I: pbuilder: network access will be disabled during build I: Current time: Mon May 20 16:55:22 +14 2024 I: pbuilder-time-stamp: 1716173722 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [biojava6-live_6.1.0+dfsg-4.dsc] I: copying [./biojava6-live_6.1.0+dfsg.orig-forester.tar.gz] I: copying [./biojava6-live_6.1.0+dfsg.orig-jcolorbrewer.tar.gz] I: copying [./biojava6-live_6.1.0+dfsg.orig.tar.gz] I: copying [./biojava6-live_6.1.0+dfsg-4.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Feb 7 10:35:54 2023 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./biojava6-live_6.1.0+dfsg-4.dsc: no acceptable signature found dpkg-source: info: extracting biojava6-live in biojava6-live-6.1.0+dfsg dpkg-source: info: unpacking biojava6-live_6.1.0+dfsg.orig.tar.gz dpkg-source: info: unpacking biojava6-live_6.1.0+dfsg.orig-forester.tar.gz dpkg-source: info: unpacking biojava6-live_6.1.0+dfsg.orig-jcolorbrewer.tar.gz dpkg-source: info: unpacking biojava6-live_6.1.0+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_itext_class_updates.patch dpkg-source: info: applying use_simple_json.patch dpkg-source: info: applying fix_import.patch dpkg-source: info: applying fix_ascii_characters_mapping.patch dpkg-source: info: applying skip_network_related_tests.patch dpkg-source: info: applying remove_openchart_use.patch dpkg-source: info: applying ignore_fake_tests.patch dpkg-source: info: applying poms.patch dpkg-source: info: applying jmol_path_in_pom.patch dpkg-source: info: applying remove_tests_needing_junitx.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3566877/tmp/hooks/D01_modify_environment starting debug: Running on codethink02-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 20 02:55 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/3566877/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3566877/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=e2836464a4d64155a454e83546e4624f LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3566877 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.nHaBZWrb/pbuilderrc_o48G --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.nHaBZWrb/b2 --logfile b2/build.log biojava6-live_6.1.0+dfsg-4.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 19 07:42 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3566877/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), javahelper, maven-debian-helper, default-jdk, default-jdk-doc, junit4, libactivation-java, libciftools-java, libcommons-codec-java, libcommons-math-java, libguava-java, libitext5-java, libjackson2-databind-java, libjaxb-api-java, libjaxb-java, libjgrapht-java, libjmol-java (>= 14.32.77+dfsg-1~), libjson-simple-java, liblog4j2-java, libmaven-antrun-plugin-java, libmaven-assembly-plugin-java, libmaven-dependency-plugin-java, libmaven-deploy-plugin-java, libmaven-enforcer-plugin-java, libmaven-install-plugin-java, libmaven-javadoc-plugin-java, libmaven-jaxb2-plugin-java, libmmtf-java, libslf4j-java, libvecmath-java, libxmlunit-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 ... 19763 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 javahelper; however: Package javahelper 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 default-jdk-doc; however: Package default-jdk-doc is not installed. pbuilder-satisfydepends-dummy depends on junit4; however: Package junit4 is not installed. pbuilder-satisfydepends-dummy depends on libactivation-java; however: Package libactivation-java is not installed. pbuilder-satisfydepends-dummy depends on libciftools-java; however: Package libciftools-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-codec-java; however: Package libcommons-codec-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-math-java; however: Package libcommons-math-java is not installed. pbuilder-satisfydepends-dummy depends on libguava-java; however: Package libguava-java is not installed. pbuilder-satisfydepends-dummy depends on libitext5-java; however: Package libitext5-java is not installed. pbuilder-satisfydepends-dummy depends on libjackson2-databind-java; however: Package libjackson2-databind-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 libjaxb-java; however: Package libjaxb-java is not installed. pbuilder-satisfydepends-dummy depends on libjgrapht-java; however: Package libjgrapht-java is not installed. pbuilder-satisfydepends-dummy depends on libjmol-java (>= 14.32.77+dfsg-1~); however: Package libjmol-java is not installed. pbuilder-satisfydepends-dummy depends on libjson-simple-java; however: Package libjson-simple-java is not installed. pbuilder-satisfydepends-dummy depends on liblog4j2-java; however: Package liblog4j2-java is not installed. pbuilder-satisfydepends-dummy depends on libmaven-antrun-plugin-java; however: Package libmaven-antrun-plugin-java is not installed. pbuilder-satisfydepends-dummy depends on libmaven-assembly-plugin-java; however: Package libmaven-assembly-plugin-java is not installed. pbuilder-satisfydepends-dummy depends on libmaven-dependency-plugin-java; however: Package libmaven-dependency-plugin-java is not installed. pbuilder-satisfydepends-dummy depends on libmaven-deploy-plugin-java; however: Package libmaven-deploy-plugin-java is not installed. pbuilder-satisfydepends-dummy depends on libmaven-enforcer-plugin-java; however: Package libmaven-enforcer-plugin-java is not installed. pbuilder-satisfydepends-dummy depends on libmaven-install-plugin-java; however: Package libmaven-install-plugin-java 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 libmaven-jaxb2-plugin-java; however: Package libmaven-jaxb2-plugin-java is not installed. pbuilder-satisfydepends-dummy depends on libmmtf-java; however: Package libmmtf-java is not installed. pbuilder-satisfydepends-dummy depends on libslf4j-java; however: Package libslf4j-java is not installed. pbuilder-satisfydepends-dummy depends on libvecmath-java; however: Package libvecmath-java is not installed. pbuilder-satisfydepends-dummy depends on libxmlunit-java; however: Package libxmlunit-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} ant-optional{a} at-spi2-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} binfmt-support{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} dctrl-tools{a} debhelper{a} default-jdk{a} default-jdk-doc{a} default-jdk-headless{a} default-jre{a} default-jre-headless{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} dwz{a} fastjar{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gnupg-utils{a} gpg{a} gpg-agent{a} gpg-wks-client{a} gpgconf{a} gpgsm{a} groff-base{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} intltool-debian{a} jarwrapper{a} java-common{a} java-wrappers{a} javahelper{a} junit{a} junit4{a} junit5{a} libactivation-java{a} libantlr4-runtime-java{a} libaopalliance-java{a} libapache-pom-java{a} libapfloat-java{a} libapiguardian-java{a} libarchive-zip-perl{a} libargs4j-java{a} libasm-java{a} libasound2-data{a} libasound2t64{a} libassuan0{a} libatinject-jsr330-api-java{a} libatk1.0-0t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libb-hooks-op-check-perl{a} libbatik-java{a} libbrotli1{a} libbsd0{a} libbsh-java{a} libcairo2{a} libcdi-api-java{a} libciftools-java{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcodemodel-java{a} libcom-err2{a} libcommons-beanutils-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-collections4-java{a} libcommons-compress-java{a} libcommons-configuration-java{a} libcommons-digester-java{a} libcommons-exec-java{a} libcommons-io-java{a} libcommons-lang-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-math-java{a} libcommons-parent-java{a} libcommons-text-java{a} libcommons-validator-java{a} libcups2t64{a} libdata-optlist-perl{a} libdatrie1{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdom4j-java{a} libdoxia-core-java{a} libdoxia-java{a} libdoxia-sitetools-java{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libdtd-parser-java{a} libdynaloader-functions-perl{a} libedit2{a} libel-api-java{a} libelf1t64{a} libencode-locale-perl{a} liberror-prone-java{a} libexec-maven-plugin-java{a} libexpat1{a} libfastinfoset-java{a} libfastutil-java{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} libfontbox2-java{a} libfontconfig1{a} libfop-java{a} libfreetype6{a} libfribidi0{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libgif7{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0t64{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgoogle-gson-java{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgtk2.0-0t64{a} libgtk2.0-common{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libhttpclient-java{a} libhttpcore-java{a} libicu72{a} libimport-into-perl{a} libinchi1{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libistack-commons-java{a} libitext1-java{a} libitext5-java{a} libjackson2-annotations-java{a} libjackson2-core-java{a} libjackson2-databind-java{a} libjakarta-activation-java{a} libjansi-java{a} libjaxb-api-java{a} libjaxb-java{a} libjaxen-java{a} libjaxp1.3-java{a} libjbig0{a} libjetty9-java{a} libjgrapht-java{a} libjgraphx-java{a} libjheaps-java{a} libjmol-java{a} libjni-inchi-java{a} libjni-inchi-jni{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-jquery-ui-theme-base{a} libjson-simple-java{a} libjsoup-java{a} libjsp-api-java{a} libjsr305-java{a} libjtidy-java{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libksba8{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblightcouch-java{a} libllvm17t64{a} liblog4j1.2-java{a} liblog4j2-java{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1t64{a} libmaven-antrun-plugin-java{a} libmaven-archiver-java{a} libmaven-artifact-transfer-java{a} libmaven-assembly-plugin-java{a} libmaven-clean-plugin-java{a} libmaven-common-artifact-filters-java{a} libmaven-compiler-plugin-java{a} libmaven-dependency-analyzer-java{a} libmaven-dependency-plugin-java{a} libmaven-dependency-tree-java{a} libmaven-deploy-plugin-java{a} libmaven-enforcer-plugin-java{a} libmaven-file-management-java{a} libmaven-filtering-java{a} libmaven-install-plugin-java{a} libmaven-invoker-java{a} libmaven-jar-plugin-java{a} libmaven-javadoc-plugin-java{a} libmaven-jaxb2-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} libmmtf-java{a} libmodule-runtime-perl{a} libmongodb-java{a} libmoo-perl{a} libmsgpack-java{a} libnaga-java{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnpth0t64{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} libparams-classify-perl{a} libparams-util-perl{a} libpcsclite1{a} libpicocli-java{a} libpipeline1{a} libpixman-1-0{a} libplexus-ant-factory-java{a} libplexus-archiver-java{a} libplexus-bsh-factory-java{a} libplexus-build-api-java{a} libplexus-cipher-java{a} libplexus-classworlds-java{a} libplexus-compiler-java{a} libplexus-component-annotations-java{a} libplexus-container-default-java{a} libplexus-container-default1.5-java{a} libplexus-i18n-java{a} libplexus-interactivity-api-java{a} libplexus-interpolation-java{a} libplexus-io-java{a} libplexus-languages-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libplexus-velocity-java{a} libpng16-16t64{a} libproc2-0{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqdox-java{a} libqdox2-java{a} libreadline8t64{a} librelaxng-datatype-java{a} librngom-java{a} librole-tiny-perl{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libservlet-api-java{a} libsharpyuv0{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libstax-ex-java{a} libstreambuffer-java{a} libsub-exporter-perl{a} libsub-install-perl{a} libsub-override-perl{a} libsub-prototype-perl{a} libsub-quote-perl{a} libsurefire-java{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libtxw2-java{a} libuchardet0{a} libunivocity-parsers-java{a} liburi-perl{a} libvecmath-java{a} libvelocity-tools-java{a} libvulkan1{a} libwagon-file-java{a} libwagon-http-java{a} libwagon-http-shaded-java{a} libwagon-provider-api-java{a} libwebp7{a} libwebsocket-api-java{a} libwww-perl{a} libwww-robotrules-perl{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} libxmlunit-java{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxsom-java{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} media-types{a} netbase{a} openjdk-17-doc{a} openjdk-17-jdk{a} openjdk-17-jdk-headless{a} openjdk-17-jre{a} openjdk-17-jre-headless{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} procps{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} tzdata{a} unzip{a} velocity{a} wdiff{a} x11-common{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf curl dbus debian-keyring dput dput-ng dupload equivs fonts-dejavu-extra icc-profiles-free javascript-common krb5-locales libarchive-cpio-perl libatk-wrapper-java-jni libdata-dump-perl libdistro-info-perl libgail-common libgdk-pixbuf2.0-bin libgit-wrapper-perl libgitlab-api-v4-perl libglib2.0-data libgtk2.0-bin libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjson-perl libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl librsvg2-common libsasl2-modules libsaxon-java libsoap-lite-perl libstring-shellquote-perl libxstring-perl libxt-dev licensecheck lintian lynx mesa-vulkan-drivers pristine-tar psmisc python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg strace wget xdg-user-dirs 0 packages upgraded, 412 newly installed, 0 to remove and 0 not upgraded. Need to get 327 MB of archives. After unpacking 1113 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 binfmt-support arm64 2.2.2-7 [61.4 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libpython3.11-minimal arm64 3.11.9-1 [813 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 python3.11-minimal arm64 3.11.9-1 [1767 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.11.8-1 [26.3 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024a-4 [255 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-4 [69.3 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libpython3.11-stdlib arm64 3.11.9-1 [1775 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 python3.11 arm64 3.11.9-1 [602 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.11.8-1 [9332 B] Get: 15 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.11.8-1 [27.4 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-4 [61.7 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-4 [869 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.2.1-3 [1324 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20240203 [158 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.1-1 [93.2 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [311 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.80.2-1 [1393 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 shared-mime-info arm64 2.4-4 [755 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3 [172 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.43-5 [272 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.20-1 [41.5 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b1 [30.4 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-4+b1 [142 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [111 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.4.0-0.1 [267 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-4 [307 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.12+dfsg-1 [130 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 gtk-update-icon-cache arm64 3.24.41-4 [46.2 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 adwaita-icon-theme all 46.0-1 [614 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 ca-certificates-java all 20240118 [11.6 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 java-common all 0.75 [6640 B] Get: 49 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.14-2+b1 [144 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libnspr4 arm64 2:4.35-1.1+b1 [101 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libnss3 arm64 2:3.100-1 [1295 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libpcsclite1 arm64 2.2.1-1 [54.1 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 openjdk-17-jre-headless arm64 17.0.11+9-1 [42.8 MB] Get: 54 http://deb.debian.org/debian unstable/main arm64 default-jre-headless arm64 2:1.17-75 [3068 B] Get: 55 http://deb.debian.org/debian unstable/main