I: pbuilder: network access will be disabled during build I: Current time: Thu Jun 20 00:09:53 -12 2024 I: pbuilder-time-stamp: 1718885393 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [biojava-live_1.9.5+dfsg-3.dsc] I: copying [./biojava-live_1.9.5+dfsg.orig.tar.xz] I: copying [./biojava-live_1.9.5+dfsg-3.debian.tar.xz] I: Extracting source gpgv: Signature made Thu May 11 21:19:05 2023 -12 gpgv: using RSA key B8CE4DE21080DCF903E16C40F513C419E4B9D0AC gpgv: issuer "ebourg@apache.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./biojava-live_1.9.5+dfsg-3.dsc: no acceptable signature found dpkg-source: info: extracting biojava-live in biojava-live-1.9.5+dfsg dpkg-source: info: unpacking biojava-live_1.9.5+dfsg.orig.tar.xz dpkg-source: info: unpacking biojava-live_1.9.5+dfsg-3.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/1691504/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='ca05f33207474fa79e3194e5465756d9' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1691504' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.cwh8ynQe/pbuilderrc_rdzM --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.cwh8ynQe/b1 --logfile b1/build.log biojava-live_1.9.5+dfsg-3.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos15-amd64 6.1.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 2023 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 2023 more -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 2023 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/1691504/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), maven-debian-helper, default-jdk, junit4, libcommons-dbcp-java, libjaxb-api-java, libjgrapht0.8-java, 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 ... 19596 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} 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{a} libasound2-data{a} libatinject-jsr330-api-java{a} libatk1.0-0{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} 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} libcups2{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} libelf1{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} libglib2.0-0{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgraphite2-3{a} libgtk2.0-0{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} liblcms2-2{a} liblerc4{a} libllvm15{a} libmagic-mgc{a} libmagic1{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} libpng16-16{a} libproc2-0{a} libqdox-java{a} libqdox2-java{a} libsensors-config{a} libsensors5{a} libservlet-api-java{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} 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 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 psmisc wget xdg-user-dirs 0 packages upgraded, 270 newly installed, 0 to remove and 0 not upgraded. Need to get 420 MB of archives. After unpacking 869 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 sgml-base all 1.31 [15.4 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libproc2-0 amd64 2:4.0.2-3 [62.8 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 procps amd64 2:4.0.2-3 [709 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.8-1 [1407 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-1 [306 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 shared-mime-info amd64 2.2-1 [729 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.1 [285 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-5 [316 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.10+dfsg-1+b1 [139 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 gtk-update-icon-cache amd64 3.24.37-2 [43.3 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 adwaita-icon-theme all 43-1 [5124 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 ca-certificates-java all 20230103 [11.4 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 java-common all 0.74 [6388 B] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libavahi-common-data amd64 0.8-10 [107 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libavahi-common3 amd64 0.8-10 [41.6 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libdbus-1-3 amd64 1.14.6-1 [200 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libavahi-client3 amd64 0.8-10 [45.5 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libcups2 amd64 2.4.2-3 [244 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [399 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 libnspr4 amd64 2:4.35-1 [113 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 libnss3 amd64 2:3.87.1-1 [1331 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libasound2-data all 1.2.8-1 [20.5 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 libasound2 amd64 1.2.8-1+b1 [362 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libpcsclite1 amd64 1.9.9-2 [49.7 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre-headless amd64 17.0.6+10-1 [43.6 MB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 default-jre-headless amd64 2:1.17-74 [2936 B] Get: 55 http://deb.debian.org/debian bookworm/main amd64 ant all 1.10.13-1 [2161 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 at-spi2-common all 2.46.0-5 [162 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 67 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 69 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 libgtk2.0-common all 2.24.33-2 [2700 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libatk1.0-0 amd64 2.46.0-5 [49.6 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2 [292 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2 [759 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 libxcomposite1 amd64 1:0.4.5-1 [16.6 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 libxfixes3 amd64 1:6.0.0-2 [22.7 kB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 libxcursor1 amd64 1:1.2.1-1 [40.9 kB] Get: 100 http://deb.debian.org/debian bookworm/main amd64 libxdamage1 amd64 1:1.1.6-1 [15.1 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 libxi6 amd64 2:1.8-1+b1 [84.2 kB] Get: 102 http://deb.debian.org/debian bookworm/main amd64 libxinerama1 amd64 2:1.1.4-3 [17.8 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 libxrandr2 amd64 2:1.5.2-2+b1 [39.2 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 libgtk2.0-0 amd64 2.24.33-2 [1855 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 libglvnd0 amd64 1.6.0-1 [51.8 kB] Get: 106 http://deb.debian.org/debian bookworm/main amd64 libdrm-common all 2.4.114-1 [7112 B] Get: 107 http://deb.debian.org/debian bookworm/main amd64 libdrm2 amd64 2.4.114-1+b1 [37.5 kB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 libglapi-mesa amd64 22.3.6-1+deb12u1 [35.7 kB] Get: 109 http://deb.debian.org/debian bookworm/main amd64 libx11-xcb1 amd64 2:1.8.4-2 [192 kB] Get: 110 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri2-0 amd64 1.15-1 [107 kB] Get: 111 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri3-0 amd64 1.15-1 [107 kB] Get: 112 http://deb.debian.org/debian bookworm/main amd64 libxcb-glx0 amd64 1.15-1 [122 kB] Get: 113 http://deb.debian.org/debian bookworm/main amd64 libxcb-present0 amd64 1.15-1 [105 kB] Get: 114 http://deb.debian.org/debian bookworm/main amd64 libxcb-randr0 amd64 1.15-1 [117 kB] Get: 115 http://deb.debian.org/debian bookworm/main amd64 libxcb-sync1 amd64 1.15-1 [109 kB] Get: 116 http://deb.debian.org/debian bookworm/main amd64 libxcb-xfixes0 amd64 1.15-1 [109 kB] Get: 117 http://deb.debian.org/debian bookworm/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get: 118 http://deb.debian.org/debian bookworm/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 119 http://deb.debian.org/debian bookworm/main amd64 libdrm-amdgpu1 amd64 2.4.114-1+b1 [20.9 kB] Get: 120 http://deb.debian.org/debian bookworm/main amd64 libpciaccess0 amd64 0.17-2 [51.4 kB] Get: 121 http://deb.debian.org/debian bookworm/main amd64 libdrm-intel1 amd64 2.4.114-1+b1 [64.0 kB] Get: 122 http://deb.debian.org/debian bookworm/main amd64 libdrm-nouveau2 amd64 2.4.114-1+b1 [19.1 kB] Get: 123 http://deb.debian.org/debian bookworm/main amd64 libdrm-radeon1 amd64 2.4.114-1+b1 [21.8 kB] Get: 124 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get: 125 http://deb.debian.org/debian bookworm/main amd64 libz3-4 amd64 4.8.12-3.1 [7216 kB] Get: 126 http://deb.debian.org/debian bookworm/main amd64 libllvm15 amd64 1:15.0.6-4+b1 [23.1 MB] Get: 127 http://deb.debian.org/debian bookworm/main amd64 libsensors-config all 1:3.6.0-7.1 [14.3 kB] Get: 128 http://deb.debian.org/debian bookworm/main amd64 libsensors5 amd64 1:3.6.0-7.1 [34.2 kB] Get: 129 http://deb.debian.org/debian bookworm/main amd64 libgl1-mesa-dri amd64 22.3.6-1+deb12u1 [7239 kB] Get: 130 http://deb.debian.org/debian bookworm/main amd64 libglx-mesa0 amd64 22.3.6-1+deb12u1 [147 kB] Get: 131 http://deb.debian.org/debian bookworm/main amd64 libglx0 amd64 1.6.0-1 [34.4 kB] Get: 132 http://deb.debian.org/debian bookworm/main amd64 libgl1 amd64 1.6.0-1 [88.4 kB] Get: 133 http://deb.debian.org/debian bookworm/main amd64 libgif7 amd64 5.2.1-2.5 [46.9 kB] Get: 134 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 135 http://deb.debian.org/debian bookworm/main amd64 libxtst6 amd64 2:1.2.3-1.1 [28.0 kB] Get: 136 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre amd64 17.0.6+10-1 [168 kB] Get: 137 http://deb.debian.org/debian bookworm/main amd64 default-jre amd64 2:1.17-74 [1056 B] Get: 138 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jdk-headless amd64 17.0.6+10-1 [230 MB] Get: 139 http://deb.debian.org/debian bookworm/main amd64 default-jdk-headless amd64 2:1.17-74 [1108 B] Get: 140 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jdk amd64 17.0.6+10-1 [4577 kB] Get: 141 http://deb.debian.org/debian bookworm/main amd64 default-jdk amd64 2:1.17-74 [1068 B] Get: 142 http://deb.debian.org/debian bookworm/main amd64 unzip amd64 6.0-28 [166 kB] Get: 143 http://deb.debian.org/debian bookworm/main amd64 java-wrappers all 0.4 [8916 B] Get: 144 http://deb.debian.org/debian bookworm/main amd64 libhamcrest-java all 2.2-1 [121 kB] Get: 145 http://deb.debian.org/debian bookworm/main amd64 junit4 all 4.13.2-3 [348 kB] Get: 146 http://deb.debian.org/debian bookworm/main amd64 libapiguardian-java all 1.1.2-1 [4656 B] Get: 147 http://deb.debian.org/debian bookworm/main amd64 libopentest4j-java all 1.2.0-4 [9516 B] Get: 148 http://deb.debian.org/debian bookworm/main amd64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 149 http://deb.debian.org/debian bookworm/main amd64 libpicocli-java all 4.6.2-2 [390 kB] Get: 150 http://deb.debian.org/debian bookworm/main amd64 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 151 http://deb.debian.org/debian bookworm/main amd64 junit5 all 5.9.2-1 [2398 kB] Get: 152 http://deb.debian.org/debian bookworm/main