386 libcommons-dbcp-java all 1.4-8 [157 kB] Get: 185 http://deb.debian.org/debian unstable/main i386 libcommons-digester-java all 1.8.1-6 [137 kB] Get: 186 http://deb.debian.org/debian unstable/main i386 libcommons-lang3-java all 3.14.0-1 [621 kB] Get: 187 http://deb.debian.org/debian unstable/main i386 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 188 http://deb.debian.org/debian unstable/main i386 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 189 http://deb.debian.org/debian unstable/main i386 libslf4j-java all 1.7.32-1 [144 kB] Get: 190 http://deb.debian.org/debian unstable/main i386 libsnappy1v5 i386 1.1.10-1+b1 [29.5 kB] Get: 191 http://deb.debian.org/debian unstable/main i386 libsnappy-jni i386 1.1.10.5-1 [6668 B] Get: 192 http://deb.debian.org/debian unstable/main i386 libsnappy-java all 1.1.10.5-1 [87.4 kB] Get: 193 http://deb.debian.org/debian unstable/main i386 libxz-java all 1.9-1 [143 kB] Get: 194 http://deb.debian.org/debian unstable/main i386 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 195 http://deb.debian.org/debian unstable/main i386 libplexus-interpolation-java all 1.26-1 [76.8 kB] Get: 196 http://deb.debian.org/debian unstable/main i386 libmaven-archiver-java all 3.6.0-1 [25.1 kB] Get: 197 http://deb.debian.org/debian unstable/main i386 libmaven-shared-utils-java all 3.3.4-1 [138 kB] Get: 198 http://deb.debian.org/debian unstable/main i386 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 199 http://deb.debian.org/debian unstable/main i386 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 200 http://deb.debian.org/debian unstable/main i386 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 201 http://deb.debian.org/debian unstable/main i386 libguava-java all 32.0.1-1 [2708 kB] Get: 202 http://deb.debian.org/debian unstable/main i386 libguice-java all 4.2.3-2 [1435 kB] Get: 203 http://deb.debian.org/debian unstable/main i386 libmaven-parent-java all 35-1 [6140 B] Get: 204 http://deb.debian.org/debian unstable/main i386 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 205 http://deb.debian.org/debian unstable/main i386 libmaven-resolver-java all 1.6.3-1 [548 kB] Get: 206 http://deb.debian.org/debian unstable/main i386 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 207 http://deb.debian.org/debian unstable/main i386 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 208 http://deb.debian.org/debian unstable/main i386 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 209 http://deb.debian.org/debian unstable/main i386 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 210 http://deb.debian.org/debian unstable/main i386 libsisu-inject-java all 0.3.4-2 [347 kB] Get: 211 http://deb.debian.org/debian unstable/main i386 libsisu-plexus-java all 0.3.4-3 [181 kB] Get: 212 http://deb.debian.org/debian unstable/main i386 libmaven3-core-java all 3.8.7-2 [1573 kB] Get: 213 http://deb.debian.org/debian unstable/main i386 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 214 http://deb.debian.org/debian unstable/main i386 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 215 http://deb.debian.org/debian unstable/main i386 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 216 http://deb.debian.org/debian unstable/main i386 libcommons-text-java all 1.11.0-1 [217 kB] Get: 217 http://deb.debian.org/debian unstable/main i386 libcommons-validator-java all 1:1.7-1 [181 kB] Get: 218 http://deb.debian.org/debian unstable/main i386 libjaxen-java all 1.1.6-4 [214 kB] Get: 219 http://deb.debian.org/debian unstable/main i386 libdom4j-java all 2.1.4-1 [312 kB] Get: 220 http://deb.debian.org/debian unstable/main i386 libhttpcore-java all 4.4.16-1 [636 kB] Get: 221 http://deb.debian.org/debian unstable/main i386 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 222 http://deb.debian.org/debian unstable/main i386 libdoxia-core-java all 1.12.0-1 [213 kB] Get: 223 http://deb.debian.org/debian unstable/main i386 libfontbox2-java all 2.0.29-1 [1510 kB] Get: 224 http://deb.debian.org/debian unstable/main i386 libqdox-java all 1.12.1-3 [172 kB] Get: 225 http://deb.debian.org/debian unstable/main i386 libfop-java all 1:2.8-3 [10.1 MB] Get: 226 http://deb.debian.org/debian unstable/main i386 libitext1-java all 1.4-7 [1257 kB] Get: 227 http://deb.debian.org/debian unstable/main i386 libxbean-reflect-java all 4.5-8 [133 kB] Get: 228 http://deb.debian.org/debian unstable/main i386 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 229 http://deb.debian.org/debian unstable/main i386 libdoxia-java all 1.12.0-1 [459 kB] Get: 230 http://deb.debian.org/debian unstable/main i386 libmaven-reporting-api-java all 3.1.1-1 [7240 B] Get: 231 http://deb.debian.org/debian unstable/main i386 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB] Get: 232 http://deb.debian.org/debian unstable/main i386 velocity all 1.7-7 [431 kB] Get: 233 http://deb.debian.org/debian unstable/main i386 libplexus-velocity-java all 1.2-3.1 [10.5 kB] Get: 234 http://deb.debian.org/debian unstable/main i386 liboro-java all 2.0.8a-14 [70.5 kB] Get: 235 http://deb.debian.org/debian unstable/main i386 libvelocity-tools-java all 2.0-9 [311 kB] Get: 236 http://deb.debian.org/debian unstable/main i386 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 237 http://deb.debian.org/debian unstable/main i386 libxerces2-java all 2.12.2-1 [1440 kB] Get: 238 http://deb.debian.org/debian unstable/main i386 libxalan2-java all 2.7.2-4 [3419 kB] Get: 239 http://deb.debian.org/debian unstable/main i386 libdoxia-sitetools-java all 1.11.1-1 [202 kB] Get: 240 http://deb.debian.org/debian unstable/main i386 libel-api-java all 3.0.0-3 [64.9 kB] Get: 241 http://deb.debian.org/debian unstable/main i386 libjansi-java all 2.4.1-2 [100 kB] Get: 242 http://deb.debian.org/debian unstable/main i386 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 243 http://deb.debian.org/debian unstable/main i386 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 244 http://deb.debian.org/debian unstable/main i386 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 245 http://deb.debian.org/debian unstable/main i386 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 246 http://deb.debian.org/debian unstable/main i386 libjetty9-java all 9.4.53-1 [2982 kB] Get: 247 http://deb.debian.org/debian unstable/main i386 libjgraph-java all 5.12.4.2+dfsg-7 [207 kB] Get: 248 http://deb.debian.org/debian unstable/main i386 libjgrapht0.8-java all 0.8.3-6 [214 kB] Get: 249 http://deb.debian.org/debian unstable/main i386 libjgrapht0.8-java-doc all 0.8.3-6 [379 kB] Get: 250 http://deb.debian.org/debian unstable/main i386 libjsoup-java all 1.15.3-1 [431 kB] Get: 251 http://deb.debian.org/debian unstable/main i386 libjtidy-java all 7+svn20110807-5 [250 kB] Get: 252 http://deb.debian.org/debian unstable/main i386 libmaven-common-artifact-filters-java all 3.3.2-1 [48.2 kB] Get: 253 http://deb.debian.org/debian unstable/main i386 libmaven-artifact-transfer-java all 0.13.1-2 [158 kB] Get: 254 http://deb.debian.org/debian unstable/main i386 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB] Get: 255 http://deb.debian.org/debian unstable/main i386 libmaven-shared-incremental-java all 1.1-4 [9924 B] Get: 256 http://deb.debian.org/debian unstable/main i386 libplexus-compiler-java all 2.12.1-2 [99.0 kB] Get: 257 http://deb.debian.org/debian unstable/main i386 libqdox2-java all 2.0.3-1 [296 kB] Get: 258 http://deb.debian.org/debian unstable/main i386 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 259 http://deb.debian.org/debian unstable/main i386 libmaven-compiler-plugin-java all 3.10.1-2 [59.0 kB] Get: 260 http://deb.debian.org/debian unstable/main i386 libplexus-build-api-java all 0.0.7-4 [10.3 kB] Get: 261 http://deb.debian.org/debian unstable/main i386 libmaven-filtering-java all 3.3.0-1 [50.2 kB] Get: 262 http://deb.debian.org/debian unstable/main i386 libmaven-invoker-java all 3.2.0-1 [28.1 kB] Get: 263 http://deb.debian.org/debian unstable/main i386 libplexus-interactivity-api-java all 1.1-2 [11.0 kB] Get: 264 http://deb.debian.org/debian unstable/main i386 libmaven-javadoc-plugin-java all 3.4.1-3 [454 kB] Get: 265 http://deb.debian.org/debian unstable/main i386 libmaven-reporting-impl-java all 3.2.0-2 [15.2 kB] Get: 266 http://deb.debian.org/debian unstable/main i386 libplexus-container-default1.5-java all 2.1.1-1 [4476 B] Get: 267 http://deb.debian.org/debian unstable/main i386 libplexus-ant-factory-java all 1.0~alpha2.1-4 [11.4 kB] Get: 268 http://deb.debian.org/debian unstable/main i386 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B] Get: 269 http://deb.debian.org/debian unstable/main i386 libmaven-plugin-tools-java all 3.7.1-1 [265 kB] Get: 270 http://deb.debian.org/debian unstable/main i386 libmaven-reporting-exec-java all 1.6.0-1 [26.8 kB] Get: 271 http://deb.debian.org/debian unstable/main i386 libmaven-resources-plugin-java all 3.3.0-1 [28.4 kB] Get: 272 http://deb.debian.org/debian unstable/main i386 libmaven-site-plugin-java all 3.12.1-2 [107 kB] Get: 273 http://deb.debian.org/debian unstable/main i386 libsurefire-java all 2.22.3-2 [1169 kB] Get: 274 http://deb.debian.org/debian unstable/main i386 libwagon-file-java all 3.5.3-1 [8388 B] Get: 275 http://deb.debian.org/debian unstable/main i386 libwagon-http-shaded-java all 3.5.3-1 [1341 kB] Get: 276 http://deb.debian.org/debian unstable/main i386 libxml2-utils i386 2.9.14+dfsg-1.3+b2 [99.4 kB] Get: 277 http://deb.debian.org/debian unstable/main i386 maven all 3.8.7-2 [19.3 kB] Get: 278 http://deb.debian.org/debian unstable/main i386 maven-repo-helper all 1.11 [142 kB] Get: 279 http://deb.debian.org/debian unstable/main i386 maven-debian-helper all 2.6.4 [108 kB] Fetched 264 MB in 7s (36.