arm64 ant all 1.10.14-1 [2162 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 ant-optional all 1.10.14-1 [455 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 at-spi2-common all 2.52.0-1 [166 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.71-3 [332 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.21-14 [496 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 dctrl-tools arm64 2.24-3 [101 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libparams-util-perl arm64 1.102-3 [23.4 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libsub-install-perl all 0.929-1 [10.5 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libsub-prototype-perl arm64 0.03-2+b2 [9776 B] Get: 73 http://deb.debian.org/debian unstable/main arm64 libsub-override-perl all 0.11-1 [10.4 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 76 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.15.3 [901 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libgtk2.0-common all 2.24.33-4 [2661 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libatk1.0-0t64 arm64 2.52.0-1 [49.2 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.2+dfsg-1+b4 [408 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libbsd0 arm64 0.12.2-1 [129 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-1 [143 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-1 [114 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-1 [105 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b1 [27.0 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.0-3+b1 [478 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libavahi-common-data arm64 0.8-13+b2 [112 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libavahi-common3 arm64 0.8-13+b2 [42.4 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libdbus-1-3 arm64 1.14.10-4+b1 [195 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libavahi-client3 arm64 0.8-13+b2 [45.7 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.20.1-6+b1 [33.0 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1~rc2-1 [22.5 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.20.1-6+b1 [80.5 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 110 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.20.1-6+b1 [315 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.20.1-6+b1 [124 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libcups2t64 arm64 2.4.7-1.2+b1 [230 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 fontconfig arm64 2.15.0-1.1 [462 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.13-3+b1 [71.3 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2 [69.2 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 8.3.0-2+b1 [2178 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libdatrie1 arm64 0.2.13-3 [37.2 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libthai0 arm64 0.1.29-2 [48.0 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 libpango-1.0-0 arm64 1.52.2+ds-1 [206 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 libpangoft2-1.0-0 arm64 1.52.2+ds-1 [45.5 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 libpangocairo-1.0-0 arm64 1.52.2+ds-1 [33.0 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 libxcomposite1 arm64 1:0.4.5-1+b1 [15.0 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 libxfixes3 arm64 1:6.0.0-2+b1 [20.5 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libxcursor1 arm64 1:1.2.1-1+b1 [35.8 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libxdamage1 arm64 1:1.1.6-1+b1 [15.6 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libxi6 arm64 2:1.8.1-1 [77.5 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libxinerama1 arm64 2:1.1.4-3+b1 [16.0 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 libxrandr2 arm64 2:1.5.4-1 [35.7 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 libgtk2.0-0t64 arm64 2.24.33-4 [1663 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 libglvnd0 arm64 1.7.0-1+b1 [41.7 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 libdrm-common all 2.4.120-2 [7688 B] Get: 133 http://deb.debian.org/debian unstable/main arm64 libdrm2 arm64 2.4.120-2 [37.5 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 libglapi-mesa arm64 24.0.7-1 [46.0 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 libx11-xcb1 arm64 2:1.8.7-1+b1 [232 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 libxcb-dri2-0 arm64 1.17.0-1 [106 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 libxcb-dri3-0 arm64 1.17.0-1 [106 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 libxcb-glx0 arm64 1.17.0-1 [122 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 libxcb-present0 arm64 1.17.0-1 [105 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 libxcb-randr0 arm64 1.17.0-1 [116 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 libxcb-sync1 arm64 1.17.0-1 [108 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 libxcb-xfixes0 arm64 1.17.0-1 [109 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 libxshmfence1 arm64 1.3-1+b1 [9080 B] Get: 144 http://deb.debian.org/debian unstable/main arm64 libxxf86vm1 arm64 1:1.1.4-1+b2 [20.1 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 libvulkan1 arm64 1.3.280.0-1 [119 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 libdrm-amdgpu1 arm64 2.4.120-2 [21.0 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 libdrm-nouveau2 arm64 2.4.120-2 [18.7 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 libdrm-radeon1 arm64 2.4.120-2 [21.1 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20230828-1+b1 [89.1 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 libz3-4 arm64 4.8.12-3.1+b2 [6508 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 libllvm17t64 arm64 1:17.0.6-12 [21.3 MB] Get: 152 http://deb.debian.org/debian unstable/main arm64 libsensors-config all 1:3.6.0-9 [14.6 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 libsensors5 arm64 1:3.6.0-9 [33.9 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 libgl1-mesa-dri arm64 24.0.7-1 [7018 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 libglx-mesa0 arm64 24.0.7-1 [150 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 libglx0 arm64 1.7.0-1+b1 [31.0 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 libgl1 arm64 1.7.0-1+b1 [90.9 kB] Get: 158 http://deb.debian.org/debian unstable/main arm64 libasound2-data all 1.2.11-1 [20.9 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 libasound2t64 arm64 1.2.11-1+b1 [334 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 libgif7 arm64 5.2.2-1 [43.7 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+23 [252 kB] Get: 162 http://deb.debian.org/debian unstable/main arm64 libxtst6 arm64 2:1.2.3-1.1+b1 [25.9 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 openjdk-17-jre arm64 17.0.11+9-1 [174 kB] Get: 164 http://deb.debian.org/debian unstable/main arm64 default-jre arm64 2:1.17-75 [1056 B] Get: 165 http://deb.debian.org/debian unstable/main arm64 openjdk-17-jdk-headless arm64 17.0.11+9-1 [70.6 MB] Get: 166 http://deb.debian.org/debian unstable/main arm64 default-jdk-headless arm64 2:1.17-75 [1108 B] Get: 167 http://deb.debian.org/debian unstable/main arm64 openjdk-17-jdk arm64 17.0.11+9-1 [10.4 kB] Get: 168 http://deb.debian.org/debian unstable/main arm64 default-jdk arm64 2:1.17-75 [1068 B] Get: 169 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 170 http://deb.debian.org/debian unstable/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 171 http://deb.debian.org/debian unstable/main arm64 libjs-jquery-ui-theme-base all 1.12.1+dfsg-1.1 [44.3 kB] Get: 172 http://deb.debian.org/debian unstable/main arm64 openjdk-17-doc all 17.0.11+9-1 [12.8 MB] Get: 173 http://deb.debian.org/debian unstable/main arm64 default-jdk-doc arm64 2:1.17-75 [3148 B] Get: 174 http://deb.debian.org/debian unstable/main arm64 libassuan0 arm64 2.5.6-1+b1 [48.0 kB] Get: 175 http://deb.debian.org/debian unstable/main arm64 gpgconf arm64 2.2.43-6 [112 kB] Get: 176 http://deb.debian.org/debian unstable/main arm64 libksba8 arm64 1.6.6-1 [122 kB] Get: 177 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-6 [20.1 kB] Get: 178 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-6 [55.3 kB] Get: 179 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.17+dfsg-1 [173 kB] Get: 180 http://deb.debian.org/debian unstable/main arm64 libnpth0t64 arm64 1.6-3.1 [17.8 kB] Get: 181 http://deb.debian.org/debian unstable/main arm64 dirmngr arm64 2.2.43-6 [340 kB] Get: 182 http://deb.debian.org/debian unstable/main arm64 gnupg-l10n all 2.2.43-6 [701 kB] Get: 183 http://deb.debian.org/debian unstable/main arm64 gnupg-utils arm64 2.2.43-6 [454 kB] Get: 184 http://deb.debian.org/debian unstable/main arm64 gpg arm64 2.2.43-6 [477 kB] Get: 185 http://deb.debian.org/debian unstable/main arm64 pinentry-curses arm64 1.2.1-3+b2 [75.9 kB] Get: 186 http://deb.debian.org/debian unstable/main arm64 gpg-agent arm64 2.2.43-6 [229 kB] Get: 187 http://deb.debian.org/debian unstable/main arm64 gpg-wks-client arm64 2.2.43-6 [93.4 kB] Get: 188 http://deb.debian.org/debian unstable/main arm64 gpgsm arm64 2.2.43-6 [227 kB] Get: 189 http://deb.debian.org/debian unstable/main arm64 gnupg all 2.2.43-6 [374 kB] Get: 190 http://deb.debian.org/debian unstable/main arm64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 191 http://deb.debian.org/debian unstable/main arm64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 192 http://deb.debian.org/debian unstable/main arm64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 193 http://deb.debian.org/debian unstable/main arm64 libfile-touch-perl all 0.12-2 [8816 B] Get: 194 http://deb.debian.org/debian unstable/main arm64 libio-pty-perl arm64 1:1.20-1+b1 [34.0 kB] Get: 195 http://deb.debian.org/debian unstable/main arm64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 196 http://deb.debian.org/debian unstable/main arm64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 197 http://deb.debian.org/debian unstable/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b3 [35.2 kB] Get: 198 http://deb.debian.org/debian unstable/main arm64 libb-hooks-op-check-perl arm64 0.22-3+b1 [10.6 kB] Get: 199 http://deb.debian.org/debian unstable/main arm64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 200 http://deb.debian.org/debian unstable/main arm64 libdevel-callchecker-perl arm64 0.009-1 [16.0 kB] Get: 201 http://deb.debian.org/debian unstable/main arm64 libparams-classify-perl arm64 0.015-2+b3 [22.3 kB] Get: 202 http://deb.debian.org/debian unstable/main arm64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 203 http://deb.debian.org/debian unstable/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 204 http://deb.debian.org/debian unstable/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 205 http://deb.debian.org/debian unstable/main arm64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 206 http://deb.debian.org/debian unstable/main arm64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 207 http://deb.debian.org/debian unstable/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 208 http://deb.debian.org/debian unstable/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 209 http://deb.debian.org/debian unstable/main arm64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 210 http://deb.debian.org/debian unstable/main arm64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 211 http://deb.debian.org/debian unstable/main arm64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 212 http://deb.debian.org/debian unstable/main arm64 liburi-perl all 5.28-1 [98.6 kB] Get: 213 http://deb.debian.org/debian unstable/main arm64 libhtml-parser-perl arm64 3.82-1 [96.9 kB] Get: 214 http://deb.debian.org/debian unstable/main arm64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 215 http://deb.debian.org/debian unstable/main arm64 libclone-perl arm64 0.46-1+b2 [13.6 kB] Get: 216 http://deb.debian.org/debian unstable/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get: 217 http://deb.debian.org/debian unstable/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 218 http://deb.debian.org/debian unstable/main arm64 libhttp-message-perl all 6.45-1 [82.0 kB] Get: 219 http://deb.debian.org/debian unstable/main arm64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 220 http://deb.debian.org/debian unstable/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 221 http://deb.debian.org/debian unstable/main arm64 perl-openssl-defaults arm64 7+b2 [6712 B] Get: 222 http://deb.debian.org/debian unstable/main arm64 libnet-ssleay-perl arm64 1.94-1+b1 [328 kB] Get: 223 http://deb.debian.org/debian unstable/main arm64 libio-socket-ssl-perl all 2.085-1 [218 kB] Get: 224 http://deb.debian.org/debian unstable/main arm64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 225 http://deb.debian.org/debian unstable/main arm64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 226 http://deb.debian.org/debian unstable/main arm64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 227 http://deb.debian.org/debian unstable/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 228 http://deb.debian.org/debian unstable/main arm64 libwww-perl all 6.77-1 [183 kB] Get: 229 http://deb.debian.org/debian unstable/main arm64 patchutils arm64 0.4.2-1 [73.5 kB] Get: 230 http://deb.debian.org/debian unstable/main arm64 wdiff arm64 1.2.2-6 [118 kB] Get: 231 http://deb.debian.org/debian unstable/main arm64 devscripts all 2.23.7 [1068 kB] Get: 232 http://deb.debian.org/debian unstable/main arm64 fastjar arm64 2:0.98-7 [75.5 kB] Get: 233 http://deb.debian.org/debian unstable/main arm64 jarwrapper all 0.79 [10.1 kB] Get: 234 http://deb.debian.org/debian unstable/main arm64 unzip arm64 6.0-28 [157 kB] Get: 235 http://deb.debian.org/debian unstable/main arm64 java-wrappers all 0.4 [8916 B] Get: 236 http://deb.debian.org/debian unstable/main arm64 javahelper all 0.79 [84.6 kB] Get: 237 http://deb.debian.org/debian unstable/main arm64 junit all 3.8.2-10 [108 kB] Get: 238 http://deb.debian.org/debian unstable/main arm64 libhamcrest-java all 2.2-2 [121 kB] Get: 239 http://deb.debian.org/debian unstable/main arm64 junit4 all 4.13.2-4 [349 kB] Get: 240 http://deb.debian.org/debian unstable/main arm64 libapiguardian-java all 1.1.2-1 [4656 B] Get: 241 http://deb.debian.org/debian unstable/main arm64 libopentest4j-java all 1.2.0-4 [9516 B] Get: 242 http://deb.debian.org/debian unstable/main arm64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 243 http://deb.debian.org/debian unstable/main arm64 libpicocli-java all 4.6.2-2 [390 kB] Get: 244 http://deb.debian.org/debian unstable/main arm64 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 245 http://deb.debian.org/debian unstable/main arm64 junit5 all 5.10.1-1 [2458 kB] Get: 246 http://deb.debian.org/debian unstable/main arm64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 247 http://deb.debian.org/debian unstable/main arm64 libantlr4-runtime-java all 4.9.2-2 [317 kB] Get: 248 http://deb.debian.org/debian unstable/main arm64 libaopalliance-java all 20070526-7 [8572 B] Get: 249 http://deb.debian.org/debian unstable/main arm64 libapache-pom-java all 29-2 [5276 B] Get: 250 http://deb.debian.org/debian unstable/main arm64 libapfloat-java all 1.13.0-1 [700 kB] Get: 251 http://deb.debian.org/debian unstable/main arm64 libargs4j-java all 2.33-2 [138 kB] Get: 252 http://deb.debian.org/debian unstable/main arm64 libasm-java all 9.7-1 [394 kB] Get: 253 http://deb.debian.org/debian unstable/main arm64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 254 http://deb.debian.org/debian unstable/main arm64 libjaxp1.3-java all 1.3.05-6 [227 kB] Get: 255 http://deb.debian.org/debian unstable/main arm64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 256 http://deb.debian.org/debian unstable/main arm64 libcommons-parent-java all 56-1 [10.8 kB] Get: 257 http://deb.debian.org/debian unstable/main arm64 libcommons-io-java all 2.16.1-1 [480 kB] Get: 258 http://deb.debian.org/debian unstable/main arm64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 259 http://deb.debian.org/debian unstable/main arm64 libxmlgraphics-commons-java all 2.8-2 [623 kB] Get: 260 