amd64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 153 http://deb.debian.org/debian bookworm/main amd64 libaopalliance-java all 20070526-7 [8572 B] Get: 154 http://deb.debian.org/debian bookworm/main amd64 libapache-pom-java all 29-2 [5276 B] Get: 155 http://deb.debian.org/debian bookworm/main amd64 libasm-java all 9.4-1 [389 kB] Get: 156 http://deb.debian.org/debian bookworm/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 157 http://deb.debian.org/debian bookworm/main amd64 libjaxp1.3-java all 1.3.05-6 [227 kB] Get: 158 http://deb.debian.org/debian bookworm/main amd64 libxml-commons-external-java all 1.4.01-5 [240 kB] Get: 159 http://deb.debian.org/debian bookworm/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 160 http://deb.debian.org/debian bookworm/main amd64 libcommons-io-java all 2.11.0-2 [319 kB] Get: 161 http://deb.debian.org/debian bookworm/main amd64 libcommons-logging-java all 1.2-3 [62.4 kB] Get: 162 http://deb.debian.org/debian bookworm/main amd64 libxmlgraphics-commons-java all 2.8-2 [623 kB] Get: 163 http://deb.debian.org/debian bookworm/main amd64 libbatik-java all 1.16+dfsg-1 [3908 kB] Get: 164 http://deb.debian.org/debian bookworm/main amd64 libbsh-java all 2.0b4-20 [291 kB] Get: 165 http://deb.debian.org/debian bookworm/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 166 http://deb.debian.org/debian bookworm/main amd64 libcdi-api-java all 1.2-3 [54.3 kB] Get: 167 http://deb.debian.org/debian bookworm/main amd64 libcommons-collections3-java all 3.2.2-2 [526 kB] Get: 168 http://deb.debian.org/debian bookworm/main amd64 libcommons-beanutils-java all 1.9.4-1 [232 kB] Get: 169 http://deb.debian.org/debian bookworm/main amd64 libcommons-cli-java all 1.5.0-1 [60.0 kB] Get: 170 http://deb.debian.org/debian bookworm/main amd64 libcommons-codec-java all 1.15-1 [292 kB] Get: 171 http://deb.debian.org/debian bookworm/main amd64 libcommons-compress-java all 1.22-1 [615 kB] Get: 172 http://deb.debian.org/debian bookworm/main amd64 libcommons-lang-java all 2.6-10 [273 kB] Get: 173 http://deb.debian.org/debian bookworm/main amd64 libcommons-configuration-java all 1.10-6 [347 kB] Get: 174 http://deb.debian.org/debian bookworm/main amd64 libcommons-pool-java all 1.6-4 [109 kB] Get: 175 http://deb.debian.org/debian bookworm/main amd64 libcommons-dbcp-java all 1.4-7 [157 kB] Get: 176 http://deb.debian.org/debian bookworm/main amd64 libcommons-digester-java all 1.8.1-5 [168 kB] Get: 177 http://deb.debian.org/debian bookworm/main amd64 libcommons-lang3-java all 3.12.0-2 [561 kB] Get: 178 http://deb.debian.org/debian bookworm/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 179 http://deb.debian.org/debian bookworm/main amd64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 180 http://deb.debian.org/debian bookworm/main amd64 libslf4j-java all 1.7.32-1 [144 kB] Get: 181 http://deb.debian.org/debian bookworm/main amd64 libsnappy1v5 amd64 1.1.9-3 [26.0 kB] Get: 182 http://deb.debian.org/debian bookworm/main amd64 libsnappy-jni amd64 1.1.8.3-1 [7152 B] Get: 183 http://deb.debian.org/debian bookworm/main amd64 libsnappy-java all 1.1.8.3-1 [98.9 kB] Get: 184 http://deb.debian.org/debian bookworm/main amd64 libxz-java all 1.9-1 [143 kB] Get: 185 http://deb.debian.org/debian bookworm/main amd64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 186 http://deb.debian.org/debian bookworm/main amd64 libplexus-interpolation-java all 1.26-1 [76.8 kB] Get: 187 http://deb.debian.org/debian bookworm/main amd64 libmaven-archiver-java all 3.6.0-1 [25.1 kB] Get: 188 http://deb.debian.org/debian bookworm/main amd64 libmaven-shared-utils-java all 3.3.4-1 [138 kB] Get: 189 http://deb.debian.org/debian bookworm/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 190 http://deb.debian.org/debian bookworm/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 191 http://deb.debian.org/debian bookworm/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 192 http://deb.debian.org/debian bookworm/main amd64 libguava-java all 31.1-1 [2613 kB] Get: 193 http://deb.debian.org/debian bookworm/main amd64 libguice-java all 4.2.3-2 [1435 kB] Get: 194 http://deb.debian.org/debian bookworm/main amd64 libmaven-parent-java all 35-1 [6140 B] Get: 195 http://deb.debian.org/debian bookworm/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 196 http://deb.debian.org/debian bookworm/main amd64 libmaven-resolver-java all 1.6.3-1 [548 kB] Get: 197 http://deb.debian.org/debian bookworm/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 198 http://deb.debian.org/debian bookworm/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 199 http://deb.debian.org/debian bookworm/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 200 http://deb.debian.org/debian bookworm/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 201 http://deb.debian.org/debian bookworm/main amd64 libsisu-inject-java all 0.3.4-2 [347 kB] Get: 202 http://deb.debian.org/debian bookworm/main amd64 libsisu-plexus-java all 0.3.4-3 [181 kB] Get: 203 http://deb.debian.org/debian bookworm/main amd64 libmaven3-core-java all 3.8.7-1 [1572 kB] Get: 204 http://deb.debian.org/debian bookworm/main amd64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 205 http://deb.debian.org/debian bookworm/main amd64 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 206 http://deb.debian.org/debian bookworm/main amd64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 207 http://deb.debian.org/debian bookworm/main amd64 libcommons-text-java all 1.10.0-1 [211 kB] Get: 208 http://deb.debian.org/debian bookworm/main amd64 libcommons-validator-java all 1:1.7-1 [181 kB] Get: 209 http://deb.debian.org/debian bookworm/main amd64 libjaxen-java all 1.1.6-4 [214 kB] Get: 210 http://deb.debian.org/debian bookworm/main amd64 libdom4j-java all 2.1.3-2 [310 kB] Get: 211 http://deb.debian.org/debian bookworm/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 212 http://deb.debian.org/debian bookworm/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 213 http://deb.debian.org/debian bookworm/main amd64 libdoxia-core-java all 1.12.0-1 [213 kB] Get: 214 http://deb.debian.org/debian bookworm/main amd64 libfontbox2-java all 2.0.27-2 [1510 kB] Get: 215 http://deb.debian.org/debian bookworm/main amd64 libqdox-java all 1.12.1-3 [172 kB] Get: 216 http://deb.debian.org/debian bookworm/main amd64 libfop-java all 1:2.8-2 [10.1 MB] Get: 217 http://deb.debian.org/debian bookworm/main amd64 libitext1-java all 1.4-7 [1257 kB] Get: 218 http://deb.debian.org/debian bookworm/main amd64 libxbean-reflect-java all 4.5-8 [133 kB] Get: 219 http://deb.debian.org/debian bookworm/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 220 http://deb.debian.org/debian bookworm/main amd64 libdoxia-java all 1.12.0-1 [459 kB] Get: 221 http://deb.debian.org/debian bookworm/main amd64 libmaven-reporting-api-java all 3.1.1-1 [7240 B] Get: 222 http://deb.debian.org/debian bookworm/main amd64 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB] Get: 223 http://deb.debian.org/debian bookworm/main amd64 velocity all 1.7-6 [429 kB] Get: 224 http://deb.debian.org/debian bookworm/main amd64 libplexus-velocity-java all 1.2-3.1 [10.5 kB] Get: 225 http://deb.debian.org/debian bookworm/main amd64 liboro-java all 2.0.8a-14 [70.5 kB] Get: 226 http://deb.debian.org/debian bookworm/main amd64 libvelocity-tools-java all 2.0-8 [308 kB] Get: 227 http://deb.debian.org/debian bookworm/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 228 http://deb.debian.org/debian bookworm/main amd64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 229 http://deb.debian.org/debian bookworm/main amd64 libxalan2-java all 2.7.2-4 [3419 kB] Get: 230 http://deb.debian.org/debian bookworm/main amd64 libdoxia-sitetools-java all 1.11.1-1 [202 kB] Get: 231 http://deb.debian.org/debian bookworm/main amd64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 232 http://deb.debian.org/debian bookworm/main amd64 libjansi-java all 2.4.0-2 [105 kB] Get: 233 http://deb.debian.org/debian bookworm/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 234 http://deb.debian.org/debian bookworm/main amd64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 235 http://deb.debian.org/debian bookworm/main amd64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 236 http://deb.debian.org/debian bookworm/main amd64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 237 http://deb.debian.org/debian bookworm/main amd64 libjetty9-java all 9.4.50-3 [2962 kB] Get: 238 http://deb.debian.org/debian bookworm/main amd64 libjgraph-java all 5.12.4.2+dfsg-7 [207 kB] Get: 239 http://deb.debian.org/debian bookworm/main amd64 libjgrapht0.8-java all 0.8.3-6 [214 kB] Get: 240 http://deb.debian.org/debian bookworm/main amd64 libjgrapht0.8-java-doc all 0.8.3-6 [379 kB] Get: 241 http://deb.debian.org/debian bookworm/main amd64 libjsoup-java all 1.15.3-1 [431 kB] Get: 242 http://deb.debian.org/debian bookworm/main amd64 libjtidy-java all 7+svn20110807-5 [250 kB] Get: 243 http://deb.debian.org/debian bookworm/main amd64 libmaven-common-artifact-filters-java all 3.3.2-1 [48.2 kB] Get: 244 http://deb.debian.org/debian bookworm/main amd64 libmaven-artifact-transfer-java all 0.13.1-2 [158 kB] Get: 245 http://deb.debian.org/debian bookworm/main amd64 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB] Get: 246 http://deb.debian.org/debian bookworm/main amd64 libmaven-shared-incremental-java all 1.1-3 [9524 B] Get: 247 http://deb.debian.org/debian bookworm/main amd64 libplexus-compiler-java all 2.12.1-1 [99.8 kB] Get: 248 http://deb.debian.org/debian bookworm/main amd64 libqdox2-java all 2.0.3-1 [296 kB] Get: 249 http://deb.debian.org/debian bookworm/main amd64 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 250 http://deb.debian.org/debian bookworm/main amd64 libmaven-compiler-plugin-java all 3.10.1-2 [59.0 kB] Get: 251 http://deb.debian.org/debian bookworm/main amd64 libplexus-build-api-java all 0.0.7-4 [10.3 kB] Get: 252 http://deb.debian.org/debian bookworm/main amd64 libmaven-filtering-java all 3.3.0-1 [50.2 kB] Get: 253 http://deb.debian.org/debian bookworm/main amd64 libmaven-invoker-java all 3.2.0-1 [28.1 kB] Get: 254 http://deb.debian.org/debian bookworm/main amd64 libplexus-interactivity-api-java all 1.1-2 [11.0 kB] Get: 255 http://deb.debian.org/debian bookworm/main amd64 libmaven-javadoc-plugin-java all 3.4.1-2 [454 kB] Get: 256 http://deb.debian.org/debian bookworm/main amd64 libmaven-reporting-impl-java all 3.2.0-2 [15.2 kB] Get: 257 http://deb.debian.org/debian bookworm/main amd64 libplexus-container-default1.5-java all 2.1.1-1 [4476 B] Get: 258 http://deb.debian.org/debian bookworm/main amd64 libplexus-ant-factory-java all 1.0~alpha2.1-4 [11.4 kB] Get: 259 http://deb.debian.org/debian bookworm/main amd64 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B] Get: 260 http://deb.debian.org/debian bookworm/main amd64 libmaven-plugin-tools-java all 3.7.1-1 [265 kB] Get: 261 http://deb.debian.org/debian bookworm/main amd64 libmaven-reporting-exec-java all 1.6.0-1 [26.8 kB] Get: 262 http://deb.debian.org/debian bookworm/main amd64 libmaven-resources-plugin-java all 3.3.0-1 [28.4 kB] Get: 263 http://deb.debian.org/debian bookworm/main amd64 libmaven-site-plugin-java all 3.12.1-2 [107 kB] Get: 264 http://deb.debian.org/debian bookworm/main amd64 libsurefire-java all 2.22.3-2 [1169 kB] Get: 265 http://deb.debian.org/debian bookworm/main amd64 libwagon-file-java all 3.5.3-1 [8388 B] Get: 266 http://deb.debian.org/debian bookworm/main amd64 libwagon-http-shaded-java all 3.5.3-1 [1341 kB] Get: 267 http://deb.debian.org/debian bookworm/main amd64 libxml2-utils amd64 2.9.14+dfsg-1.2 [98.8 kB] Get: 268 http://deb.debian.org/debian bookworm/main amd64 maven all 3.8.7-1 [18.9 kB] Get: 269 http://deb.debian.org/debian bookworm/main amd64 maven-repo-helper all 1.11 [142 kB] Get: 270 http://deb.debian.org/debian bookworm/main amd64 maven-debian-helper all 2.6.3 [108 kB] Fetched 420 MB in 5s (84.6 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 ... 