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sgml-base. (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 ... 19703 files and directories currently installed.) Preparing to unpack .../000-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:i386. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-4_i386.deb ... Unpacking libproc2-0:i386 (2:4.0.4-4) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.4-4_i386.deb ... 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Setting up libcdi-api-java (1.2-3) ... Setting up libsnappy-jni (1.1.10.5-1) ... Setting up libxml2:i386 (2.9.14+dfsg-1.3+b2) ... 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 (1.13.1-1) ... Setting up libwagon-provider-api-java (3.5.3-1) ... Setting up libcommons-dbcp-java (1.4-8) ... Setting up libxdmcp6:i386 (1:1.1.2-3) ... Setting up libxcb1:i386 (1.15-1) ... Setting up gettext (0.21-14+b1) ... Setting up libjetty9-java (9.4.53-1) ... Setting up libxcb-xfixes0:i386 (1.15-1) ... Setting up java-wrappers (0.4) ... Setting up libatk1.0-0t64:i386 (2.52.0-1) ... Setting up libplexus-languages-java (1.1.1-2) ... Setting up libjgrapht0.8-java (0.8.3-6) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:i386 (1.15-1) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libxcb-glx0:i386 (1.15-1) ... Setting up libmaven-parent-java (35-1) ... Setting up libedit2:i386 (3.1-20230828-1) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:i386 (0.8-13+b2) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libsisu-inject-java (0.3.4-2) ... Setting up libnss3:i386 (2:3.99-1) ... Setting up libxcb-shm0:i386 (1.15-1) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libxcb-present0:i386 (1.15-1) ... Setting up dh-autoreconf (20) ... Setting up libthai0:i386 (0.1.29-2) ... 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 libllvm17t64:i386 (1:17.0.6-9+b1) ... Setting up libfreetype6:i386 (2.13.2+dfsg-1+b2) ... Setting up libxcb-sync1:i386 (1.15-1) ... Setting up libxalan2-java (2.7.2-4) ... Setting up shared-mime-info (2.4-4) ... Setting up libgssapi-krb5-2:i386 (1.20.1-6+b1) ... Setting up libcommons-lang3-java (3.14.0-1) ... Setting up libxcb-dri2-0:i386 (1.15-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libdrm2:i386 (2.4.120-2) ... Setting up libmaven-common-artifact-filters-java (3.3.2-1) ... Setting up groff-base (1.23.0-3+b1) ... Setting up libxcb-randr0:i386 (1.15-1) ... Setting up libcommons-beanutils-java (1.9.4-2) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libx11-6:i386 (2:1.8.7-1) ... Setting up libharfbuzz0b:i386 (8.3.0-2+b1) ... Setting up libgdk-pixbuf-2.0-0:i386 (2.42.10+dfsg-3+b2) ... Setting up libsnappy-java (1.1.10.5-1) ... Setting up libfontconfig1:i386 (2.15.0-1.1) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libcommons-configuration-java (1.10-6) ... Setting up libwagon-file-java (3.5.3-1) ... Setting up libxml2-utils (2.9.14+dfsg-1.3+b2) ... Setting up libcommons-codec-java (1.16.0-1) ... Setting up libxcomposite1:i386 (1:0.4.5-1) ... Setting up libavahi-client3:i386 (0.8-13+b2) ... Setting up libdrm-amdgpu1:i386 (2.4.120-2) ... Setting up libxcb-dri3-0:i386 (1.15-1) ... Setting up gtk-update-icon-cache (3.24.41-4) ... Setting up libx11-xcb1:i386 (2:1.8.7-1) ... Setting up velocity (1.7-7) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libdrm-nouveau2:i386 (2.4.120-2) ... Setting up libxdamage1:i386 (1:1.1.6-1) ... Setting up libxrender1:i386 (1:0.9.10-1.1) ... Setting up libcommons-compress-java (1.25.0-1) ... Setting up libcommons-io-java (2.11.0-2) ... Setting up libdrm-radeon1:i386 (2.4.120-2) ... Setting up libcommons-digester-java (1.8.1-6) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:i386 (1.52.1+ds-1) ... Setting up libdrm-intel1:i386 (2.4.120-2) ... Setting up libgl1-mesa-dri:i386 (24.0.4-1) ... Setting up libxext6:i386 (2:1.3.4-1+b1) ... Setting up libxmlgraphics-commons-java (2.8-2) ... Setting up man-db (2.12.0-4) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:i386 (1.18.0-3) ... Setting up libxxf86vm1:i386 (1:1.1.4-1+b2) ... Setting up libmaven-filtering-java (3.3.0-1) ... Setting up libmaven-resolver-java (1.6.3-1) ... Setting up adwaita-icon-theme (46.0-1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up libxfixes3:i386 (1:6.0.0-2) ... Setting up libxinerama1:i386 (2:1.1.4-3) ... Setting up libxrandr2:i386 (2:1.5.4-1) ... Setting up openjdk-17-jre-headless:i386 (17.0.11~7ea-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libhttpclient-java (4.5.14-1) ... Setting up libmaven-shared-utils-java (3.3.4-1) ... Setting up libpangoft2-1.0-0:i386 (1.52.1+ds-1) ... Setting up libmaven-resources-plugin-java (3.3.0-1) ... Setting up libcups2t64:i386 (2.4.7-1.2+b1) ... Setting up libpangocairo-1.0-0:i386 (1.52.1+ds-1) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up libglx-mesa0:i386 (24.0.4-1) ... Setting up libxi6:i386 (2:1.8.1-1) ... Setting up libglx0:i386 (1.7.0-1) ... Setting up libcommons-validator-java (1:1.7-1) ... Setting up libxtst6:i386 (2:1.2.3-1.1) ... Setting up libbatik-java (1.17+dfsg-1) ... Setting up libxcursor1:i386 (1:1.2.1-1) ... Setting up libmaven-invoker-java (3.2.0-1) ... Setting up debhelper (13.15.3) ... Setting up libgl1:i386 (1.7.0-1) ... Setting up libgtk2.0-0t64:i386 (2.24.33-4) ... Setting up libmaven-clean-plugin-java (3.2.0-2) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libfop-java (1:2.8-3) ... Setting up libmaven-archiver-java (3.6.0-1) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libguava-java (32.0.1-1) ... Setting up libplexus-container-default-java (2.1.1-1) ... Setting up libguice-java (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-interactivity-api-java (1.1-2) ... Setting up libplexus-velocity-java (1.2-3.1) ... Setting up libmaven3-core-java (3.8.7-2) ... Setting up libmaven-shared-incremental-java (1.1-4) ... 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 (2.12.1-2) ... Setting up libmaven-compiler-plugin-java (3.10.1-2) ... Setting up libmaven-artifact-transfer-java (0.13.1-2) ... 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 (1.11.0-1) ... Setting up libdoxia-core-java (1.12.0-1) ... Setting up libdoxia-java (1.12.0-1) ... Setting up libmaven-reporting-api-java (3.1.1-1) ... Setting up libmaven-reporting-exec-java (1.6.0-1) ... Processing triggers for libc-bin (2.37-15.1) ... 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 (3.8.7-2) ... update-alternatives: using /usr/share/maven/bin/mvn to provide /usr/bin/mvn (mvn) in auto mode Setting up openjdk-17-jdk-headless:i386 (17.0.11~7ea-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up ant (1.10.14-1) ... Setting up junit4 (4.13.2-4) ... Setting up default-jre-headless (2:1.17-75) ... Setting up openjdk-17-jre:i386 (17.0.11~7ea-1) ... Setting up default-jre (2:1.17-75) ... Setting up openjdk-17-jdk:i386 (17.0.11~7ea-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up libplexus-ant-factory-java (1.0~alpha2.1-4) ... Setting up default-jdk-headless (2:1.17-75) ... Setting up junit5 (5.10.1-1) ... Setting up default-jdk (2:1.17-75) ... Processing triggers for sgml-base (1.31) ... Setting up libvelocity-tools-java (2.0-9) ... Setting up libdoxia-sitetools-java (1.11.1-1) ... Setting up libmaven-site-plugin-java (3.12.1-2) ... Setting up libmaven-javadoc-plugin-java (3.4.1-3) ... Setting up libmaven-reporting-impl-java (3.2.0-2) ... Setting up libmaven-plugin-tools-java (3.7.1-1) ... Setting up libsurefire-java (2.22.3-2) ... Setting up maven-debian-helper (2.6.4) ... 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/45107/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/45107/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-1_source.changes dpkg-buildpackage: info: source package biojava-live dpkg-buildpackage: info: source version 1:1.9.7+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Pierre Gruet 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 javadoc:jar javadoc:aggregate -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] [WARNING] The POM for org.apache.maven.plugins:maven-install-plugin:jar:2.4 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-install-plugin:2.4: Plugin org.apache.maven.plugins:maven-install-plugin:2.4 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-install-plugin:jar:2.4 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-deploy-plugin:2.7: Plugin org.apache.maven.plugins:maven-deploy-plugin:2.7 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-antrun-plugin:1.3: Plugin org.apache.maven.plugins:maven-antrun-plugin:1.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5: Plugin org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-dependency-plugin:2.8: Plugin org.apache.maven.plugins:maven-dependency-plugin:2.8 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-install-plugin:jar:2.4 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-install-plugin:2.4: Plugin org.apache.maven.plugins:maven-install-plugin:2.4 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-install-plugin:jar:2.4 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-deploy-plugin:2.7: Plugin org.apache.maven.plugins:maven-deploy-plugin:2.7 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-antrun-plugin:1.3: Plugin org.apache.maven.plugins:maven-antrun-plugin:1.