http://deb.debian.org/debian unstable/main arm64 libbatik-java all 1.17+dfsg-1 [3923 kB] Get: 261 http://deb.debian.org/debian unstable/main arm64 libbsh-java all 2.0b4-20 [291 kB] Get: 262 http://deb.debian.org/debian unstable/main arm64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 263 http://deb.debian.org/debian unstable/main arm64 libcdi-api-java all 1.2-3 [54.3 kB] Get: 264 http://deb.debian.org/debian unstable/main arm64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 265 http://deb.debian.org/debian unstable/main arm64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 266 http://deb.debian.org/debian unstable/main arm64 libciftools-java all 6.0.0-1 [2211 kB] Get: 267 http://deb.debian.org/debian unstable/main arm64 libjaxen-java all 1.1.6-4 [214 kB] Get: 268 http://deb.debian.org/debian unstable/main arm64 libdom4j-java all 2.1.4-1 [312 kB] Get: 269 http://deb.debian.org/debian unstable/main arm64 libmaven-shared-utils-java all 3.3.4-1 [138 kB] Get: 270 http://deb.debian.org/debian unstable/main arm64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 271 http://deb.debian.org/debian unstable/main arm64 libcommons-lang3-java all 3.14.0-1 [621 kB] Get: 272 http://deb.debian.org/debian unstable/main arm64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 273 http://deb.debian.org/debian unstable/main arm64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 274 http://deb.debian.org/debian unstable/main arm64 libguava-java all 32.0.1-1 [2708 kB] Get: 275 http://deb.debian.org/debian unstable/main arm64 libguice-java all 4.2.3-2 [1435 kB] Get: 276 http://deb.debian.org/debian unstable/main arm64 libmaven-parent-java all 35-1 [6140 B] Get: 277 http://deb.debian.org/debian unstable/main arm64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 278 http://deb.debian.org/debian unstable/main arm64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 279 http://deb.debian.org/debian unstable/main arm64 libmaven-resolver-java all 1.6.3-1 [548 kB] Get: 280 http://deb.debian.org/debian unstable/main arm64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 281 http://deb.debian.org/debian unstable/main arm64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 282 http://deb.debian.org/debian unstable/main arm64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 283 http://deb.debian.org/debian unstable/main arm64 libplexus-interpolation-java all 1.26-1 [76.8 kB] Get: 284 http://deb.debian.org/debian unstable/main arm64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 285 http://deb.debian.org/debian unstable/main arm64 libslf4j-java all 1.7.32-1 [144 kB] Get: 286 http://deb.debian.org/debian unstable/main arm64 libsisu-inject-java all 0.3.4-2 [347 kB] Get: 287 http://deb.debian.org/debian unstable/main arm64 libsisu-plexus-java all 0.3.4-3 [181 kB] Get: 288 http://deb.debian.org/debian unstable/main arm64 libmaven3-core-java all 3.8.7-2 [1573 kB] Get: 289 http://deb.debian.org/debian unstable/main arm64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 290 http://deb.debian.org/debian unstable/main arm64 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 291 http://deb.debian.org/debian unstable/main arm64 libcommons-compress-java all 1.25.0-1 [635 kB] Get: 292 http://deb.debian.org/debian unstable/main arm64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 293 http://deb.debian.org/debian unstable/main arm64 libsnappy1v5 arm64 1.2.0-2 [28.3 kB] Get: 294 http://deb.debian.org/debian unstable/main arm64 libsnappy-jni arm64 1.1.10.5-2 [6440 B] Get: 295 http://deb.debian.org/debian unstable/main arm64 libsnappy-java all 1.1.10.5-2 [87.5 kB] Get: 296 http://deb.debian.org/debian unstable/main arm64 libxz-java all 1.9-1 [143 kB] Get: 297 http://deb.debian.org/debian unstable/main arm64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 298 http://deb.debian.org/debian unstable/main arm64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 299 http://deb.debian.org/debian unstable/main arm64 libcommons-codec-java all 1.16.0-1 [297 kB] Get: 300 http://deb.debian.org/debian unstable/main arm64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 301 http://deb.debian.org/debian unstable/main arm64 libjsoup-java all 1.15.3-1 [431 kB] Get: 302 http://deb.debian.org/debian unstable/main arm64 libwagon-http-java all 3.5.3-1 [49.5 kB] Get: 303 http://deb.debian.org/debian unstable/main arm64 libistack-commons-java all 3.0.6-5 [145 kB] Get: 304 http://deb.debian.org/debian unstable/main arm64 libcodemodel-java all 2.6+jaxb2.3.0.1-10.1 [164 kB] Get: 305 http://deb.debian.org/debian unstable/main arm64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 306 http://deb.debian.org/debian unstable/main arm64 libcommons-beanutils-java all 1.9.4-2 [233 kB] Get: 307 http://deb.debian.org/debian unstable/main arm64 libcommons-collections4-java all 4.4-2 [682 kB] Get: 308 http://deb.debian.org/debian unstable/main arm64 libcommons-lang-java all 2.6-10 [273 kB] Get: 309 http://deb.debian.org/debian unstable/main arm64 libcommons-configuration-java all 1.10-6 [347 kB] Get: 310 http://deb.debian.org/debian unstable/main arm64 libcommons-digester-java all 1.8.1-6 [137 kB] Get: 311 http://deb.debian.org/debian unstable/main arm64 libcommons-exec-java all 1.3-2 [48.1 kB] Get: 312 http://deb.debian.org/debian unstable/main arm64 libcommons-math-java all 2.2-8 [926 kB] Get: 313 http://deb.debian.org/debian unstable/main arm64 libmaven-archiver-java all 3.6.0-1 [25.1 kB] Get: 314 http://deb.debian.org/debian unstable/main arm64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 315 http://deb.debian.org/debian unstable/main arm64 libcommons-text-java all 1.11.0-1 [217 kB] Get: 316 http://deb.debian.org/debian unstable/main arm64 libcommons-validator-java all 1:1.7-1 [181 kB] Get: 317 http://deb.debian.org/debian unstable/main arm64 libdoxia-core-java all 1.12.0-1 [213 kB] Get: 318 http://deb.debian.org/debian unstable/main arm64 libfontbox2-java all 2.0.29-1 [1510 kB] Get: 319 http://deb.debian.org/debian unstable/main arm64 libqdox-java all 1.12.1-3 [172 kB] Get: 320 http://deb.debian.org/debian unstable/main arm64 libfop-java all 1:2.8-3 [10.1 MB] Get: 321 http://deb.debian.org/debian unstable/main arm64 libitext1-java all 1.4-7 [1257 kB] Get: 322 http://deb.debian.org/debian unstable/main arm64 libxbean-reflect-java all 4.5-8 [133 kB] Get: 323 http://deb.debian.org/debian unstable/main arm64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 324 http://deb.debian.org/debian unstable/main arm64 libdoxia-java all 1.12.0-1 [459 kB] Get: 325 http://deb.debian.org/debian unstable/main arm64 libmaven-reporting-api-java all 3.1.1-1 [7240 B] Get: 326 http://deb.debian.org/debian unstable/main arm64 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB] Get: 327 http://deb.debian.org/debian unstable/main arm64 velocity all 1.7-7 [431 kB] Get: 328 http://deb.debian.org/debian unstable/main arm64 libplexus-velocity-java all 1.2-3.1 [10.5 kB] Get: 329 http://deb.debian.org/debian unstable/main arm64 liboro-java all 2.0.8a-14 [70.5 kB] Get: 330 http://deb.debian.org/debian unstable/main arm64 libvelocity-tools-java all 2.0-9 [311 kB] Get: 331 http://deb.debian.org/debian unstable/main arm64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 332 http://deb.debian.org/debian unstable/main arm64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 333 http://deb.debian.org/debian unstable/main arm64 libxalan2-java all 2.7.2-4 [3419 kB] Get: 334 http://deb.debian.org/debian unstable/main arm64 libdoxia-sitetools-java all 1.11.1-1 [202 kB] Get: 335 http://deb.debian.org/debian unstable/main arm64 libdtd-parser-java all 1.2-1 [64.9 kB] Get: 336 http://deb.debian.org/debian unstable/main arm64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 337 http://deb.debian.org/debian unstable/main arm64 libexec-maven-plugin-java all 3.1.0-2 [66.7 kB] Get: 338 http://deb.debian.org/debian unstable/main arm64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 339 http://deb.debian.org/debian unstable/main arm64 libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 