19596 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:amd64. Preparing to unpack .../001-libproc2-0_2%3a4.0.2-3_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.2-3_amd64.deb ... 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Unpacking shared-mime-info (2.2-1) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../021-libjpeg62-turbo_1%3a2.1.5-2_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-2) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../022-libpng16-16_1.6.39-2_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.39-2) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../023-libdeflate0_1.14-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.14-1) ... Selecting previously unselected package libjbig0:amd64. Preparing to unpack .../024-libjbig0_2.1-6.1_amd64.deb ... Unpacking libjbig0:amd64 (2.1-6.1) ... Selecting previously unselected package liblerc4:amd64. Preparing to unpack .../025-liblerc4_4.0.0+ds-2_amd64.deb ... Unpacking liblerc4:amd64 (4.0.0+ds-2) ... Selecting previously unselected package libwebp7:amd64. Preparing to unpack .../026-libwebp7_1.2.4-0.1_amd64.deb ... Unpacking libwebp7:amd64 (1.2.4-0.1) ... Selecting previously unselected package libtiff6:amd64. Preparing to unpack .../027-libtiff6_4.5.0-5_amd64.deb ... Unpacking libtiff6:amd64 (4.5.0-5) ... Selecting previously unselected package libgdk-pixbuf-2.0-0:amd64. Preparing to unpack .../028-libgdk-pixbuf-2.0-0_2.42.10+dfsg-1+b1_amd64.deb ... Unpacking libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-1+b1) ... Selecting previously unselected package gtk-update-icon-cache. Preparing to unpack .../029-gtk-update-icon-cache_3.24.37-2_amd64.deb ... Unpacking gtk-update-icon-cache (3.24.37-2) ... Selecting previously unselected package adwaita-icon-theme. Preparing to unpack .../030-adwaita-icon-theme_43-1_all.deb ... Unpacking adwaita-icon-theme (43-1) ... Selecting previously unselected package ca-certificates-java. Preparing to unpack .../031-ca-certificates-java_20230103_all.deb ... Unpacking ca-certificates-java (20230103) ... Selecting previously unselected package java-common. 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Selecting previously unselected package libharfbuzz0b:amd64. Preparing to unpack .../050-libharfbuzz0b_6.0.0+dfsg-3_amd64.deb ... Unpacking libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Selecting previously unselected package libpcsclite1:amd64. Preparing to unpack .../051-libpcsclite1_1.9.9-2_amd64.deb ... Unpacking libpcsclite1:amd64 (1.9.9-2) ... Selecting previously unselected package openjdk-17-jre-headless:amd64. Preparing to unpack .../052-openjdk-17-jre-headless_17.0.6+10-1_amd64.deb ... Unpacking openjdk-17-jre-headless:amd64 (17.0.6+10-1) ... Selecting previously unselected package default-jre-headless. Preparing to unpack .../053-default-jre-headless_2%3a1.17-74_amd64.deb ... Unpacking default-jre-headless (2:1.17-74) ... Selecting previously unselected package ant. Preparing to unpack .../054-ant_1.10.13-1_all.deb ... Unpacking ant (1.10.13-1) ... Selecting previously unselected package at-spi2-common. Preparing to unpack .../055-at-spi2-common_2.46.0-5_all.deb ... Unpacking at-spi2-common (2.46.0-5) ... Selecting previously unselected package m4. Preparing to unpack .../056-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../057-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../058-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../059-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../060-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../061-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. 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Selecting previously unselected package libelf1:amd64. Preparing to unpack .../068-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../069-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package gettext. Preparing to unpack .../070-gettext_0.21-12_amd64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../071-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../072-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../073-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package libgtk2.0-common. 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Setting up sgml-base (1.31) ... Setting up libgtk2.0-common (2.24.33-2) ... Setting up libatk1.0-0:amd64 (2.46.0-5) ... Setting up libwagon-http-shaded-java (3.5.3-1) ... Setting up libhttpcore-java (4.4.16-1) ... Setting up libxerces2-java (2.12.2-1) ... Setting up libjaxp1.3-java (1.3.05-6) ... Setting up openssl (3.0.8-1) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up libdrm-common (2.4.114-1) ... Setting up libcdi-api-java (1.2-3) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libsnappy-jni (1.1.8.3-1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... 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 (2.1.3-2) ... 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 (1.4-7) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libjetty9-java (9.4.50-3) ... Setting up libxcb-xfixes0:amd64 (1.15-1) ... Setting up java-wrappers (0.4) ... Setting up libplexus-languages-java (1.1.1-2) ... Setting up libjgrapht0.8-java (0.8.3-6) ... Setting up libtool (2.4.7-5) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libxcb-glx0:amd64 (1.15-1) ... Setting up libmaven-parent-java (35-1) ... Setting up libedit2:amd64 (3.1-20221030-2) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-10) ... Setting up libcommons-logging-java (1.2-3) ... Setting up libsisu-inject-java (0.3.4-2) ... Setting up libnss3:amd64 (2:3.87.1-1) ... Setting up libxcb-shm0:amd64 (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:amd64 (1.15-1) ... Setting up dh-autoreconf (20) ... Setting up libthai0:amd64 (0.1.29-1) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.4-3) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-5) ... Setting up libxcb-sync1:amd64 (1.15-1) ... Setting up libxalan2-java (2.7.2-4) ... Setting up shared-mime-info (2.2-1) ... Setting up libcommons-lang3-java (3.12.0-2) ... Setting up libxcb-dri2-0:amd64 (1.15-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libdrm2:amd64 (2.4.114-1+b1) ... Setting up dwz (0.15-1) ... Setting up libmaven-common-artifact-filters-java (3.3.2-1) ... Setting up groff-base (1.22.4-10) ... Setting up libxcb-randr0:amd64 (1.15-1) ... Setting up libllvm15:amd64 (1:15.0.6-4+b1) ... Setting up libcommons-beanutils-java (1.9.4-1) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libx11-6:amd64 (2:1.8.4-2) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-1+b1) ... Setting up libsnappy-java (1.1.8.3-1) ... Setting up libfontconfig1:amd64 (2.14.1-4) ... 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-1.2) ... Setting up libcommons-codec-java (1.15-1) ... Setting up libxcomposite1:amd64 (1:0.4.5-1) ... Setting up libavahi-client3:amd64 (0.8-10) ... Setting up libdrm-amdgpu1:amd64 (2.4.114-1+b1) ... Setting up libxcb-dri3-0:amd64 (1.15-1) ... Setting up gtk-update-icon-cache (3.24.37-2) ... Setting up libx11-xcb1:amd64 (2:1.8.4-2) ... Setting up velocity (1.7-6) ... Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libdrm-nouveau2:amd64 (2.4.114-1+b1) ... Setting up libxdamage1:amd64 (1:1.1.6-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up libcommons-compress-java (1.22-1) ... Setting up libcommons-io-java (2.11.0-2) ... Setting up libdrm-radeon1:amd64 (2.4.114-1+b1) ... Setting up libcommons-digester-java (1.8.1-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libdrm-intel1:amd64 (2.4.114-1+b1) ... Setting up libgl1-mesa-dri:amd64 (22.3.6-1+deb12u1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libxmlgraphics-commons-java (2.8-2) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.16.0-7) ... Setting up libxxf86vm1:amd64 (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 (43-1) ... 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:amd64 (1:6.0.0-2) ... Setting up libxinerama1:amd64 (2:1.1.4-3) ... Setting up libxrandr2:amd64 (2:1.5.2-2+b1) ... Setting up libcups2:amd64 (2.4.2-3) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up libmaven-shared-utils-java (3.3.4-1) ... Setting up libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libmaven-resources-plugin-java (3.3.0-1) ... Setting up libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up libglx-mesa0:amd64 (22.3.6-1+deb12u1) ... Setting up libxi6:amd64 (2:1.8-1+b1) ... Setting up libglx0:amd64 (1.6.0-1) ... Setting up libcommons-validator-java (1:1.7-1) ... Setting up libxtst6:amd64 (2:1.2.3-1.1) ... Setting up libbatik-java (1.16+dfsg-1) ... Setting up libxcursor1:amd64 (1:1.2.1-1) ... Setting up libmaven-invoker-java (3.2.0-1) ... Setting up debhelper (13.11.4) ... Setting up libgl1:amd64 (1.6.0-1) ... Setting up libmaven-clean-plugin-java (3.2.0-2) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libfop-java (1:2.8-2) ... Setting up libgtk2.0-0:amd64 (2.24.33-2) ... Setting up libmaven-archiver-java (3.6.0-1) ... Setting up openjdk-17-jre-headless:amd64 (17.0.6+10-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up ca-certificates-java (20230103) ... 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:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068_2.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: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:E-Tugra_Certification_Authority.pem Adding debian:E-Tugra_Global_Root_CA_ECC_v3.pem Adding debian:E-Tugra_Global_Root_CA_RSA_v3.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_1.