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5: Plugin org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-dependency-plugin:2.8: Plugin org.apache.maven.plugins:maven-dependency-plugin:2.8 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before. [INFO] [INFO] ---------------------< org.biojava:biojava-legacy >--------------------- [INFO] Building biojava-legacy 1.9.7 [1/9] [INFO] --------------------------------[ pom ]--------------------------------- [WARNING] The POM for org.apache.maven.plugins:maven-install-plugin:jar:2.4 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-install-plugin:2.4: Plugin org.apache.maven.plugins:maven-install-plugin:2.4 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-install-plugin:jar:2.4 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-deploy-plugin:2.7: Plugin org.apache.maven.plugins:maven-deploy-plugin:2.7 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-antrun-plugin:1.3: Plugin org.apache.maven.plugins:maven-antrun-plugin:1.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5: Plugin org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-dependency-plugin:2.8: Plugin org.apache.maven.plugins:maven-dependency-plugin:2.8 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before. [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-legacy --- [INFO] Not executing Javadoc as the project is not a Java classpath-capable package [INFO] [INFO] ------------------------< org.biojava:bytecode >------------------------ [INFO] Building bytecode 1.9.7 [2/9] [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The POM for org.apache.maven.plugins:maven-install-plugin:jar:2.4 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-install-plugin:2.4: Plugin org.apache.maven.plugins:maven-install-plugin:2.4 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-install-plugin:jar:2.4 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-deploy-plugin:2.7: Plugin org.apache.maven.plugins:maven-deploy-plugin:2.7 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-antrun-plugin:1.3: Plugin org.apache.maven.plugins:maven-antrun-plugin:1.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5: Plugin org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-dependency-plugin:2.8: Plugin org.apache.maven.plugins:maven-dependency-plugin:2.8 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0: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:3.10.1:compile (default-compile) @ bytecode --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 44 source files to /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/target/classes [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/MethodRootContext.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/MethodRootContext.java: Recompile with -Xlint:removal for details. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/ConstantPool.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/ConstantPool.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0: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:3.10.1: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] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ bytecode --- [INFO] Adding the --ignore-source-errors option [INFO] No previous run data found, generating javadoc. [WARNING] Javadoc Warnings [WARNING] warning: The -footer option is no longer supported and will be ignored. [WARNING] It may be removed in a future release. [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/ByteCode.java:1347: warning: @param argument "lockVar" is not a parameter name. [WARNING] * @param lockVar Label for the local variable to lock on [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/package.html:146: warning: invalid input: '<' [WARNING] This will need a constructor. Remember, constructors have the name >init<:, [WARNING] ^ [WARNING] 3 warnings [INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/target/bytecode-1.9.7-javadoc.jar [INFO] [INFO] --------------------------< org.biojava:core >-------------------------- [INFO] Building core 1.9.7 [3/9] [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The POM for org.apache.maven.plugins:maven-install-plugin:jar:2.4 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-install-plugin:2.4: Plugin org.apache.maven.plugins:maven-install-plugin:2.4 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-install-plugin:jar:2.4 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-deploy-plugin:2.7: Plugin org.apache.maven.plugins:maven-deploy-plugin:2.7 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-antrun-plugin:1.3: Plugin org.apache.maven.plugins:maven-antrun-plugin:1.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5: Plugin org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-dependency-plugin:2.8: Plugin org.apache.maven.plugins:maven-dependency-plugin:2.8 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ core --- [INFO] Copying 29 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ core --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1063 source files to /build/reproducible-path/biojava-live-1.9.7+dfsg/core/target/classes [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/bio/symbol/SuffixTree.java: Some input files 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/bio/symbol/SuffixTree.java: Recompile with -Xlint:removal for details. [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:3.3.0:testResources (default-testResources) @ core --- [INFO] Copying 53 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ core --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 148 source files to /build/reproducible-path/biojava-live-1.9.7+dfsg/core/target/test-classes [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/biojavax/ontology/SimpleComparableTermTest.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/ontology/SimpleComparableTermTest.java: Recompile with -Xlint:removal 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] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ core --- [INFO] Adding the --ignore-source-errors option [INFO] No previous run data found, generating javadoc. [WARNING] Javadoc Warnings [WARNING] warning: The -footer option is no longer supported and will be ignored. [WARNING] It may be removed in a future release. [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/proteomics/aaindex/AAindexStreamReader.java:55: warning: invalid input: '<' [WARNING] * for (int i = 1; i <= symbols.length(); i++) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/AbstractAlphabet.java:51: warning: invalid input: '<' [WARNING] * This provides the frame-work for maintaining the SymbolParser <-> name [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&' [WARNING] * be transient and lazily instantiated. Be sure to register & unregister the [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&' [WARNING] * be transient and lazily instantiated. Be sure to register & unregister the [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&' [WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&' [WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&' [WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&' [WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&' [WARNING] * be transient and lazily instantiated. Be sure to register & unregister the [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&' [WARNING] * be transient and lazily instantiated. Be sure to register & unregister the [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&' [WARNING] * be transient and lazily instantiated. Be sure to register & unregister the [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&' [WARNING] * be transient and lazily instantiated. Be sure to register & unregister the [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/AlphabetIndex.java:60: warning: invalid input: '&' [WARNING] * The previous & changed fields should be arrays of symbols in the order they [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bibliography/BibRefQuery.java:625: warning: invalid input: '&' [WARNING] * @param properties FIXME: docs & params out of sync [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&' [WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&' [WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/stats/svm/tools/ClassifierExample.java:150: warning: invalid input: '&' [WARNING] * An extention of JComponent that contains the points & encapsulates the [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/stats/svm/tools/ClassifierExample.java:150: warning: invalid input: '&' [WARNING] * An extention of JComponent that contains the points & encapsulates the [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/stats/svm/tools/ClassifierExample.java:331: warning: invalid input: '&' [WARNING] * Hooks up the mouse listener & cursor. [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/stats/svm/tools/ClassifierExample.java:332: warning: invalid input: '&' [WARNING] * Chooses default colors & Shapes. [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&' [WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&' [WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/DNATools.java:255: warning: invalid input: '&' [WARNING] * The index for a symbol is stable accross virtual machines & [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/DNATools.java:284: warning: invalid input: '&' [WARNING] * The index for a symbol is stable accross virtual machines & [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&cvsroot' [WARNING] * the odda formats specification.

[WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&content' [WARNING] * the odda formats specification.

[WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:486: warning: invalid input: '<' [WARNING] * <123 or >123 [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:492: warning: invalid input: '<' [WARNING] * <123..567 or 123..>567 or <123..>567 [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:492: warning: invalid input: '<' [WARNING] * <123..567 or 123..>567 or <123..>567 [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:503: warning: invalid input: '<' [WARNING] * @param sb a StringBuffer123 [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/EmblLikeLocationParser.java:55: warning: invalid input: '<' [WARNING] * <123..567 or 123..>567 or <123..>567 [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/EmblLikeLocationParser.java:55: warning: invalid input: '<' [WARNING] * <123..567 or 123..>567 or <123..>567 [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/EmblProcessor.java:47: warning: invalid input: '<' [WARNING] * <123 or >123 [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/EmblProcessor.java:53: warning: invalid input: '<' [WARNING] * <123..567 or 123..>567 or <123..>567 [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/EmblProcessor.java:53: warning: invalid input: '<' [WARNING] * <123..567 or 123..>567 or <123..>567 [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&' [WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&' [WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&cvsroot' [WARNING] * the odda formats specification.

[WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&content' [WARNING] * the odda formats specification.

[WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/FeatureFilter.java:1657: warning: invalid input: '<' [WARNING] * SimilarityPairFeature and its score is <= filter's minimum [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/FeatureFilter.java:1657: warning: invalid input: '<' [WARNING] * SimilarityPairFeature and its score is <= filter's minimum [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&' [WARNING] * be transient and lazily instantiated. Be sure to register & unregister the [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&cvsroot' [WARNING] * the odda formats specification.

[WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&content' [WARNING] * the odda formats specification.

[WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/FuzzyPointLocation.java:34: warning: invalid input: '<' [WARNING] * the '<123' or '>123' type, which represent an unbounded location, [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:486: warning: invalid input: '<' [WARNING] * <123 or >123 [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:492: warning: invalid input: '<' [WARNING] * <123..567 or 123..>567 or <123..>567 [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:492: warning: invalid input: '<' [WARNING] * <123..567 or 123..>567 or <123..>567 [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:503: warning: invalid input: '<' [WARNING] * @param sb a StringBuffer delete transitions allowed [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/blast2html/HTMLRenderer.java:116: warning: invalid input: '<' [WARNING] * formats specification.

[WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&content' [WARNING] * the odda formats specification.

[WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&cvsroot' [WARNING] * the odda formats specification.

[WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&content' [WARNING] * the odda formats specification.

[WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&cvsroot' [WARNING] * the odda formats specification.

[WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&content' [WARNING] * the odda formats specification.

[WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&' [WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&' [WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&' [WARNING] * be transient and lazily instantiated. Be sure to register & unregister the [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&' [WARNING] * be transient and lazily instantiated. Be sure to register & unregister the [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/NucleotideTools.java:380: warning: invalid input: '&' [WARNING] * The index for a symbol is stable accross virtual machines & [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/NucleotideTools.java:442: warning: invalid input: '&' [WARNING] * The index for a symbol is stable accross virtual machines & [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:49: warning: invalid input: '&view' [WARNING] * http://geneontology.cvs.sourceforge.net/geneontology/go-dev/java/oboedit/sources/org/geneontology/oboedit/dataadapter/OBOParseEngine.java?revision=1.10&view=markup [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&' [WARNING] * be transient and lazily instantiated. Be sure to register & unregister the [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/process/OutputHandler.java:33: warning: invalid usage of tag {@linkplain java.lang.Process#getOutputStream()() [WARNING] * {@linkplain java.lang.Process#getOutputStream()() STDOUT} output and/or the [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&' [WARNING] * be transient and lazily instantiated. Be sure to register & unregister the [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:486: warning: invalid input: '<' [WARNING] * <123 or >123 [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:492: warning: invalid input: '<' [WARNING] * <123..567 or 123..>567 or <123..>567 [WARNING] ^ [WARNING] 100 warnings [INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/core/target/core-1.9.7-javadoc.jar [INFO] [INFO] -----------------------< org.biojava:alignment >------------------------ [INFO] Building alignment 1.9.7 [4/9] [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The POM for org.apache.maven.plugins:maven-install-plugin:jar:2.4 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-install-plugin:2.4: Plugin org.apache.maven.plugins:maven-install-plugin:2.4 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-install-plugin:jar:2.4 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-deploy-plugin:2.7: Plugin org.apache.maven.plugins:maven-deploy-plugin:2.7 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-antrun-plugin:1.3: Plugin org.apache.maven.plugins:maven-antrun-plugin:1.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5: Plugin org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-dependency-plugin:2.8: Plugin org.apache.maven.plugins:maven-dependency-plugin:2.8 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ alignment --- [INFO] Copying 89 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ alignment --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 14 source files to /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/target/classes [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/main/java/org/biojava/bio/alignment/SubstitutionMatrix.java: /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/main/java/org/biojava/bio/alignment/SubstitutionMatrix.java uses or overrides a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/main/java/org/biojava/bio/alignment/SubstitutionMatrix.java: Recompile with -Xlint:removal for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ alignment --- [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ alignment --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 5 source files to /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/target/test-classes [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] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ alignment --- [INFO] Adding the --ignore-source-errors option [INFO] No previous run data found, generating javadoc. [WARNING] Javadoc Warnings [WARNING] warning: The -footer option is no longer supported and will be ignored. [WARNING] It may be removed in a future release. [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/main/java/org/biojava/bio/alignment/AlignmentAlgorithm.java:39: warning: invalid input: '<' [WARNING] * @author Andreas Dräger [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:217: warning: @param argument "queryLength" is not a parameter name. [WARNING] * @param queryLength [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/main/java/org/biojava/bio/alignment/EditableAlignment.java:35: warning: invalid input: '<' [WARNING] * shifted to the right with offset > 1 to the left with offset < [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/main/java/org/biojava/bio/alignment/SubstitutionMatrix.java:65: warning: invalid input: '<' [WARNING] * @author Andreas Dräger [WARNING] ^ [WARNING] 5 warnings [INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/target/alignment-1.9.7-javadoc.jar [INFO] [INFO] -------------------------< org.biojava:biosql >------------------------- [INFO] Building biosql 1.9.7 [5/9] [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The POM for org.apache.maven.plugins:maven-install-plugin:jar:2.4 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-install-plugin:2.4: Plugin org.apache.maven.plugins:maven-install-plugin:2.4 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-install-plugin:jar:2.4 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-deploy-plugin:2.7: Plugin org.apache.maven.plugins:maven-deploy-plugin:2.7 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-antrun-plugin:1.3: Plugin org.apache.maven.plugins:maven-antrun-plugin:1.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5: Plugin org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-dependency-plugin:2.8: Plugin org.apache.maven.plugins:maven-dependency-plugin:2.8 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0: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:3.10.1:compile (default-compile) @ biosql --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 35 source files to /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/target/classes [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/BioSQLSequenceDB.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.java: Recompile with -Xlint:removal 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:3.3.0: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:3.10.1:testCompile (default-testCompile) @ biosql --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 2 source files to /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/target/test-classes [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] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biosql --- [INFO] Adding the --ignore-source-errors option [INFO] No previous run data found, generating javadoc. [WARNING] Javadoc Warnings [WARNING] warning: The -footer option is no longer supported and will be ignored. [WARNING] It may be removed in a future release. [WARNING] 1 warning [INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/target/biosql-1.9.7-javadoc.jar [INFO] [INFO] -------------------------< org.biojava:blast >-------------------------- [INFO] Building blast 1.9.7 [6/9] [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The POM for org.apache.maven.plugins:maven-install-plugin:jar:2.4 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-install-plugin:2.4: Plugin org.apache.maven.plugins:maven-install-plugin:2.4 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-install-plugin:jar:2.4 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-deploy-plugin:2.7: Plugin org.apache.maven.plugins:maven-deploy-plugin:2.7 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-antrun-plugin:1.3: Plugin org.apache.maven.plugins:maven-antrun-plugin:1.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5: Plugin org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-dependency-plugin:2.8: Plugin org.apache.maven.plugins:maven-dependency-plugin:2.8 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ blast --- [INFO] Copying 3 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ blast --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 56 source files to /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/target/classes [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/src/main/java/org/biojava/bio/program/sax/GenericSAXParserTest.java: /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/src/main/java/org/biojava/bio/program/sax/GenericSAXParserTest.java uses or overrides a deprecated API. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/src/main/java/org/biojava/bio/program/sax/GenericSAXParserTest.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:3.3.0:testResources (default-testResources) @ blast --- [INFO] Copying 22 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ blast --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 19 source files to /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/target/test-classes [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] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ blast --- [INFO] Adding the --ignore-source-errors option [INFO] No previous run data found, generating javadoc. [WARNING] Javadoc Warnings [WARNING] warning: The -footer option is no longer supported and will be ignored. [WARNING] It may be removed in a future release. [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/src/main/java/org/biojava/bio/program/BlastLikeToXMLConverter.java:61: warning: invalid input: '<' [WARNING] * * looks something like then, [WARNING] ^ [WARNING] 2 warnings [INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/target/blast-1.9.7-javadoc.jar [INFO] [INFO] -----------------------< org.biojava:sequencing >----------------------- [INFO] Building sequencing 1.9.7 [7/9] [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The POM for org.apache.maven.plugins:maven-install-plugin:jar:2.4 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-install-plugin:2.4: Plugin org.apache.maven.plugins:maven-install-plugin:2.4 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-install-plugin:jar:2.4 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-deploy-plugin:2.7: Plugin org.apache.maven.plugins:maven-deploy-plugin:2.7 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-antrun-plugin:1.3: Plugin org.apache.maven.plugins:maven-antrun-plugin:1.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5: Plugin org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-dependency-plugin:2.8: Plugin org.apache.maven.plugins:maven-dependency-plugin:2.8 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0: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:3.10.1:compile (default-compile) @ sequencing --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 33 source files to /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/target/classes [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/scf/SCF.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/program/scf/SCF.java: Recompile with -Xlint:removal 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:3.3.0:testResources (default-testResources) @ sequencing --- [INFO] Copying 77 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ sequencing --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 15 source files to /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/target/test-classes [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] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ sequencing --- [INFO] Adding the --ignore-source-errors option [INFO] No previous run data found, generating javadoc. [WARNING] Javadoc Warnings [WARNING] warning: The -footer option is no longer supported and will be ignored. [WARNING] It may be removed in a future release. [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.java:1074: warning: invalid input: '&' [WARNING] * Default value: {@link BasicStroke} with width 1.0, default cap & join. [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/ChromatogramTools.java:67: warning: invalid input: '<' [WARNING] * for (int i = m ; i < n ; i++) [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/program/scf/SCF.java:169: warning: invalid input: '&returned' [WARNING] * PROB_UNDERCALL are just reversed &returned. [WARNING] ^ [WARNING] 4 warnings [INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/target/sequencing-1.9.7-javadoc.jar [INFO] [INFO] --------------------------< org.biojava:gui >--------------------------- [INFO] Building gui 1.9.7 [8/9] [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The POM for org.apache.maven.plugins:maven-install-plugin:jar:2.4 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-install-plugin:2.4: Plugin org.apache.maven.plugins:maven-install-plugin:2.4 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-install-plugin:jar:2.4 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-deploy-plugin:2.7: Plugin org.apache.maven.plugins:maven-deploy-plugin:2.7 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-antrun-plugin:1.3: Plugin org.apache.maven.plugins:maven-antrun-plugin:1.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5: Plugin org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-dependency-plugin:2.8: Plugin org.apache.maven.plugins:maven-dependency-plugin:2.8 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 has not been downloaded from it before. [WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0: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:3.10.1:compile (default-compile) @ gui --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 99 source files to /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/target/classes [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 or override a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/LineInfo.java: Recompile with -Xlint:removal 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:3.3.0: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:3.10.1: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] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ gui --- [INFO] Adding the --ignore-source-errors option [INFO] No previous run data found, generating javadoc. [WARNING] Javadoc Warnings [WARNING] warning: The -footer option is no longer supported and will be ignored. [WARNING] It may be removed in a future release. [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/LogoPainter.java:30: warning: invalid input: '&' [WARNING] * calculations for sizes & information and the like. The LogoPainter renders [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/glyph/RectangleGlyph.java:32: warning: invalid input: '<' [WARNING] * @author then, [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&' [WARNING] * be transient and lazily instantiated. Be sure to register & unregister the [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/ByteCode.java:1347: warning: @param argument "lockVar" is not a parameter name. [WARNING] * @param lockVar Label for the local variable to lock on [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.java:1074: warning: invalid input: '&' [WARNING] * Default value: {@link BasicStroke} with width 1.0, default cap & join. [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/ChromatogramTools.java:67: warning: invalid input: '<' [WARNING] * for (int i = m ; i < n ; i++) [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&' [WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&' [WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/stats/svm/tools/ClassifierExample.java:150: warning: invalid input: '&' [WARNING] * An extention of JComponent that contains the points & encapsulates the [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/stats/svm/tools/ClassifierExample.java:150: warning: invalid input: '&' [WARNING] * An extention of JComponent that contains the points & encapsulates the [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/stats/svm/tools/ClassifierExample.java:331: warning: invalid input: '&' [WARNING] * Hooks up the mouse listener & cursor. [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/stats/svm/tools/ClassifierExample.java:332: warning: invalid input: '&' [WARNING] * Chooses default colors & Shapes. [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&' [WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&' [WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/DNATools.java:255: warning: invalid input: '&' [WARNING] * The index for a symbol is stable accross virtual machines & [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/DNATools.java:284: warning: invalid input: '&' [WARNING] * The index for a symbol is stable accross virtual machines & [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/main/java/org/biojava/bio/alignment/EditableAlignment.java:35: warning: invalid input: '<' [WARNING] * shifted to the right with offset > 1 to the left with offset < [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&cvsroot' [WARNING] * the odda formats specification.

[WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&content' [WARNING] * the odda formats specification.

[WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:486: warning: invalid input: '<' [WARNING] * <123 or >123 [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:492: warning: invalid input: '<' [WARNING] * <123..567 or 123..>567 or <123..>567 [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:492: warning: invalid input: '<' [WARNING] * <123..567 or 123..>567 or <123..>567 [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:503: warning: invalid input: '<' [WARNING] * @param sb a StringBuffer123 [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/EmblLikeLocationParser.java:55: warning: invalid input: '<' [WARNING] * <123..567 or 123..>567 or <123..>567 [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/EmblLikeLocationParser.java:55: warning: invalid input: '<' [WARNING] * <123..567 or 123..>567 or <123..>567 [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/EmblProcessor.java:47: warning: invalid input: '<' [WARNING] * <123 or >123 [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/EmblProcessor.java:53: warning: invalid input: '<' [WARNING] * <123..567 or 123..>567 or <123..>567 [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/EmblProcessor.java:53: warning: invalid input: '<' [WARNING] * <123..567 or 123..>567 or <123..>567 [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&' [WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&' [WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&cvsroot' [WARNING] * the odda formats specification.

[WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&content' [WARNING] * the odda formats specification.

[WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&' [WARNING] * be transient and lazily instantiated. Be sure to register & unregister the [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/FeatureFilter.java:1657: warning: invalid input: '<' [WARNING] * SimilarityPairFeature and its score is <= filter's minimum [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/FeatureFilter.java:1657: warning: invalid input: '<' [WARNING] * SimilarityPairFeature and its score is <= filter's minimum [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&' [WARNING] * be transient and lazily instantiated. Be sure to register & unregister the [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&' [WARNING] * be transient and lazily instantiated. Be sure to register & unregister the [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&cvsroot' [WARNING] * the odda formats specification.

[WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&content' [WARNING] * the odda formats specification.

[WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/FuzzyPointLocation.java:34: warning: invalid input: '<' [WARNING] * the '<123' or '>123' type, which represent an unbounded location, [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:486: warning: invalid input: '<' [WARNING] * <123 or >123 [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:492: warning: invalid input: '<' [WARNING] * <123..567 or 123..>567 or <123..>567 [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:492: warning: invalid input: '<' [WARNING] * <123..567 or 123..>567 or <123..>567 [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:503: warning: invalid input: '<' [WARNING] * @param sb a StringBuffer delete transitions allowed [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/blast2html/HTMLRenderer.java:116: warning: invalid input: '<' [WARNING] * formats specification.

[WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&content' [WARNING] * the odda formats specification.

[WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&cvsroot' [WARNING] * the odda formats specification.

[WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&content' [WARNING] * the odda formats specification.

[WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&cvsroot' [WARNING] * the odda formats specification.

[WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&content' [WARNING] * the odda formats specification.

[WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&' [WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&' [WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/LogoPainter.java:30: warning: invalid input: '&' [WARNING] * calculations for sizes & information and the like. The LogoPainter renders [WARNING] ^ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&' [WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) { [WARNING] ^ [WARNING] 100 warnings [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava-legacy 1.9.7: [INFO] [INFO] biojava-legacy ..................................... SUCCESS [ 45.091 s] [INFO] bytecode ........................................... SUCCESS [ 7.063 s] [INFO] core ............................................... SUCCESS [ 54.534 s] [INFO] alignment .......................................... SUCCESS [ 4.252 s] [INFO] biosql ............................................. SUCCESS [ 6.339 s] [INFO] blast .............................................. SUCCESS [ 7.041 s] [INFO] sequencing ......................................... SUCCESS [ 6.986 s] [INFO] gui ................................................ SUCCESS [ 7.933 s] [INFO] phylo .............................................. SUCCESS [ 6.426 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 02:27 min [INFO] Finished at: 2024-04-02T21:18:03Z [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] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] ------------------------< org.biojava:bytecode >------------------------ [INFO] Building bytecode 1.9.7 [2/9] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0: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:3.10.1:compile (default-compile) @ bytecode --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0: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:3.10.1: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] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ core --- [INFO] Copying 29 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ core --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ core --- [INFO] Copying 53 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1: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.seq.FeatureHolderUtilsTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.435 s - in org.biojava.bio.seq.FeatureHolderUtilsTest [INFO] Running org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 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: 0.04 s - in org.biojava.bio.seq.NewSimpleAssemblyTest [INFO] Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 s - in org.biojava.bio.seq.project.ProjectedFeatureHolderTest [INFO] Running org.biojava.bio.seq.MergeFeatureHolderTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.MergeFeatureHolderTest [INFO] Running org.biojava.bio.seq.CircularSequenceTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.seq.CircularSequenceTest [INFO] Running org.biojava.bio.seq.SeqSerializationTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.169 s - in org.biojava.bio.seq.SeqSerializationTest [INFO] Running org.biojava.bio.seq.RNAToolsTest [INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s - in org.biojava.bio.seq.RNAToolsTest [INFO] Running org.biojava.bio.seq.FilterUtilsTest [INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 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.FeatureFilterTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.FeatureFilterTest [INFO] Running org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest [INFO] Running org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest [INFO] Running org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest [INFO] Running org.biojava.bio.seq.db.TestHashSequenceDB [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 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: 0.023 s - in org.biojava.bio.seq.db.EmblCDROMIndexStoreTest [INFO] Running org.biojava.bio.seq.db.HashSequenceDBTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.db.HashSequenceDBTest [INFO] Running org.biojava.bio.seq.impl.GappedSequenceTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.seq.impl.GappedSequenceTest [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: 0.004 s - in org.biojava.bio.seq.impl.ViewSequenceTest [INFO] Running org.biojava.bio.seq.impl.ViewSeqSerializationTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 s - in org.biojava.bio.seq.impl.ViewSeqSerializationTest [INFO] Running org.biojava.bio.seq.impl.SubSequenceTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.bio.seq.impl.SubSequenceTest [INFO] Running org.biojava.bio.seq.DNAToolsTest [INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.DNAToolsTest [INFO] Running org.biojava.bio.seq.io.SeqIOToolsTest idb length: 79 [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.987 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.MSFAlignmentFormatTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.io.MSFAlignmentFormatTest [INFO] Running org.biojava.bio.seq.io.filterxml.FilterXMLTest [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 s - in org.biojava.bio.seq.io.filterxml.FilterXMLTest [INFO] Running org.biojava.bio.seq.io.SmartSequenceBuilderTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.099 s - in org.biojava.bio.seq.io.SmartSequenceBuilderTest [INFO] Running org.biojava.bio.seq.io.LocationFormatterTest [INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.bio.seq.io.LocationFormatterTest [INFO] Running org.biojava.bio.seq.filter.FilterTransformerTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojava.bio.seq.filter.FilterTransformerTest [INFO] Running org.biojava.bio.seq.ProteinToolsTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.ProteinToolsTest [INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 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.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.search.SimpleSeqSimilaritySearchResultTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest [INFO] Running org.biojava.bio.search.SeqContentPatternTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.search.SeqContentPatternTest [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.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:568) 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.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:568) 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.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:568) at junit.framework.TestCase.runTest(TestCase.java:177) at junit.framework.TestCase.runBare(TestCase.java:142) at junit.framework.TestResult$1.protect(TestResult.java:122) at junit.framework.TestResult.runProtected(TestResult.java:142) at junit.framework.TestResult.run(TestResult.java:125) at junit.framework.TestCase.run(TestCase.java:130) at junit.framework.TestSuite.runTest(TestSuite.java:241) at junit.framework.TestSuite.run(TestSuite.java:236) at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90) at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365) at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273) at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238) at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159) at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384) at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345) at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126) at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418) [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 s - in org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest [INFO] Running org.biojava.bio.proteomics.aaindex.AAindexTest org.biojava.bio.symbol.IllegalSymbolException: Symbol adenine not found in alphabet PROTEIN at org.biojava.bio.symbol.AbstractAlphabet.validate(AbstractAlphabet.java:327) at org.biojava.bio.symbol.AlphabetManager$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.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:568) at junit.framework.TestCase.runTest(TestCase.java:177) at junit.framework.TestCase.runBare(TestCase.java:142) at junit.framework.TestResult$1.protect(TestResult.java:122) at junit.framework.TestResult.runProtected(TestResult.java:142) at junit.framework.TestResult.run(TestResult.java:125) at junit.framework.TestCase.run(TestCase.java:130) at junit.framework.TestSuite.runTest(TestSuite.java:241) at junit.framework.TestSuite.run(TestSuite.java:236) at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90) at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365) at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273) at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238) at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159) at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384) at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345) at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126) at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418) [INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojava.bio.proteomics.aaindex.AAindexTest [INFO] Running org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 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: 0.004 s - in org.biojava.bio.proteomics.MassCalcTest [INFO] Running org.biojava.bio.proteomics.IsoelectricPointCalcTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.proteomics.IsoelectricPointCalcTest [INFO] Running org.biojava.bio.dist.TranslatedDistributionTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.dist.TranslatedDistributionTest [INFO] Running org.biojava.bio.dist.DistSerTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 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: 0.043 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: 0.003 s - in org.biojava.bio.dist.DistributionTest [INFO] Running org.biojava.bio.dp.EmissionStateEventTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.dp.EmissionStateEventTest [INFO] Running org.biojava.bio.dp.MarkovModelEventTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 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: 0.035 s - in org.biojava.bio.dp.DPSerializationTest [INFO] Running org.biojava.bio.MergeAnnotationTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.MergeAnnotationTest [INFO] Running org.biojava.bio.molbio.RestrictionEnzymeManagerTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 s - in org.biojava.bio.molbio.RestrictionEnzymeManagerTest [INFO] Running org.biojava.bio.molbio.RestrictionEnzymeTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.molbio.RestrictionEnzymeTest [INFO] Running org.biojava.bio.symbol.SimpleAtomicSymbolEventTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.SimpleAtomicSymbolEventTest [INFO] Running org.biojava.bio.symbol.DoubleAlphabetTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.DoubleAlphabetTest [INFO] Running org.biojava.bio.symbol.NameTokenizationTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.symbol.NameTokenizationTest [INFO] Running org.biojava.bio.symbol.BetweenLocationTest [INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.symbol.BetweenLocationTest [INFO] Running org.biojava.bio.symbol.SimpleCodonPrefTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s - in org.biojava.bio.symbol.SimpleCodonPrefTest [INFO] Running org.biojava.bio.symbol.GappedSymbolListTest [INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.symbol.GappedSymbolListTest [INFO] Running org.biojava.bio.symbol.CodonPrefToolsTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.CodonPrefToolsTest [INFO] Running org.biojava.bio.symbol.CrossProductAlphabetIndexTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.808 s - in org.biojava.bio.symbol.CrossProductAlphabetIndexTest [INFO] Running org.biojava.bio.symbol.CircularLocationTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.symbol.CircularLocationTest [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.CrossProductTokenizationTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.CrossProductTokenizationTest [INFO] Running org.biojava.bio.symbol.TranslationTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.TranslationTest [INFO] Running org.biojava.bio.symbol.PointLocationTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.PointLocationTest [INFO] Running org.biojava.bio.symbol.AlphabetManagerTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.AlphabetManagerTest [INFO] Running org.biojava.bio.symbol.SymbolSerializationTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.SymbolSerializationTest [INFO] Running org.biojava.bio.symbol.TestSoftMaskedAlphabet [INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.TestSoftMaskedAlphabet [INFO] Running org.biojava.bio.symbol.SimpleWobbleDistributionTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.SimpleWobbleDistributionTest [INFO] Running org.biojava.bio.symbol.SymbolListTest [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.127 s - in org.biojava.bio.symbol.SymbolListTest [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.UkkonenSuffixTreeTest Adding symbol list taccaccagga$ Adding symbol list taccaccagga$ [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.bio.symbol.UkkonenSuffixTreeTest [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.IndexedNoAmbPackTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.IndexedNoAmbPackTest [INFO] Running org.biojava.bio.symbol.