340 http://deb.debian.org/debian unstable/main arm64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB] Get: 341 http://deb.debian.org/debian unstable/main arm64 librelaxng-datatype-java all 1.0+ds1-3.1 [11.7 kB] Get: 342 http://deb.debian.org/debian unstable/main arm64 libxsom-java all 2.3.0.1-10.1 [400 kB] Get: 343 http://deb.debian.org/debian unstable/main arm64 libfastinfoset-java all 1.2.12-3 [343 kB] Get: 344 http://deb.debian.org/debian unstable/main arm64 libfastutil-java all 8.5.12+dfsg-2 [19.6 MB] Get: 345 http://deb.debian.org/debian unstable/main arm64 libinchi1 arm64 1.03+dfsg-4 [387 kB] Get: 346 http://deb.debian.org/debian unstable/main arm64 libitext5-java all 5.5.13.3-4 [2667 kB] Get: 347 http://deb.debian.org/debian unstable/main arm64 libjackson2-annotations-java all 2.14.0-1 [68.8 kB] Get: 348 http://deb.debian.org/debian unstable/main arm64 libjackson2-core-java all 2.14.1-1 [447 kB] Get: 349 http://deb.debian.org/debian unstable/main arm64 libjackson2-databind-java all 2.14.0-1 [1584 kB] Get: 350 http://deb.debian.org/debian unstable/main arm64 libjakarta-activation-java all 2.0.0-1 [59.8 kB] Get: 351 http://deb.debian.org/debian unstable/main arm64 libjansi-java all 2.4.1-2 [100 kB] Get: 352 http://deb.debian.org/debian unstable/main arm64 librngom-java all 2.3.0.1-10.1 [290 kB] Get: 353 http://deb.debian.org/debian unstable/main arm64 libtxw2-java all 2.3.0.1-10.1 [134 kB] Get: 354 http://deb.debian.org/debian unstable/main arm64 libjaxb-java all 2.3.0.1-10.1 [1973 kB] Get: 355 http://deb.debian.org/debian unstable/main arm64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 356 http://deb.debian.org/debian unstable/main arm64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 357 http://deb.debian.org/debian unstable/main arm64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 358 http://deb.debian.org/debian unstable/main arm64 libjetty9-java all 9.4.54-1 [2980 kB] Get: 359 http://deb.debian.org/debian unstable/main arm64 libjheaps-java all 0.14-2 [144 kB] Get: 360 http://deb.debian.org/debian unstable/main arm64 libjgraphx-java all 2.1.0.7-3 [807 kB] Get: 361 http://deb.debian.org/debian unstable/main arm64 libjgrapht-java all 1.5.2-1 [1610 kB] Get: 362 http://deb.debian.org/debian unstable/main arm64 libjni-inchi-jni arm64 0.8+dfsg-7 [9312 B] Get: 363 http://deb.debian.org/debian unstable/main arm64 libmaven-shared-incremental-java all 1.1-4 [9924 B] Get: 364 http://deb.debian.org/debian unstable/main arm64 libplexus-compiler-java all 2.12.1-2 [99.0 kB] Get: 365 http://deb.debian.org/debian unstable/main arm64 libqdox2-java all 2.0.3-1 [296 kB] Get: 366 http://deb.debian.org/debian unstable/main arm64 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 367 http://deb.debian.org/debian unstable/main arm64 libmaven-compiler-plugin-java all 3.10.1-2 [59.0 kB] Get: 368 http://deb.debian.org/debian unstable/main arm64 liblog4j1.2-java all 1.2.17-11 [444 kB] Get: 369 http://deb.debian.org/debian unstable/main arm64 libjni-inchi-java all 0.8+dfsg-7 [33.2 kB] Get: 370 http://deb.debian.org/debian unstable/main arm64 libnaga-java all 3.0+svn80-5 [43.5 kB] Get: 371 http://deb.debian.org/debian unstable/main arm64 libjmol-java all 16.2.9+dfsg-1 [8951 kB] Get: 372 http://deb.debian.org/debian unstable/main arm64 libjson-simple-java all 2.3.0-1 [63.8 kB] Get: 373 http://deb.debian.org/debian unstable/main arm64 libjtidy-java all 7+svn20110807-5 [250 kB] Get: 374 http://deb.debian.org/debian unstable/main arm64 liblightcouch-java all 0.2.0-1 [75.0 kB] Get: 375 http://deb.debian.org/debian unstable/main arm64 libmongodb-java all 3.6.3-2 [1901 kB] Get: 376 http://deb.debian.org/debian unstable/main arm64 liblog4j2-java all 2.19.0-2 [2310 kB] Get: 377 http://deb.debian.org/debian unstable/main arm64 libmaven-antrun-plugin-java all 3.1.0-1 [36.9 kB] Get: 378 http://deb.debian.org/debian unstable/main arm64 libmaven-common-artifact-filters-java all 3.3.2-1 [48.2 kB] Get: 379 http://deb.debian.org/debian unstable/main arm64 libmaven-artifact-transfer-java all 0.13.1-2 [158 kB] Get: 380 http://deb.debian.org/debian unstable/main arm64 libplexus-build-api-java all 0.0.7-4 [10.3 kB] Get: 381 http://deb.debian.org/debian unstable/main arm64 libmaven-filtering-java all 3.3.0-1 [50.2 kB] Get: 382 http://deb.debian.org/debian unstable/main arm64 libmaven-assembly-plugin-java all 3.4.2-1 [242 kB] Get: 383 http://deb.debian.org/debian unstable/main arm64 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB] Get: 384 http://deb.debian.org/debian unstable/main arm64 libmaven-dependency-analyzer-java all 1.13.0-1 [30.4 kB] Get: 385 http://deb.debian.org/debian unstable/main arm64 libmaven-dependency-tree-java all 3.2.1-1 [34.7 kB] Get: 386 http://deb.debian.org/debian unstable/main arm64 libmaven-reporting-impl-java all 3.2.0-2 [15.2 kB] Get: 387 http://deb.debian.org/debian unstable/main arm64 libmaven-dependency-plugin-java all 3.5.0-1 [173 kB] Get: 388 http://deb.debian.org/debian unstable/main arm64 libmaven-deploy-plugin-java all 3.1.1-1 [36.4 kB] Get: 389 http://deb.debian.org/debian unstable/main arm64 libmaven-enforcer-plugin-java all 3.1.0-1 [135 kB] Get: 390 http://deb.debian.org/debian unstable/main arm64 libmaven-install-plugin-java all 3.1.1-1 [28.7 kB] Get: 391 http://deb.debian.org/debian unstable/main arm64 libmaven-invoker-java all 3.2.0-1 [28.1 kB] Get: 392 http://deb.debian.org/debian unstable/main arm64 libplexus-interactivity-api-java all 1.1-2 [11.0 kB] Get: 393 http://deb.debian.org/debian unstable/main arm64 libmaven-javadoc-plugin-java all 3.4.1-3 [454 kB] Get: 394 http://deb.debian.org/debian unstable/main arm64 libplexus-container-default1.5-java all 2.1.1-1 [4476 B] Get: 395 http://deb.debian.org/debian unstable/main arm64 libplexus-ant-factory-java all 1.0~alpha2.1-4 [11.4 kB] Get: 396 http://deb.debian.org/debian unstable/main arm64 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B] Get: 397 http://deb.debian.org/debian unstable/main arm64 libmaven-plugin-tools-java all 3.7.1-1 [265 kB] Get: 398 http://deb.debian.org/debian unstable/main arm64 libmaven-jaxb2-plugin-java all 0.15.1-1 [118 kB] Get: 399 http://deb.debian.org/debian unstable/main arm64 libmaven-reporting-exec-java all 1.6.0-1 [26.8 kB] Get: 400 http://deb.debian.org/debian unstable/main arm64 libmaven-resources-plugin-java all 3.3.0-1 [28.4 kB] Get: 401 http://deb.debian.org/debian unstable/main arm64 libmaven-site-plugin-java all 3.12.1-2 [107 kB] Get: 402 http://deb.debian.org/debian unstable/main arm64 libmsgpack-java all 0.9.6-1 [161 kB] Get: 403 http://deb.debian.org/debian unstable/main arm64 libmmtf-java all 1.0.11-1 [187 kB] Get: 404 http://deb.debian.org/debian unstable/main arm64 libsurefire-java all 2.22.3-2 [1169 kB] Get: 405 http://deb.debian.org/debian unstable/main arm64 libvecmath-java all 1.5.2-7 [97.0 kB] Get: 406 http://deb.debian.org/debian unstable/main arm64 libwagon-file-java all 3.5.3-1 [8388 B] Get: 407 http://deb.debian.org/debian unstable/main arm64 libwagon-http-shaded-java all 3.5.3-1 [1341 kB] Get: 408 http://deb.debian.org/debian unstable/main arm64 libxml2-utils arm64 2.9.14+dfsg-1.3+b3 [97.5 kB] Get: 409 http://deb.debian.org/debian unstable/main arm64 libxmlunit-java all 1.6-2 [100 kB] Get: 410 http://deb.debian.org/debian unstable/main arm64 maven all 3.8.7-2 [19.3 kB] Get: 411 http://deb.debian.org/debian unstable/main arm64 maven-repo-helper all 1.11 [142 kB] Get: 412 http://deb.debian.org/debian unstable/main arm64 maven-debian-helper all 2.6.4 [108 kB] Fetched 327 MB in 2s (197 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1:arm64. 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_arm64.deb ... Unpacking python3.11 (3.11.9-1) ... 