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:SZAFIR_ROOT_CA2.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:TrustCor_ECA-1.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_RootCert_CA-2.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 junit4 (4.13.2-3) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up default-jre-headless (2:1.17-74) ... Setting up openjdk-17-jre:amd64 (17.0.6+10-1) ... Setting up maven-repo-helper (1.11) ... Setting up default-jre (2:1.17-74) ... Setting up libguava-java (31.1-1) ... Setting up openjdk-17-jdk-headless:amd64 (17.0.6+10-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up ant (1.10.13-1) ... Setting up junit5 (5.9.2-1) ... Setting up libplexus-container-default-java (2.1.1-1) ... Setting up openjdk-17-jdk:amd64 (17.0.6+10-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up libguice-java (4.2.3-2) ... Setting up default-jdk-headless (2:1.17-74) ... 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 (3.8.7-1) ... Setting up libmaven-shared-incremental-java (1.1-3) ... Setting up libmaven-shared-io-java (3.0.0-4) ... Setting up libplexus-bsh-factory-java (1.0~alpha7-5) ... Setting up default-jdk (2:1.17-74) ... Setting up maven (3.8.7-1) ... update-alternatives: using /usr/share/maven/bin/mvn to provide /usr/bin/mvn (mvn) in auto mode Setting up libplexus-ant-factory-java (1.0~alpha2.1-4) ... Setting up libplexus-compiler-java (2.12.1-1) ... 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 (1.10.0-1) ... 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 (2.36-9) ... Processing triggers for sgml-base (1.31) ... Setting up libvelocity-tools-java (2.0-8) ... 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 (3.4.1-2) ... 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 (2.6.3) ... Processing triggers for ca-certificates (20230311) ... 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 (20230103) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/biojava-live-1.9.5+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../biojava-live_1.9.5+dfsg-3_source.changes dpkg-buildpackage: info: source package biojava-live dpkg-buildpackage: info: source version 1:1.9.5+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Emmanuel Bourg dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean bash -c "for dir in \$(find . -name target -type d); do if [ -f \$(echo \$dir | sed -e s/target\$/pom.xml/) ]; then rm -Rf \$dir; fi done" mh_unpatchpoms -plibbiojava1.9-java dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure mh_patchpoms -plibbiojava1.9-java --debian-build --keep-pom-version --maven-repo=/build/biojava-live-1.9.5\+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/biojava-live-1.9.5\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/biojava-live-1.9.5\+dfsg/debian -Dmaven.repo.local=/build/biojava-live-1.9.5\+dfsg/debian/maven-repo --batch-mode package javadoc:jar javadoc:aggregate -DskipTests -Dnotimestamp=true -Dlocale=en_US OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release. [INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] biojava-legacy [pom] [INFO] bytecode [jar] [INFO] core [jar] [INFO] alignment [jar] [INFO] biosql [jar] [INFO] blast [jar] [INFO] sequencing [jar] [INFO] gui [jar] [INFO] phylo [jar] [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 1.9.5 [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 1.9.5 [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/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/bytecode/target/classes [INFO] /build/biojava-live-1.9.5+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/ChildContext.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/biojava-live-1.9.5+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/ChildContext.java: Recompile with -Xlint:removal for details. [INFO] /build/biojava-live-1.9.5+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/GeneratedClassLoader.java: Some input files use unchecked or unsafe operations. [INFO] /build/biojava-live-1.9.5+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/GeneratedClassLoader.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/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/bytecode/target/bytecode-1.9.5.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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/bytecode/target/bytecode-1.9.5-javadoc.jar [INFO] [INFO] --------------------------< org.biojava:core >-------------------------- [INFO] Building core 1.9.5 [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/biojava-live-1.9.5+dfsg/core/target/classes [INFO] /build/biojava-live-1.9.5+dfsg/core/src/main/java/org/biojava/bio/dist/DistributionTools.java: Some input files use or override a deprecated API. [INFO] /build/biojava-live-1.9.5+dfsg/core/src/main/java/org/biojava/bio/dist/DistributionTools.java: Recompile with -Xlint:deprecation for details. [INFO] /build/biojava-live-1.9.5+dfsg/core/src/main/java/org/biojava/bio/symbol/IntegerAlphabet.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/biojava-live-1.9.5+dfsg/core/src/main/java/org/biojava/bio/symbol/IntegerAlphabet.java: Recompile with -Xlint:removal for details. [INFO] /build/biojava-live-1.9.5+dfsg/core/src/main/java/org/biojava/utils/ChangeType.java: Some input files use unchecked or unsafe operations. [INFO] /build/biojava-live-1.9.5+dfsg/core/src/main/java/org/biojava/utils/ChangeType.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/biojava-live-1.9.5+dfsg/core/target/test-classes [INFO] /build/biojava-live-1.9.5+dfsg/core/src/test/java/org/biojava/bio/seq/io/SeqIOToolsTest.java: Some input files use or override a deprecated API. [INFO] /build/biojava-live-1.9.5+dfsg/core/src/test/java/org/biojava/bio/seq/io/SeqIOToolsTest.java: Recompile with -Xlint:deprecation for details. [INFO] /build/biojava-live-1.9.5+dfsg/core/src/test/java/org/biojavax/bio/SimpleBioEntryTest.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/biojava-live-1.9.5+dfsg/core/src/test/java/org/biojavax/bio/SimpleBioEntryTest.java: Recompile with -Xlint:removal for details. [INFO] /build/biojava-live-1.9.5+dfsg/core/src/test/java/org/biojava/bio/symbol/AlphabetManagerTest.java: Some input files use unchecked or unsafe operations. [INFO] /build/biojava-live-1.9.5+dfsg/core/src/test/java/org/biojava/bio/symbol/AlphabetManagerTest.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/biojava-live-1.9.5+dfsg/core/target/core-1.9.5.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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/core/src/main/java/org/biojava/stats/svm/tools/ClassifierExample.java:332: warning: invalid input: '&' [WARNING] * Chooses default colors & Shapes. [WARNING] ^ [WARNING] /build/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:486: warning: invalid input: '<' [WARNING] * <123 or >123 [WARNING] ^ [WARNING] /build/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:503: warning: invalid input: '<' [WARNING] * @param sb a StringBuffer123 [WARNING] ^ [WARNING] /build/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/core/src/main/java/org/biojava/bio/seq/io/EmblProcessor.java:47: warning: invalid input: '<' [WARNING] * <123 or >123 [WARNING] ^ [WARNING] /build/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:486: warning: invalid input: '<' [WARNING] * <123 or >123 [WARNING] ^ [WARNING] /build/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/core/src/main/java/org/biojava/bio/program/blast2html/HTMLRenderer.java:116: warning: invalid input: '<' [WARNING] * formats specification.

[WARNING] ^ [WARNING] /build/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:486: warning: invalid input: '<' [WARNING] * <123 or >123 [WARNING] ^ [WARNING] /build/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/core/target/core-1.9.5-javadoc.jar [INFO] [INFO] -----------------------< org.biojava:alignment >------------------------ [INFO] Building alignment 1.9.5 [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/biojava-live-1.9.5+dfsg/alignment/target/classes [INFO] /build/biojava-live-1.9.5+dfsg/alignment/src/main/java/org/biojava/bio/alignment/SubstitutionMatrix.java: /build/biojava-live-1.9.5+dfsg/alignment/src/main/java/org/biojava/bio/alignment/SubstitutionMatrix.java uses or overrides a deprecated API that is marked for removal. [INFO] /build/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/alignment/target/test-classes [INFO] /build/biojava-live-1.9.5+dfsg/alignment/src/test/java/org/biojava/bio/alignment/FlexibleAlignmentTest.java: /build/biojava-live-1.9.5+dfsg/alignment/src/test/java/org/biojava/bio/alignment/FlexibleAlignmentTest.java uses unchecked or unsafe operations. [INFO] /build/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/alignment/target/alignment-1.9.5.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/biojava-live-1.9.5+dfsg/alignment/src/main/java/org/biojava/bio/alignment/AlignmentAlgorithm.java:39: warning: invalid input: '<' [WARNING] * @author Andreas Dräger [WARNING] ^ [WARNING] /build/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/alignment/target/alignment-1.9.5-javadoc.jar [INFO] [INFO] -------------------------< org.biojava:biosql >------------------------- [INFO] Building biosql 1.9.5 [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/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/biosql/target/classes [INFO] /build/biojava-live-1.9.5+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.java: Some input files use or override a deprecated API. [INFO] /build/biojava-live-1.9.5+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.java: Recompile with -Xlint:deprecation for details. [INFO] /build/biojava-live-1.9.5+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLFeatureAnnotationChangeHub.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/biojava-live-1.9.5+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLFeatureAnnotationChangeHub.java: Recompile with -Xlint:removal for details. [INFO] /build/biojava-live-1.9.5+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.java: Some input files use unchecked or unsafe operations. [INFO] /build/biojava-live-1.9.5+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.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/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/biosql/target/test-classes [INFO] /build/biojava-live-1.9.5+dfsg/biosql/src/test/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceDBTest.java: /build/biojava-live-1.9.5+dfsg/biosql/src/test/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceDBTest.java uses or overrides a deprecated API. [INFO] /build/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/biosql/target/biosql-1.9.5.