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.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.FundamentalAtomicSymbolEventTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest [INFO] Running org.biojava.bio.symbol.LinearAlphabetIndexTest symbolForIndex getAlphabet indexForSymbol [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.LinearAlphabetIndexTest [INFO] Running org.biojava.bio.symbol.AlphabetSerializationTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.bio.symbol.AlphabetSerializationTest [INFO] Running org.biojava.bio.symbol.MergeLocationTest [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.MergeLocationTest [INFO] Running org.biojava.bio.symbol.MotifToolsTest [INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.MotifToolsTest [INFO] Running org.biojava.bio.symbol.CompoundLocationTest [INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.bio.symbol.CompoundLocationTest [INFO] Running org.biojava.bio.program.phred.PhredToolsTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 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: 0.046 s - in org.biojava.bio.program.indexdb.IndexToolsTest [INFO] Running org.biojava.bio.AnnotationTypeTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.AnnotationTypeTest [INFO] Running org.biojava.directory.OBDARegistryParserTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.directory.OBDARegistryParserTest [INFO] Running org.biojava.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: 0.037 s - in org.biojava.directory.SystemRegistryTest [INFO] Running org.biojava.ontology.TermImplTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.ontology.TermImplTest [INFO] Running org.biojava.ontology.OntologyTest [INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.ontology.OntologyTest [INFO] Running org.biojava.ontology.ParseOBOFileTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.19 s - in org.biojava.ontology.ParseOBOFileTest [INFO] Running org.biojava.ontology.TripleImplTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.ontology.TripleImplTest [INFO] Running org.biojava.utils.ListToolsTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.utils.ListToolsTest [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.walker.WalkerFactoryTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 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: 0.011 s - in org.biojava.utils.walker.WalkerTest [INFO] Running org.biojava.utils.regex.RegexTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.utils.regex.RegexTest [INFO] Running org.biojava.utils.regex.PatternCheckerTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.regex.PatternCheckerTest [INFO] Running org.biojava.utils.process.AllTests [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 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: 0.038 s - in org.biojava.utils.process.ExternalProcessTest [INFO] Running org.biojava.utils.SmallMapTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.utils.SmallMapTest [INFO] Running org.biojava.utils.RepeatedCharSequenceTest JAM [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.utils.RepeatedCharSequenceTest [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.naming.ObdaInitialContextFactoryTest Reached Attributes: No attributes Binding: urn -> org.biojava.naming.ObdaContext@14e5a39 Reached urn Attributes: No attributes Binding: open-bio.org -> org.biojava.naming.ObdaContext@1de7f3d 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@166ae3a 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@f4b83d 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@131289 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@5e69a5 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@a1116a 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@1e17893 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@1eea77c 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@82e6a5 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@c4915e 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@fb4575 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@c2c551 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@184b3a2 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@1648d2d 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@1ccb12d} My component is urn:open-bio.org:format:embl lookup: 'open-bio.org:format:embl' for {open-bio.org=org.biojava.naming.ObdaContext@1ca495} My component is open-bio.org:format:embl lookup: 'format:embl' for {type=org.biojava.naming.ObdaContext@19d4443, format=org.biojava.naming.ObdaContext@13eca84, alphabet=org.biojava.naming.ObdaContext@147dfed} My component is format:embl lookup: 'embl' for {enzyme=org.biojava.naming.ObdaContext@38e4dc, genbank=org.biojava.naming.ObdaContext@1fc0084, swissprot=org.biojava.naming.ObdaContext@1788d5, embl=org.biojava.naming.ObdaContext@1ec9f8d} My component is embl [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 s - in org.biojava.naming.ObdaInitialContextFactoryTest [INFO] Running org.biojava.naming.ObdaUriParserTest urn:obda.org:format:embl/ac :trail oneName lead: [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.naming.ObdaUriParserTest [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: 0.008 s - in org.biojavax.SimpleNoteTest [INFO] Running org.biojavax.SimpleDocRefAuthorTest testIsConsortium testToString testCompareTo testGetName testHashCode testEquals testGetExtendedName [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.SimpleDocRefAuthorTest [INFO] Running org.biojavax.SimpleRichAnnotationTest testGetNoteSet testAddNote testAsMap testClear testKeys testToString testGetNote testSetNoteSet testContains testGetPropertys testSetProperty testRemoveNote testGetProperty testRemoveProperty testRemoveProperty2 testContainsProperty [INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojavax.SimpleRichAnnotationTest [INFO] Running org.biojavax.ga.impl.SimplePopulationTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 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: 0.001 s - in org.biojavax.ga.impl.SimpleOrganismTest [INFO] Running org.biojavax.ga.util.WeightedSetTest [INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.ga.util.WeightedSetTest [INFO] Running org.biojavax.ga.util.GAToolsTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.util.GAToolsTest [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.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.ProportionalSelectionTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.ga.functions.ProportionalSelectionTest [INFO] Running org.biojavax.ga.functions.SimpleMutationFunctionTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.functions.SimpleMutationFunctionTest [INFO] Running org.biojavax.ga.functions.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.SimpleCommentTest testSetComment testToString testCompareTo testGetRank testHashCode testGetComment testEquals testSetRank [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.SimpleCommentTest [INFO] Running org.biojavax.bio.seq.RichLocationToolsTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.bio.seq.RichLocationToolsTest [INFO] Running org.biojavax.bio.seq.SimpleRichFeatureTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojavax.bio.seq.SimpleRichFeatureTest [INFO] Running org.biojavax.bio.seq.CompoundRichLocationTest testEquals [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.seq.CompoundRichLocationTest [INFO] Running org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest testEquals [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest [INFO] Running org.biojavax.bio.seq.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.io.Bug2249_2248Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 s - in org.biojavax.bio.seq.io.Bug2249_2248Test [INFO] Running org.biojavax.bio.seq.io.GenbankFormatTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 s - in org.biojavax.bio.seq.io.GenbankFormatTest [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: 0.003 s - in org.biojavax.bio.seq.io.GenbankLocationParserTest [INFO] Running org.biojavax.bio.seq.io.Bug2255Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojavax.bio.seq.io.Bug2255Test [INFO] Running org.biojavax.bio.seq.io.Bug2250_2256Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 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: 0.012 s - in org.biojavax.bio.seq.io.UniProtFormatTest [INFO] Running org.biojavax.bio.seq.io.EMBLFormatTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.bio.seq.io.EMBLFormatTest [INFO] Running org.biojavax.bio.seq.io.INSDseqFormatTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.033 s - in org.biojavax.bio.seq.io.INSDseqFormatTest [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: 0.001 s - in org.biojavax.bio.taxa.SimpleNCBITaxonNameTest [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: 0.005 s - in org.biojavax.bio.SimpleBioEntryTest [INFO] Running org.biojavax.SimpleRankedCrossRefTest testToString testGetCrossRef testCompareTo testGetRank testHashCode testEquals testSetRank [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.SimpleRankedCrossRefTest [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.SimpleCrossRefTest testGetNoteSet testGetAccession testToString testCompareTo testGetAnnotation testSetNoteSet testGetVersion testHashCode testGetDbname testEquals [INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.SimpleCrossRefTest [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: 0.002 s - in org.biojavax.SimpleRankedDocRefTest [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.SimpleNamespaceTest testGetAuthority testSetDescription testToString testGetAcronym testCompareTo testGetName testSetAuthority testGetDescription testHashCode testSetAcronym testEquals testGetURI testSetURI [INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojavax.SimpleNamespaceTest [INFO] Running org.biojavax.