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Setting up liboro-java (2.0.8a-14) ... Setting up libjakarta-activation-java (2.0.0-1) ... Setting up libsnappy1v5:arm64 (1.2.0-2) ... Setting up libkrb5support0:arm64 (1.20.1-6+b1) ... Setting up libexec-maven-plugin-java (3.1.0-2) ... Setting up libfontbox2-java (2.0.29-1) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-6) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Mon May 20 02:56:51 UTC 2024. Universal Time is now: Mon May 20 02:56:51 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... Setting up libgeronimo-interceptor-3.0-spec-java (1.0.1-4) ... Setting up libcommons-collections3-java (3.2.2-3) ... Setting up libasound2-data (1.2.11-1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:arm64 (4.8.12-3.1+b2) ... Setting up libglib2.0-0t64:arm64 (2.80.2-1) ... No schema files found: doing nothing. Setting up libasound2t64:arm64 (1.2.11-1+b1) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-3) ... Setting up junit (3.8.2-10) ... Setting up libjaxen-java (1.1.6-4) ... Setting up libapiguardian-java (1.1.2-1) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libnspr4:arm64 (2:4.35-1.1+b1) ... Setting up gnupg-l10n (2.2.43-6) ... Setting up libjtidy-java (7+svn20110807-5) ... Setting up libjansi-java (2.4.1-2) ... Setting up libapache-pom-java (29-2) ... Setting up libavahi-common-data:arm64 (0.8-13+b2) ... Setting up libatinject-jsr330-api-java (1.0+ds1-5) ... Setting up libdbus-1-3:arm64 (1.14.10-4+b1) ... Setting up libwebsocket-api-java (1.1-2) ... Setting up libfribidi0:arm64 (1.0.13-3+b1) ... Setting up libproc2-0:arm64 (2:4.0.4-4) ... Setting up libplexus-interpolation-java (1.26-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libitext5-java (5.5.13.3-4) ... Setting up libpng16-16t64:arm64 (1.6.43-5) ... Setting up libxml-commons-resolver1.1-java (1.2-11) ... Setting up libxz-java (1.9-1) ... Setting up libitext1-java (1.4-7) ... Setting up libio-html-perl (1.004-3) ... Setting up autopoint (0.21-14) ... Setting up binfmt-support (2.2.2-7) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libb-hooks-op-check-perl:arm64 (0.22-3+b1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up libpcsclite1:arm64 (2.2.1-1) ... Setting up libsensors5:arm64 (1:3.6.0-9) ... Setting up libmongodb-java (3.6.3-2) ... Setting up libk5crypto3:arm64 (1.20.1-6+b1) ... Setting up libactivation-java (1.2.0-2) ... Setting up libhamcrest-java (2.2-2) ... Setting up libglapi-mesa:arm64 (24.0.7-1) ... Setting up libbsh-java (2.0b4-20) ... Setting up libjsp-api-java (2.3.4-3) ... Setting up libparams-util-perl (1.102-3) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-6) ... Setting up libvulkan1:arm64 (1.3.280.0-1) ... Setting up autoconf (2.71-3) ... Setting up libapfloat-java (1.13.0-1) ... Setting up libwebp7:arm64 (1.4.0-0.1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libgif7:arm64 (5.2.2-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libxshmfence1:arm64 (1.3-1+b1) ... Setting up libjsoup-java (1.15.3-1) ... Setting up at-spi2-common (2.52.0-1) ... Setting up libcommons-math-java (2.2-8) ... Setting up libtiff6:arm64 (4.5.1+git230720-4) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up libxml-commons-external-java (1.4.01-6) ... Setting up procps (2:4.0.4-4) ... Setting up libxbean-reflect-java (4.5-8) ... Setting up libservlet-api-java (4.0.1-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libopentest4j-java (1.2.0-4) ... Setting up libjackson2-core-java (2.14.1-1) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b3) ... Setting up libgtk2.0-common (2.24.33-4) ... Setting up libkrb5-3:arm64 (1.20.1-6+b1) ... Setting up libwagon-http-shaded-java (3.5.3-1) ... Setting up libhttpcore-java (4.4.16-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libxerces2-java (2.12.2-1) ... Setting up libfile-dirlist-perl (0.05-3) ... Setting up libjaxp1.3-java (1.3.05-6) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up librelaxng-datatype-java (1.0+ds1-3.1) ... Setting up openssl (3.2.1-3) ... Setting up libbsd0:arm64 (0.12.2-1) ... Setting up libdrm-common (2.4.120-2) ... Setting up libcdi-api-java (1.2-3) ... Setting up libsnappy-jni (1.1.10.5-2) ... Setting up readline-common (8.2-4) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Setting up liburi-perl (5.28-1) ... Setting up libargs4j-java (2.33-2) ... Setting up libfile-touch-perl (0.12-2) ... Setting up dctrl-tools (2.24-3) ... Setting up libinchi1 (1.03+dfsg-4) ... Setting up libnaga-java (3.0+svn80-5) ... Setting up libnet-ssleay-perl:arm64 (1.94-1+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up pinentry-curses (1.2.1-3+b2) ... Setting up libdom4j-java (2.1.4-1) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up libwagon-provider-api-java (3.5.3-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3+b1) ... Setting up libxcb1:arm64 (1.17.0-1) ... Setting up gettext (0.21-14+b1) ... Setting up libjetty9-java (9.4.54-1) ... Setting up libxcb-xfixes0:arm64 (1.17.0-1) ... Setting up java-wrappers (0.4) ... Setting up libatk1.0-0t64:arm64 (2.52.0-1) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libplexus-languages-java (1.1.1-2) ... Setting up jarwrapper (0.79) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:arm64 (1.17.0-1) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libstax-ex-java (1.7.8-3) ... Setting up libxcb-glx0:arm64 (1.17.0-1) ... Setting up libmaven-parent-java (35-1) ... Setting up libedit2:arm64 (3.1-20230828-1+b1) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:arm64 (0.8-13+b2) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libnet-http-perl (6.23-1) ... Setting up libsisu-inject-java (0.3.4-2) ... Setting up libnss3:arm64 (2:3.100-1) ... Setting up libxcb-shm0:arm64 (1.17.0-1) ... Setting up libciftools-java (6.0.0-1) ... Setting up libdevel-callchecker-perl:arm64 (0.009-1) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libldap-2.5-0:arm64 (2.5.17+dfsg-1) ... Setting up libjackson2-databind-java (2.14.0-1) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libxmlunit-java (1.6-2) ... Setting up libxcb-present0:arm64 (1.17.0-1) ... Setting up dh-autoreconf (20) ... Setting up patchutils (0.4.2-1) ... Setting up libthai0:arm64 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.4-3) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libllvm17t64:arm64 (1:17.0.6-12) ... Setting up libfreetype6:arm64 (2.13.2+dfsg-1+b4) ... Setting up libxcb-sync1:arm64 (1.17.0-1) ... Setting up libxalan2-java (2.7.2-4) ... Setting up shared-mime-info (2.4-4) ... Setting up libstreambuffer-java (1.5.4-1.1) ... Setting up libgssapi-krb5-2:arm64 (1.20.1-6+b1) ... Setting up libdata-optlist-perl (0.114-1) ... Setting up libcommons-collections4-java (4.4-2) ... Setting up libcommons-lang3-java (3.14.0-1) ... Setting up libreadline8t64:arm64 (8.2-4) ... Setting up libxcb-dri2-0:arm64 (1.17.0-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up librngom-java (2.3.0.1-10.1) ... Setting up libdrm2:arm64 (2.4.120-2) ... Setting up libjni-inchi-jni (0.8+dfsg-7) ... Setting up libmaven-common-artifact-filters-java (3.3.2-1) ... Setting up libjgraphx-java (2.1.0.7-3) ... Setting up groff-base (1.23.0-4) ... Setting up libxcb-randr0:arm64 (1.17.0-1) ... Setting up libhtml-parser-perl:arm64 (3.82-1) ... Setting up gpgconf (2.2.43-6) ... Setting up openjdk-17-doc (17.0.11+9-1) ... Setting up libcommons-beanutils-java (1.9.4-2) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libx11-6:arm64 (2:1.8.7-1+b1) ... Setting up libharfbuzz0b:arm64 (8.3.0-2+b1) ... Setting up libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-1) ... Setting up libsnappy-java (1.1.10.5-2) ... Setting up libfontconfig1:arm64 (2.15.0-1.1) ... Setting up libxsom-java (2.3.0.1-10.1) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libcommons-configuration-java (1.10-6) ... Setting up libwagon-file-java (3.5.3-1) ... Setting up libxml2-utils (2.9.14+dfsg-1.3+b3) ... Setting up libcommons-codec-java (1.16.0-1) ... Setting up libxcomposite1:arm64 (1:0.4.5-1+b1) ... Setting up libavahi-client3:arm64 (0.8-13+b2) ... Setting up libio-socket-ssl-perl (2.085-1) ... Setting up gpg (2.2.43-6) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up gnupg-utils (2.2.43-6) ... Setting up libhttp-message-perl (6.45-1) ... Setting up libdrm-amdgpu1:arm64 (2.4.120-2) ... Setting up libxcb-dri3-0:arm64 (1.17.0-1) ... Setting up