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/biojava-live-1.9.5+dfsg/biosql/target/biosql-1.9.5-javadoc.jar [INFO] [INFO] -------------------------< org.biojava:blast >-------------------------- [INFO] Building blast 1.9.5 [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/biojava-live-1.9.5+dfsg/blast/target/classes [INFO] /build/biojava-live-1.9.5+dfsg/blast/src/main/java/org/biojava/bio/program/sax/GenericSAXParserTest.java: /build/biojava-live-1.9.5+dfsg/blast/src/main/java/org/biojava/bio/program/sax/GenericSAXParserTest.java uses or overrides a deprecated API. [INFO] /build/biojava-live-1.9.5+dfsg/blast/src/main/java/org/biojava/bio/program/sax/GenericSAXParserTest.java: Recompile with -Xlint:deprecation for details. [INFO] /build/biojava-live-1.9.5+dfsg/blast/src/main/java/org/biojava/bio/program/sax/blastxml/StAXFeatureHandler.java: Some input files use unchecked or unsafe operations. [INFO] /build/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/blast/target/blast-1.9.5.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/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/blast/target/blast-1.9.5-javadoc.jar [INFO] [INFO] -----------------------< org.biojava:sequencing >----------------------- [INFO] Building sequencing 1.9.5 [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/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/sequencing/target/classes [INFO] /build/biojava-live-1.9.5+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/AbstractChromatogram.java: Some input files use or override a deprecated API. [INFO] /build/biojava-live-1.9.5+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/AbstractChromatogram.java: Recompile with -Xlint:deprecation for details. [INFO] /build/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/sequencing/src/main/java/org/biojava/bio/program/scf/SCF.java: Recompile with -Xlint:removal for details. [INFO] /build/biojava-live-1.9.5+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/AbstractChromatogram.java: Some input files use unchecked or unsafe operations. [INFO] /build/biojava-live-1.9.5+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/AbstractChromatogram.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/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/sequencing/target/sequencing-1.9.5.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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/sequencing/target/sequencing-1.9.5-javadoc.jar [INFO] [INFO] --------------------------< org.biojava:gui >--------------------------- [INFO] Building gui 1.9.5 [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/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/gui/target/classes [INFO] /build/biojava-live-1.9.5+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/SequencePanel.java: Some input files use or override a deprecated API. [INFO] /build/biojava-live-1.9.5+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/SequencePanel.java: Recompile with -Xlint:deprecation for details. [INFO] /build/biojava-live-1.9.5+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/RectangularImapRenderer.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/biojava-live-1.9.5+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/RectangularImapRenderer.java: Recompile with -Xlint:removal for details. [INFO] /build/biojava-live-1.9.5+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/AbstractBeadRenderer.java: Some input files use unchecked or unsafe operations. [INFO] /build/biojava-live-1.9.5+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/AbstractBeadRenderer.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/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/gui/target/gui-1.9.5.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/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/gui/src/main/java/org/biojava/bio/gui/glyph/RectangleGlyph.java:32: warning: invalid input: '<' [WARNING] * @author then, [WARNING] ^ [WARNING] /build/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/core/src/main/java/org/biojava/stats/svm/tools/ClassifierExample.java:332: warning: invalid input: '&' [WARNING] * Chooses default colors & Shapes. [WARNING] ^ [WARNING] /build/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:486: warning: invalid input: '<' [WARNING] * <123 or >123 [WARNING] ^ [WARNING] /build/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:503: warning: invalid input: '<' [WARNING] * @param sb a StringBuffer123 [WARNING] ^ [WARNING] /build/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/core/src/main/java/org/biojava/bio/seq/io/EmblProcessor.java:47: warning: invalid input: '<' [WARNING] * <123 or >123 [WARNING] ^ [WARNING] /build/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:486: warning: invalid input: '<' [WARNING] * <123 or >123 [WARNING] ^ [WARNING] /build/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+dfsg/core/src/main/java/org/biojava/bio/program/blast2html/HTMLRenderer.java:116: warning: invalid input: '<' [WARNING] * formats specification.

[WARNING] ^ [WARNING] /build/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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 1.9.5: [INFO] [INFO] biojava-legacy ..................................... SUCCESS [01:24 min] [INFO] bytecode ........................................... SUCCESS [ 17.344 s] [INFO] core ............................................... SUCCESS [01:01 min] [INFO] alignment .......................................... SUCCESS [ 10.289 s] [INFO] biosql ............................................. SUCCESS [ 16.253 s] [INFO] blast .............................................. SUCCESS [ 17.106 s] [INFO] sequencing ......................................... SUCCESS [ 17.604 s] [INFO] gui ................................................ SUCCESS [ 24.265 s] [INFO] phylo .............................................. SUCCESS [ 17.735 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 04:30 min [INFO] Finished at: 2024-06-20T00:17:45-12:00 [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/biojava-live-1.9.5\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/biojava-live-1.9.5\+dfsg/debian -Dmaven.repo.local=/build/biojava-live-1.9.5\+dfsg/debian/maven-repo --batch-mode test OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release. [INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] biojava-legacy [pom] [INFO] bytecode [jar] [INFO] core [jar] [INFO] alignment [jar] [INFO] biosql [jar] [INFO] blast [jar] [INFO] sequencing [jar] [INFO] gui [jar] [INFO] phylo [jar] [INFO] [INFO] ---------------------< org.biojava:biojava-legacy >--------------------- [INFO] Building biojava-legacy 1.9.5 [1/9] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] ------------------------< org.biojava:bytecode >------------------------ [INFO] Building bytecode 1.9.5 [2/9] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ bytecode --- [INFO] skip non existing resourceDirectory /build/biojava-live-1.9.5+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/biojava-live-1.9.5+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 1.9.5 [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.biojavax.SimpleRankedDocRefTest testGetStart testSetLocation testToString testGetDocumentReference testCompareTo testGetRank testHashCode testEquals testGetEnd testSetRank [INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.156 s - in org.biojavax.SimpleRankedDocRefTest [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.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: 0.003 s - in org.biojavax.SimpleDocRefTest [INFO] Running org.biojavax.DummyCrossReferenceResolverTest testGetRemoteBioEntry testGetRemoteSymbolList [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.795 s - in org.biojavax.DummyCrossReferenceResolverTest [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: 0.073 s - in org.biojavax.SimpleNoteTest [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: 0.032 s - in org.biojavax.SimpleNamespaceTest [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: 0.017 s - in org.biojavax.EmptyRichAnnotationTest [INFO] Running org.biojavax.SimpleDocRefAuthorTest testIsConsortium testToString testCompareTo testGetName testHashCode testEquals testGetExtendedName [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.SimpleDocRefAuthorTest [INFO] Running org.biojavax.SimpleCommentTest testSetComment testToString testCompareTo testGetRank testHashCode testGetComment testEquals testSetRank [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 s - in org.biojavax.SimpleCommentTest [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: 0.027 s - in org.biojavax.ontology.SimpleComparableTermTest [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: 0.015 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: 0.009 s - in org.biojavax.ontology.SimpleComparableOntologyTest [INFO] Running org.biojavax.SimpleRankedCrossRefTest testToString testGetCrossRef testCompareTo testGetRank testHashCode testEquals testSetRank [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.SimpleRankedCrossRefTest [INFO] Running org.biojavax.SimpleCrossRefTest testGetNoteSet testGetAccession testToString testCompareTo testGetAnnotation testSetNoteSet testGetVersion testHashCode testGetDbname testEquals [INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojavax.SimpleCrossRefTest [INFO] Running org.biojavax.bio.taxa.SimpleNCBITaxonNameTest testGetNameClass testToString testCompareTo testSetNameClass testGetName testHashCode testEquals testSetName [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 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: 0.056 s - in org.biojavax.bio.SimpleBioEntryTest [INFO] Running org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest testEquals [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest [INFO] Running org.biojavax.bio.seq.SimpleRichFeatureTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 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: 0.009 s - in org.biojavax.bio.seq.CompoundRichLocationTest [INFO] Running org.biojavax.bio.seq.RichLocationToolsTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojavax.bio.seq.RichLocationToolsTest [INFO] Running org.biojavax.bio.seq.io.Bug2255Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 s - in org.biojavax.bio.seq.io.Bug2255Test [INFO] Running org.biojavax.bio.seq.io.GenbankFormatTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.422 s - in org.biojavax.bio.seq.io.GenbankFormatTest [INFO] Running org.biojavax.bio.seq.io.INSDseqFormatTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.159 s - in org.biojavax.bio.seq.io.INSDseqFormatTest [INFO] Running org.biojavax.bio.seq.io.UniProtFormatTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.19 s - in org.biojavax.bio.seq.io.UniProtFormatTest [INFO] Running org.biojavax.bio.seq.io.GenbankLocationParserTest Location 467: 467 Location 340..565: 340..565 Location <345..500: <345..500 Location <1..888: <1..888 Location (102.110): (102.110) Location (23.45)..600: (23.45)..600 Location (122.133)..