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: 0.002 s - in org.biojavax.ontology.SimpleComparableTripleTest [INFO] Running org.biojavax.ontology.SimpleComparableOntologyTest testSetTripleSet testCreateTriple testContainsTriple testGetTerms testCreateVariable testContainsTerm testGetTermSet testSetDescription testToString testGetOrCreateTerm testCompareTo testGetTriples testGetName testGetTerm testGetOrImportTerm testGetTripleSet testCreateTerm testGetDescription testSetTermSet testHashCode testDeleteTerm testEquals testGetOps testImportTerm [INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojavax.ontology.SimpleComparableOntologyTest [INFO] Running org.biojavax.ontology.SimpleComparableTermTest testSetDescription testGetRankedCrossRefs testToString testGetSynonyms testCompareTo testAddSynonym testGetName testGetOntology testSetRankedCrossRefs testGetIdentifier testGetAnnotation testRemoveRankedCrossRef testGetDescription testSetIdentifier testHashCode testEquals testAddRankedCrossRef testRemoveSynonym testSetObsolete testGetObsolete [INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojavax.ontology.SimpleComparableTermTest [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: 0.002 s - in org.biojavax.EmptyRichAnnotationTest [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: 0.006 s - in org.biojavax.SimpleDocRefTest [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] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ alignment --- [INFO] Copying 89 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ alignment --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ alignment --- [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.10.1: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: 0.78 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: 0.03 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: 0.014 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] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0: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:3.10.1:compile (default-compile) @ biosql --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0: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:3.10.1: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: 0.035 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] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ blast --- [INFO] Copying 3 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ blast --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ blast --- [INFO] Copying 22 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1: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.SSBindNCBIblastx2_2_3Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.729 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.553 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: 1.336 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.532 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.101 s - in org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.226 s - in org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.848 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.668 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.109 s - in org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.153 s - in org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.573 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.799 s - in org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.573 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: 3.314 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.336 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.109 s - in org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test [INFO] Running org.biojava.bio.program.sax.BlastTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 s - in org.biojava.bio.program.sax.BlastTest [INFO] Running org.biojava.bio.program.sax.blastxml.BlastXMLTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.312 s - in org.biojava.bio.program.sax.blastxml.BlastXMLTest [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] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0: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:3.10.1:compile (default-compile) @ sequencing --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ sequencing --- [INFO] Copying 77 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1: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.scf.SCFTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.091 s - in org.biojava.bio.program.scf.SCFTest [INFO] Running org.biojava.bio.program.fastq.IlluminaFastqReaderTest [INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.613 s - in org.biojava.bio.program.fastq.IlluminaFastqReaderTest [INFO] Running org.biojava.bio.program.fastq.FastqVariantTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.program.fastq.FastqVariantTest [INFO] Running org.biojava.bio.program.fastq.SolexaFastqReaderTest [INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.136 s - in org.biojava.bio.program.fastq.SolexaFastqReaderTest [INFO] Running org.biojava.bio.program.fastq.FastqTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.program.fastq.FastqTest [INFO] Running org.biojava.bio.program.fastq.ConvertTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.593 s - in org.biojava.bio.program.fastq.ConvertTest [INFO] Running org.biojava.bio.program.fastq.IlluminaFastqWriterTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.144 s - in org.biojava.bio.program.fastq.IlluminaFastqWriterTest [INFO] Running org.biojava.bio.program.fastq.FastqToolsTest [INFO] Tests run: 38, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.202 s - in org.biojava.bio.program.fastq.FastqToolsTest [INFO] Running org.biojava.bio.program.fastq.SangerFastqReaderTest [INFO] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.06 s - in org.biojava.bio.program.fastq.SangerFastqReaderTest [INFO] Running org.biojava.bio.program.fastq.StreamingFastqParserTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.program.fastq.StreamingFastqParserTest [INFO] Running org.biojava.bio.program.fastq.FastqBuilderTest [INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.bio.program.fastq.FastqBuilderTest [INFO] Running org.biojava.bio.program.fastq.SolexaFastqWriterTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojava.bio.program.fastq.SolexaFastqWriterTest [INFO] Running org.biojava.bio.program.fastq.SangerFastqWriterTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.bio.program.fastq.SangerFastqWriterTest [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] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0: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:3.10.1:compile (default-compile) @ gui --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0: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:3.10.1: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] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0: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:3.10.1:compile (default-compile) @ phylo --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ phylo --- [INFO] Copying 3 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1: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: 0.58 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 [ 0.003 s] [INFO] bytecode ........................................... SUCCESS [ 0.885 s] [INFO] core ............................................... SUCCESS [ 10.600 s] [INFO] alignment .......................................... SUCCESS [ 10.161 s] [INFO] biosql ............................................. SUCCESS [ 10.145 s] [INFO] blast .............................................. SUCCESS [ 20.193 s] [INFO] sequencing ......................................... SUCCESS [ 10.392 s] [INFO] gui ................................................ SUCCESS [ 0.117 s] [INFO] phylo .............................................. SUCCESS [ 10.187 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:12 min [INFO] Finished at: 2024-04-02T21:19:18Z [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] --------------------------------[ 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] --------------------------------[ 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] --------------------------------[ 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] --------------------------------[ 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] --------------------------------[ 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] --------------------------------[ 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] --------------------------------[ 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] --------------------------------[ 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] --------------------------------[ 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 [ 0.907 s] [INFO] bytecode ........................................... SUCCESS [ 0.199 s] [INFO] core ............................................... SUCCESS [ 0.219 s] [INFO] alignment .......................................... SUCCESS [ 0.164 s] [INFO] biosql ............................................. SUCCESS [ 0.200 s] [INFO] blast .............................................. SUCCESS [ 0.188 s] [INFO] sequencing ......................................... SUCCESS [ 0.168 s] [INFO] gui ................................................ SUCCESS [ 0.256 s] [INFO] phylo .............................................. SUCCESS [ 0.196 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 3.235 s [INFO] Finished at: 2024-04-02T21:19:26Z [INFO] ------------------------------------------------------------------------ mh_resolve_dependencies --non-interactive --offline --build -plibbiojava1.9-java --javadoc --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 Checking dependencies for documentation packages... > dpkg --search /usr/share/doc/libcommons-dbcp-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-dbcp-java/api/index.html > dpkg --search /usr/share/doc/libcommons-dbcp-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-dbcp-java-doc/api/index.html > dpkg --search /usr/share/doc/libcommons-dbcp-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-dbcp-java/apidocs/index.html > dpkg --search /usr/share/doc/libcommons-dbcp-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-dbcp-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libguava-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libguava-java/api/index.html > dpkg --search /usr/share/doc/libguava-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libguava-java-doc/api/index.html > dpkg --search /usr/share/doc/libguava-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libguava-java/apidocs/index.html > dpkg --search /usr/share/doc/libguava-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libguava-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libjgrapht0.8-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjgrapht0.8-java/api/index.html > dpkg --search /usr/share/doc/libjgrapht0.8-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjgrapht0.8-java-doc/api/index.html > dpkg --search /usr/share/doc/libjgrapht0.8-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjgrapht0.8-java/apidocs/index.html > dpkg --search /usr/share/doc/libjgrapht0.8-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjgrapht0.8-java-doc/apidocs/index.html bash -c "rm -f target/apidocs/*.sh target/apidocs/options" mh_unpatchpoms -plibbiojava1.9-java dh_install 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 dpkg-gencontrol: warning: package libbiojava1.9-java: substitution variable ${maven:CompileDepends} unused, but is defined dpkg-gencontrol: warning: package libbiojava1.9-java: substitution variable ${maven:DocDepends} unused, but is defined dpkg-gencontrol: warning: package libbiojava-java-doc: substitution variable ${maven:CompileDepends} unused, but is defined dpkg-gencontrol: warning: package libbiojava-java-doc: substitution variable ${maven:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'libbiojava1.9-java' in '../libbiojava1.9-java_1.9.7+dfsg-1_all.deb'. dpkg-deb: building package 'libbiojava-java' in '../libbiojava-java_1.9.7+dfsg-1_all.deb'. dpkg-deb: building package 'libbiojava-java-doc' in '../libbiojava-java-doc_1.9.7+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../biojava-live_1.9.7+dfsg-1_i386.buildinfo dpkg-genchanges --build=binary -O../biojava-live_1.9.7+dfsg-1_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: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/45107/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/45107/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/45107 and its subdirectories I: Current time: Wed Apr 3 11:22:51 +14 2024 I: pbuilder-time-stamp: 1712092971