(204.221): (122.133)..(204.221) Location 123^124: 123^124 Location 145^177: 145^177 Location join(12..78,134..202): join(12..78,134..202) Location complement(1..23): complement(1..23) Location complement(join(2691..4571,4918..5163): complement(join(2691..4571,4918..5163)) Location join(complement(4918..5163),complement(2691..4571)): complement(join(2691..4571,4918..5163)) Location complement(34..(122.126)): complement(34..(122.126)) Location complement((122.126)..34): complement((122.126)..34) Location J00194:100..202: J00194:100..202 Location (8298.8300)..10206: (8298.8300)..10206 Location join((8298.8300)..10206,1..855): join((8298.8300)..10206,1..855) [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojavax.bio.seq.io.GenbankLocationParserTest [INFO] Running org.biojavax.bio.seq.io.Bug2249_2248Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 s - in org.biojavax.bio.seq.io.Bug2249_2248Test [INFO] Running org.biojavax.bio.seq.io.EMBLFormatTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojavax.bio.seq.io.EMBLFormatTest [INFO] Running org.biojavax.bio.seq.io.Bug2250_2256Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.502 s - in org.biojavax.bio.seq.io.Bug2250_2256Test [INFO] Running org.biojavax.bio.seq.SimpleRichLocationTest testEquals [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.seq.SimpleRichLocationTest [INFO] Running org.biojavax.ga.util.GAToolsTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 s - in org.biojavax.ga.util.GAToolsTest [INFO] Running org.biojavax.ga.util.WeightedSetTest [INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 s - in org.biojavax.ga.util.WeightedSetTest [INFO] Running org.biojavax.ga.impl.SimplePopulationTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 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 s - in org.biojavax.ga.impl.SimpleOrganismTest [INFO] Running org.biojavax.ga.functions.ProportionalSelectionTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojavax.ga.functions.ProportionalSelectionTest [INFO] Running org.biojavax.ga.functions.AbstractCrossOverFunctionTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojavax.ga.functions.AbstractCrossOverFunctionTest [INFO] Running org.biojavax.ga.functions.SimpleMutationFunctionTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 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: 0.006 s - in org.biojavax.ga.functions.SimpleCrossOverFunctionTest [INFO] Running org.biojavax.ga.functions.AbstractMutationFunctionTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.functions.AbstractMutationFunctionTest [INFO] Running org.biojavax.SimpleRichAnnotationTest testGetNoteSet testAddNote testAsMap testClear testKeys testToString testGetNote testSetNoteSet testContains testGetPropertys testSetProperty testRemoveNote testGetProperty testRemoveProperty testRemoveProperty2 testContainsProperty [INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.SimpleRichAnnotationTest [INFO] Running org.biojava.naming.ObdaUriParserTest urn:obda.org:format:embl/ac :trail oneName lead: [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.naming.ObdaUriParserTest [INFO] Running org.biojava.naming.ObdaInitialContextFactoryTest Reached Attributes: No attributes Binding: urn -> org.biojava.naming.ObdaContext@130f889 Reached urn Attributes: No attributes Binding: open-bio.org -> org.biojava.naming.ObdaContext@1188e820 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@166fa74d 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@40f08448 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@276438c9 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@588df31b 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@33b37288 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@77a57272 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@7181ae3f 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@46238e3f 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@6e2c9341 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@32464a14 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@4e4aea35 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@1442d7b5 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@1efee8e7 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@d6da883} My component is urn:open-bio.org:format:embl lookup: 'open-bio.org:format:embl' for {open-bio.org=org.biojava.naming.ObdaContext@799d4f69} My component is open-bio.org:format:embl lookup: 'format:embl' for {type=org.biojava.naming.ObdaContext@49c43f4e, format=org.biojava.naming.ObdaContext@290dbf45, alphabet=org.biojava.naming.ObdaContext@12028586} My component is format:embl lookup: 'embl' for {enzyme=org.biojava.naming.ObdaContext@17776a8, genbank=org.biojava.naming.ObdaContext@69a10787, swissprot=org.biojava.naming.ObdaContext@2d127a61, embl=org.biojava.naming.ObdaContext@2bbaf4f0} My component is embl [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.137 s - in org.biojava.naming.ObdaInitialContextFactoryTest [INFO] Running org.biojava.utils.RepeatedCharSequenceTest JAM [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.utils.RepeatedCharSequenceTest [INFO] Running org.biojava.utils.walker.WalkerFactoryTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 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: 0.06 s - in org.biojava.utils.walker.WalkerTest [INFO] Running org.biojava.utils.process.AllTests [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.361 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: 0.155 s - in org.biojava.utils.process.ExternalProcessTest [INFO] Running org.biojava.utils.ListToolsTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.ListToolsTest [INFO] Running org.biojava.utils.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.regex.RegexTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojava.utils.regex.RegexTest [INFO] Running org.biojava.utils.automata.NfaTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.utils.automata.NfaTest [INFO] Running org.biojava.utils.lsid.LifeScienceIdentifierTest [INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 s - in org.biojava.utils.lsid.LifeScienceIdentifierTest [INFO] Running org.biojava.utils.SmallMapTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.utils.SmallMapTest [INFO] Running org.biojava.ontology.ParseOBOFileTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.429 s - in org.biojava.ontology.ParseOBOFileTest [INFO] Running org.biojava.ontology.TermImplTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.ontology.TermImplTest [INFO] Running org.biojava.ontology.OntologyTest [INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.ontology.OntologyTest [INFO] Running org.biojava.ontology.TripleImplTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.ontology.TripleImplTest [INFO] Running org.biojava.bio.AnnotationTypeTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojava.bio.AnnotationTypeTest [INFO] Running org.biojava.bio.search.MaxMismatchPatternTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.search.MaxMismatchPatternTest [INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest [INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest [INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest [INFO] Running org.biojava.bio.search.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.MergeAnnotationTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.MergeAnnotationTest [INFO] Running org.biojava.bio.dist.TranslatedDistributionTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.dist.TranslatedDistributionTest [INFO] Running org.biojava.bio.dist.DistributionTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.dist.DistributionTest [INFO] Running org.biojava.bio.dist.DistSerTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.325 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: 0.11 s - in org.biojava.bio.dist.DistributionToolsTest [INFO] Running org.biojava.bio.dp.DPSerializationTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.158 s - in org.biojava.bio.dp.DPSerializationTest [INFO] Running org.biojava.bio.dp.EmissionStateEventTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 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: 0.014 s - in org.biojava.bio.dp.MarkovModelEventTest [INFO] Running org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest [INFO] Running org.biojava.bio.symbol.SimpleCodonPrefTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.182 s - in org.biojava.bio.symbol.SimpleCodonPrefTest [INFO] Running org.biojava.bio.symbol.AlphabetSerializationTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.207 s - in org.biojava.bio.symbol.AlphabetSerializationTest [INFO] Running org.biojava.bio.symbol.GappedSymbolListTest [INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.141 s - in org.biojava.bio.symbol.GappedSymbolListTest [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.BetweenLocationTest [INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 s - in org.biojava.bio.symbol.BetweenLocationTest [INFO] Running org.biojava.bio.symbol.CompoundLocationTest [INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.107 s - in org.biojava.bio.symbol.CompoundLocationTest [INFO] Running org.biojava.bio.symbol.LinearAlphabetIndexTest symbolForIndex getAlphabet indexForSymbol [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.LinearAlphabetIndexTest [INFO] Running org.biojava.bio.symbol.NameTokenizationTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 s - in org.biojava.bio.symbol.NameTokenizationTest [INFO] Running org.biojava.bio.symbol.RangeLocationTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.RangeLocationTest [INFO] Running org.biojava.bio.symbol.TestSoftMaskedAlphabet [INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojava.bio.symbol.TestSoftMaskedAlphabet [INFO] Running org.biojava.bio.symbol.CircularLocationTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 s - in org.biojava.bio.symbol.CircularLocationTest [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.SimpleWobbleDistributionTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.symbol.SimpleWobbleDistributionTest [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: 0.111 s - in org.biojava.bio.symbol.UkkonenSuffixTreeTest [INFO] Running org.biojava.bio.symbol.IndexedNoAmbPackTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.IndexedNoAmbPackTest [INFO] Running org.biojava.bio.symbol.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: 6.069 s - in org.biojava.bio.symbol.CrossProductAlphabetIndexTest [INFO] Running org.biojava.bio.symbol.MotifToolsTest [INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.symbol.MotifToolsTest [INFO] Running org.biojava.bio.symbol.SymbolSerializationTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.bio.symbol.SymbolSerializationTest [INFO] Running org.biojava.bio.symbol.SimpleBasisSymbolEventTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.SimpleBasisSymbolEventTest [INFO] Running org.biojava.bio.symbol.CrossProductTokenizationTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.CrossProductTokenizationTest [INFO] Running org.biojava.bio.symbol.SimpleSymbolListTest [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.SimpleSymbolListTest [INFO] Running org.biojava.bio.symbol.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.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.SimpleAtomicSymbolEventTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.SimpleAtomicSymbolEventTest [INFO] Running org.biojava.bio.symbol.SimpleSymbolEventTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.SimpleSymbolEventTest [INFO] Running org.biojava.bio.symbol.SymbolListTest [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.121 s - in org.biojava.bio.symbol.SymbolListTest [INFO] Running org.biojava.bio.symbol.DoubleAlphabetTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.DoubleAlphabetTest [INFO] Running org.biojava.bio.symbol.AlphabetManagerTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.AlphabetManagerTest [INFO] Running org.biojava.bio.molbio.RestrictionEnzymeTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 s - in org.biojava.bio.molbio.RestrictionEnzymeTest [INFO] Running org.biojava.bio.molbio.RestrictionEnzymeManagerTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojava.bio.molbio.RestrictionEnzymeManagerTest [INFO] Running org.biojava.bio.program.phred.PhredToolsTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.program.phred.PhredToolsTest [INFO] Running org.biojava.bio.program.indexdb.IndexToolsTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.252 s - in org.biojava.bio.program.indexdb.IndexToolsTest [INFO] Running org.biojava.bio.proteomics.IsoelectricPointCalcTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.bio.proteomics.IsoelectricPointCalcTest [INFO] Running org.biojava.bio.proteomics.MassCalcTest [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojava.bio.proteomics.MassCalcTest [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: 0.018 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: 0.141 s - in org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest [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.seq.DNAToolsTest [INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.DNAToolsTest [INFO] Running org.biojava.bio.seq.SimpleAssemblyTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.033 s - in org.biojava.bio.seq.SimpleAssemblyTest [INFO] Running org.biojava.bio.seq.FilterUtilsTest [INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 s - in org.biojava.bio.seq.FilterUtilsTest [INFO] Running org.biojava.bio.seq.RNAToolsTest [INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojava.bio.seq.RNAToolsTest [INFO] Running org.biojava.bio.seq.filter.FilterTransformerTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.043 s - in org.biojava.bio.seq.filter.FilterTransformerTest [INFO] Running org.biojava.bio.seq.CircularSequenceTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.CircularSequenceTest [INFO] Running org.biojava.bio.seq.FeatureFilterTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.seq.FeatureFilterTest [INFO] Running org.biojava.bio.seq.MergeFeatureHolderTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.seq.MergeFeatureHolderTest [INFO] Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 s - in org.biojava.bio.seq.project.ProjectedFeatureHolderTest [INFO] Running org.biojava.bio.seq.ProteinToolsTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.bio.seq.ProteinToolsTest [INFO] Running org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest [INFO] Running org.biojava.bio.seq.io.MSFAlignmentFormatTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.seq.io.MSFAlignmentFormatTest [INFO] Running org.biojava.bio.seq.io.LocationFormatterTest [INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.118 s - in org.biojava.bio.seq.io.LocationFormatterTest [INFO] Running org.biojava.bio.seq.io.filterxml.FilterXMLTest [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.144 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: 1.66 s - in org.biojava.bio.seq.io.SmartSequenceBuilderTest [INFO] Running org.biojava.bio.seq.io.SymbolListCharSequenceTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.io.SymbolListCharSequenceTest [INFO] Running org.biojava.bio.seq.io.SeqIOToolsTest idb length: 79 [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.941 s - in org.biojava.bio.seq.io.SeqIOToolsTest [INFO] Running org.biojava.bio.seq.NewSimpleAssemblyTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojava.bio.seq.NewSimpleAssemblyTest [INFO] Running org.biojava.bio.seq.SeqSerializationTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.134 s - in org.biojava.bio.seq.SeqSerializationTest [INFO] Running org.biojava.bio.seq.FeatureHolderUtilsTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojava.bio.seq.FeatureHolderUtilsTest [INFO] Running org.biojava.bio.seq.impl.GappedSequenceTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojava.bio.seq.impl.GappedSequenceTest [INFO] Running org.biojava.bio.seq.impl.SubSequenceTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 s - in org.biojava.bio.seq.impl.SubSequenceTest [INFO] Running org.biojava.bio.seq.impl.ViewSeqSerializationTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 s - in org.biojava.bio.seq.impl.ViewSeqSerializationTest [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: 0.013 s - in org.biojava.bio.seq.impl.ViewSequenceTest [INFO] Running org.biojava.bio.seq.db.HashSequenceDBTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.seq.db.HashSequenceDBTest [INFO] Running org.biojava.bio.seq.db.EmblCDROMIndexStoreTest [INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 s - in org.biojava.bio.seq.db.EmblCDROMIndexStoreTest [INFO] Running org.biojava.bio.seq.db.TestHashSequenceDB [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojava.bio.seq.db.TestHashSequenceDB [INFO] Running org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest [INFO] Running org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest [INFO] Running org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest [INFO] Running org.biojava.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.SystemRegistryTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 s - in org.biojava.directory.SystemRegistryTest [INFO] Running org.biojava.directory.RegistryConfigurationTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.directory.RegistryConfigurationTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 890, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] -----------------------< org.biojava:alignment >------------------------ [INFO] Building alignment 1.9.5 [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.FlexibleAlignmentTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.12 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: 0.078 s - in org.biojava.bio.alignment.AlignmentPairTest [INFO] Running org.biojava.bio.alignment.SubstitutionMatrixTest [INFO] Tests run: 96, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.769 s - in org.biojava.bio.alignment.SubstitutionMatrixTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 102, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] -------------------------< org.biojava:biosql >------------------------- [INFO] Building biosql 1.9.5 [5/9] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biosql --- [INFO] skip non existing resourceDirectory /build/biojava-live-1.9.5+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/biojava-live-1.9.5+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: 0.12 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 1.9.5 [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.sax.BlastTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.495 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: 0.344 s - in org.biojava.bio.program.sax.blastxml.BlastXMLTest [INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.335 s - in org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.894 s - in org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.276 s - in org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.821 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.957 s - in org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.564 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.285 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.238 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.529 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.108 s - in org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.27 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.333 s - in org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.749 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.745 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test [INFO] [INFO] Results: [INFO] [INFO] Tests run: 118, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] -----------------------< org.biojava:sequencing >----------------------- [INFO] Building sequencing 1.9.5 [7/9] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ sequencing --- [INFO] skip non existing resourceDirectory /build/biojava-live-1.9.5+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.fastq.SangerFastqReaderTest [INFO] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.577 s - in org.biojava.bio.program.fastq.SangerFastqReaderTest [INFO] Running org.biojava.bio.program.fastq.FastqToolsTest [INFO] Tests run: 38, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.973 s - in org.biojava.bio.program.fastq.FastqToolsTest [INFO] Running org.biojava.bio.program.fastq.SolexaFastqWriterTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 s - in org.biojava.bio.program.fastq.SolexaFastqWriterTest [INFO] Running org.biojava.bio.program.fastq.ConvertTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.104 s - in org.biojava.bio.program.fastq.ConvertTest [INFO] Running org.biojava.bio.program.fastq.FastqBuilderTest [INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 s - in org.biojava.bio.program.fastq.FastqBuilderTest [INFO] Running org.biojava.bio.program.fastq.SangerFastqWriterTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojava.bio.program.fastq.SangerFastqWriterTest [INFO] Running org.biojava.bio.program.fastq.FastqTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.bio.program.fastq.FastqTest [INFO] Running org.biojava.bio.program.fastq.SolexaFastqReaderTest [INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 s - in org.biojava.bio.program.fastq.SolexaFastqReaderTest [INFO] Running org.biojava.bio.program.fastq.IlluminaFastqWriterTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.biojava.bio.program.fastq.IlluminaFastqWriterTest [INFO] Running org.biojava.bio.program.fastq.IlluminaFastqReaderTest [INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.06 s - in org.biojava.bio.program.fastq.IlluminaFastqReaderTest [INFO] Running org.biojava.bio.program.fastq.StreamingFastqParserTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 s - in org.biojava.bio.program.fastq.StreamingFastqParserTest [INFO] Running org.biojava.bio.program.fastq.FastqVariantTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 s - in org.biojava.bio.program.fastq.FastqVariantTest [INFO] Running org.biojava.bio.program.scf.SCFTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.224 s - in org.biojava.bio.program.scf.SCFTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 192, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] --------------------------< org.biojava:gui >--------------------------- [INFO] Building gui 1.9.5 [8/9] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ gui --- [INFO] skip non existing resourceDirectory /build/biojava-live-1.9.5+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/biojava-live-1.9.5+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 1.9.5 [9/9] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ phylo --- [INFO] skip non existing resourceDirectory /build/biojava-live-1.9.5+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: 0.759 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 1.9.5: [INFO] [INFO] biojava-legacy ..................................... SUCCESS [ 0.023 s] [INFO] bytecode ........................................... SUCCESS [ 2.288 s] [INFO] core ............................................... SUCCESS [ 21.225 s] [INFO] alignment .......................................... SUCCESS [ 10.424 s] [INFO] biosql ............................................. SUCCESS [ 10.323 s] [INFO] blast .............................................. SUCCESS [ 30.241 s] [INFO] sequencing ......................................... SUCCESS [ 10.337 s] [INFO] gui ................................................ SUCCESS [ 0.170 s] [INFO] phylo .............................................. SUCCESS [ 10.307 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:35 min [INFO] Finished at: 2024-06-20T00:19:27-12:00 [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/biojava-live-1.9.5\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/biojava-live-1.9.5\+dfsg/debian -Dmaven.repo.local=/build/biojava-live-1.9.5\+dfsg/debian/maven-repo --batch-mode -Ddebian.dir=/build/biojava-live-1.9.5\+dfsg/debian -Ddebian.package=libbiojava1.9-java -Dmaven.repo.local=/build/biojava-live-1.9.5\+dfsg/debian/maven-repo -Dinstall.to.usj=true org.debian.maven:debian-maven-plugin:2.6:install OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release. [INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] biojava-legacy [pom] [INFO] bytecode [jar] [INFO] core [jar] [INFO] alignment [jar] [INFO] biosql [jar] [INFO] blast [jar] [INFO] sequencing [jar] [INFO] gui [jar] [INFO] phylo [jar] [INFO] [INFO] ---------------------< org.biojava:biojava-legacy >--------------------- [INFO] Building biojava-legacy 1.9.5 [1/9] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-legacy --- [INFO] Cleaning pom file: /build/biojava-live-1.9.5+dfsg/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava1.9-java [INFO] --rules=/build/biojava-live-1.9.5+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/biojava-live-1.9.5+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/biojava-live-1.9.5+dfsg/debian/maven.publishedRules [INFO] --no-parent [INFO] [INFO] ------------------------< org.biojava:bytecode >------------------------ [INFO] Building bytecode 1.9.5 [2/9] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ bytecode --- [INFO] Cleaning pom file: /build/biojava-live-1.9.5+dfsg/bytecode/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava1.9-java [INFO] --rules=/build/biojava-live-1.9.5+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/biojava-live-1.9.5+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/biojava-live-1.9.5+dfsg/debian/maven.publishedRules [INFO] Install jar for bytecode into /usr/share/java [INFO] [INFO] --------------------------< org.biojava:core >-------------------------- [INFO] Building core 1.9.5 [3/9] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ core --- [INFO] Cleaning pom file: /build/biojava-live-1.9.5+dfsg/core/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava1.9-java [INFO] --rules=/build/biojava-live-1.9.5+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/biojava-live-1.9.5+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/biojava-live-1.9.5+dfsg/debian/maven.publishedRules [INFO] Install jar for core into /usr/share/java [INFO] [INFO] -----------------------< org.biojava:alignment >------------------------ [INFO] Building alignment 1.9.5 [4/9] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ alignment --- [INFO] Cleaning pom file: /build/biojava-live-1.9.5+dfsg/alignment/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava1.9-java [INFO] --rules=/build/biojava-live-1.9.5+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/biojava-live-1.9.5+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/biojava-live-1.9.5+dfsg/debian/maven.publishedRules [INFO] Install jar for alignment into /usr/share/java [INFO] [INFO] -------------------------< org.biojava:biosql >------------------------- [INFO] Building biosql 1.9.5 [5/9] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biosql --- [INFO] Cleaning pom file: /build/biojava-live-1.9.5+dfsg/biosql/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava1.9-java [INFO] --rules=/build/biojava-live-1.9.5+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/biojava-live-1.9.5+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/biojava-live-1.9.5+dfsg/debian/maven.publishedRules [INFO] Install jar for biosql into /usr/share/java [INFO] [INFO] -------------------------< org.biojava:blast >-------------------------- [INFO] Building blast 1.9.5 [6/9] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ blast --- [INFO] Cleaning pom file: /build/biojava-live-1.9.5+dfsg/blast/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava1.9-java [INFO] --rules=/build/biojava-live-1.9.5+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/biojava-live-1.9.5+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/biojava-live-1.9.5+dfsg/debian/maven.publishedRules [INFO] Install jar for blast into /usr/share/java [INFO] [INFO] -----------------------< org.biojava:sequencing >----------------------- [INFO] Building sequencing 1.9.5 [7/9] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ sequencing --- [INFO] Cleaning pom file: /build/biojava-live-1.9.5+dfsg/sequencing/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava1.9-java [INFO] --rules=/build/biojava-live-1.9.5+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/biojava-live-1.9.5+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/biojava-live-1.9.5+dfsg/debian/maven.publishedRules [INFO] Install jar for sequencing into /usr/share/java [INFO] [INFO] --------------------------< org.biojava:gui >--------------------------- [INFO] Building gui 1.9.5 [8/9] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ gui --- [INFO] Cleaning pom file: /build/biojava-live-1.9.5+dfsg/gui/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava1.9-java [INFO] --rules=/build/biojava-live-1.9.5+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/biojava-live-1.9.5+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/biojava-live-1.9.5+dfsg/debian/maven.publishedRules [INFO] Install jar for gui into /usr/share/java [INFO] [INFO] -------------------------< org.biojava:phylo >-------------------------- [INFO] Building phylo 1.9.5 [9/9] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ phylo --- [INFO] Cleaning pom file: /build/biojava-live-1.9.5+dfsg/phylo/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava1.9-java [INFO] --rules=/build/biojava-live-1.9.5+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/biojava-live-1.9.5+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/biojava-live-1.9.5+dfsg/debian/maven.publishedRules [INFO] Install jar for phylo into /usr/share/java [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava-legacy 1.9.5: [INFO] [INFO] biojava-legacy ..................................... SUCCESS [ 1.829 s] [INFO] bytecode ........................................... SUCCESS [ 0.244 s] [INFO] core ............................................... SUCCESS [ 0.228 s] [INFO] alignment .......................................... SUCCESS [ 0.140 s] [INFO] biosql ............................................. SUCCESS [ 0.168 s] [INFO] blast .............................................. SUCCESS [ 0.172 s] [INFO] sequencing ......................................... SUCCESS [ 0.180 s] [INFO] gui ................................................ SUCCESS [ 0.180 s] [INFO] phylo .............................................. SUCCESS [ 0.180 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 4.153 s [INFO] Finished at: 2024-06-20T00:19:37-12:00 [INFO] ------------------------------------------------------------------------  mh_resolve_dependencies --non-interactive --offline --build -plibbiojava1.9-java --javadoc --base-directory=/build/biojava-live-1.9.5\+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/biojava-live-1.9.5+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/biojava-live-1.9.5+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 'libbiojava-java' in '../libbiojava-java_1.9.5+dfsg-3_all.deb'. dpkg-deb: building package 'libbiojava1.9-java' in '../libbiojava1.9-java_1.9.5+dfsg-3_all.deb'. dpkg-deb: building package 'libbiojava-java-doc' in '../libbiojava-java-doc_1.9.5+dfsg-3_all.deb'. dpkg-genbuildinfo --build=binary -O../biojava-live_1.9.5+dfsg-3_amd64.buildinfo dpkg-genchanges --build=binary -O../biojava-live_1.9.5+dfsg-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1691504 and its subdirectories I: Current time: Thu Jun 20 00:22:37 -12 2024 I: pbuilder-time-stamp: 1718886157