gtk-update-icon-cache (3.24.41-4) ... Setting up libx11-xcb1:arm64 (2:1.8.7-1+b1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up velocity (1.7-7) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libdrm-nouveau2:arm64 (2.4.120-2) ... Setting up libxdamage1:arm64 (1:1.1.6-1+b1) ... Setting up gpg-agent (2.2.43-6) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b1) ... Setting up libcommons-compress-java (1.25.0-1) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up libcommons-io-java (2.16.1-1) ... Setting up libdrm-radeon1:arm64 (2.4.120-2) ... Setting up libcommons-digester-java (1.8.1-6) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libpython3.11-stdlib:arm64 (3.11.9-1) ... Setting up libparams-classify-perl:arm64 (0.015-2+b3) ... Setting up gpgsm (2.2.43-6) ... Setting up libpango-1.0-0:arm64 (1.52.2+ds-1) ... Setting up libgl1-mesa-dri:arm64 (24.0.7-1) ... Setting up libxext6:arm64 (2:1.3.4-1+b1) ... Setting up libxmlgraphics-commons-java (2.8-2) ... Setting up libsub-prototype-perl (0.03-2+b2) ... Setting up default-jdk-doc (2:1.17-75) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.18.0-3+b1) ... Setting up libxxf86vm1:arm64 (1:1.1.4-1+b2) ... Setting up dirmngr (2.2.43-6) ... Setting up libmaven-filtering-java (3.3.0-1) ... Setting up libmaven-resolver-java (1.6.3-1) ... Setting up adwaita-icon-theme (46.0-1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up libmodule-runtime-perl (0.016-2) ... Setting up libxfixes3:arm64 (1:6.0.0-2+b1) ... Setting up libxinerama1:arm64 (2:1.1.4-3+b1) ... Setting up libxrandr2:arm64 (2:1.5.4-1) ... Setting up openjdk-17-jre-headless:arm64 (17.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libhttpclient-java (4.5.14-1) ... Setting up libmaven-dependency-tree-java (3.2.1-1) ... Setting up libsub-override-perl (0.11-1) ... Setting up liblightcouch-java (0.2.0-1) ... Setting up libwagon-http-java (3.5.3-1) ... Setting up libmaven-shared-utils-java (3.3.4-1) ... Setting up libfastinfoset-java (1.2.12-3) ... Setting up libpangoft2-1.0-0:arm64 (1.52.2+ds-1) ... Setting up libmaven-resources-plugin-java (3.3.0-1) ... Setting up libcups2t64:arm64 (2.4.7-1.2+b1) ... Setting up libpangocairo-1.0-0:arm64 (1.52.2+ds-1) ... Setting up libpython3-stdlib:arm64 (3.11.8-1) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.11 (3.11.9-1) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up libglx-mesa0:arm64 (24.0.7-1) ... Setting up libxi6:arm64 (2:1.8.1-1) ... Setting up gpg-wks-client (2.2.43-6) ... Setting up libglx0:arm64 (1.7.0-1+b1) ... Setting up libmaven-install-plugin-java (3.1.1-1) ... Setting up libcommons-validator-java (1:1.7-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libxtst6:arm64 (2:1.2.3-1.1+b1) ... Setting up libbatik-java (1.17+dfsg-1) ... Setting up libmoo-perl (2.005005-1) ... Setting up liblog4j2-java (2.19.0-2) ... Setting up libxcursor1:arm64 (1:1.2.1-1+b1) ... Setting up libmaven-invoker-java (3.2.0-1) ... Setting up python3 (3.11.8-1) ... Setting up libmaven-deploy-plugin-java (3.1.1-1) ... Setting up libgl1:arm64 (1.7.0-1+b1) ... Setting up libgtk2.0-0t64:arm64 (2.24.33-4) ... Setting up libmaven-clean-plugin-java (3.2.0-2) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up gnupg (2.2.43-6) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libfop-java (1:2.8-3) ... Setting up libmaven-archiver-java (3.6.0-1) ... Setting up debhelper (13.15.3) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libwww-perl (6.77-1) ... Setting up devscripts (2.23.7) ... Setting up libguava-java (32.0.1-1) ... Setting up javahelper (0.79) ... Setting up libplexus-container-default-java (2.1.1-1) ... Setting up libguice-java (4.2.3-2) ... Setting up libplexus-i18n-java (1.0-beta-10-6) ... Setting up libplexus-container-default1.5-java (2.1.1-1) ... Setting up libplexus-interactivity-api-java (1.1-2) ... Setting up libplexus-velocity-java (1.2-3.1) ... Setting up libmaven3-core-java (3.8.7-2) ... Setting up libmaven-shared-incremental-java (1.1-4) ... Setting up libmaven-shared-io-java (3.0.0-4) ... Setting up libplexus-bsh-factory-java (1.0~alpha7-5) ... Setting up libmaven-dependency-analyzer-java (1.13.0-1) ... Setting up libplexus-compiler-java (2.12.1-2) ... Setting up libmaven-compiler-plugin-java (3.10.1-2) ... Setting up libjni-inchi-java (0.8+dfsg-7) ... Setting up libmaven-artifact-transfer-java (0.13.1-2) ... Setting up libmaven-file-management-java (3.0.0-1) ... Setting up libjmol-java (16.2.9+dfsg-1) ... Setting up libmaven-enforcer-plugin-java (3.1.0-1) ... Setting up libmaven-jar-plugin-java (3.3.0-2) ... Setting up libmaven-assembly-plugin-java (3.4.2-1) ... Setting up libcommons-text-java (1.11.0-1) ... Setting up libmsgpack-java (0.9.6-1) ... Setting up libmmtf-java (1.0.11-1) ... Setting up libjgrapht-java (1.5.2-1) ... 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 (2.38-11) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up maven-repo-helper (1.11) ... Setting up maven (3.8.7-2) ... update-alternatives: using /usr/share/maven/bin/mvn to provide /usr/bin/mvn (mvn) in auto mode Setting up openjdk-17-jdk-headless:arm64 (17.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up ant (1.10.14-1) ... Setting up junit4 (4.13.2-4) ... Setting up default-jre-headless (2:1.17-75) ... Setting up openjdk-17-jre:arm64 (17.0.11+9-1) ... Setting up default-jre (2:1.17-75) ... Setting up openjdk-17-jdk:arm64 (17.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up libmaven-antrun-plugin-java (3.1.0-1) ... Setting up libplexus-ant-factory-java (1.0~alpha2.1-4) ... Setting up ant-optional (1.10.14-1) ... Setting up default-jdk-headless (2:1.17-75) ... Setting up junit5 (5.10.1-1) ... Setting up libistack-commons-java (3.0.6-5) ... Setting up default-jdk (2:1.17-75) ... Setting up libcodemodel-java (2.6+jaxb2.3.0.1-10.1) ... Setting up libtxw2-java (2.3.0.1-10.1) ... Setting up libjaxb-java (2.3.0.1-10.1) ... Processing triggers for sgml-base (1.31) ... Setting up libvelocity-tools-java (2.0-9) ... Setting up libdoxia-sitetools-java (1.11.1-1) ... Setting up libmaven-site-plugin-java (3.12.1-2) ... Setting up libmaven-javadoc-plugin-java (3.4.1-3) ... Setting up libmaven-reporting-impl-java (3.2.0-2) ... Setting up libmaven-dependency-plugin-java (3.5.0-1) ... Setting up libmaven-plugin-tools-java (3.7.1-1) ... Setting up libmaven-jaxb2-plugin-java (0.15.1-1) ... Setting up libsurefire-java (2.22.3-2) ... Setting up maven-debian-helper (2.6.4) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/3566877/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/3566877/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/biojava6-live-6.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../biojava6-live_6.1.0+dfsg-4_source.changes dpkg-buildpackage: info: source package biojava6-live dpkg-buildpackage: info: source version 6.1.0+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Pierre Gruet dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dpkg: warning: --compare-versions used with obsolete relation operator '>' dh clean --with javahelper 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 -plibbiojava6-java jh_clean debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg' dpkg: warning: --compare-versions used with obsolete relation operator '>' dh_clean rm -rf target rm -rf biojava-*/target find . -type f -name \*.java.json-simple \ -exec sh -c 'file={} && mv $file ${file%.json-simple}' \; -print rm -rf biojava-forester rm -rf biojava-jcolorbrewer make[1]: Leaving directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg' debian/rules binary dpkg: warning: --compare-versions used with obsolete relation operator '>' dh binary --with javahelper dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg' dpkg: warning: --compare-versions used with obsolete relation operator '>' # Creating the directories for forester and jcolorbrewer, with symlinks. mkdir -p biojava-forester/src/main/java/ cp -a forester/org biojava-forester/src/main/java/ mkdir -p biojava-jcolorbrewer/src/main/java/ cp -a jcolorbrewer/org biojava-jcolorbrewer/src/main/java/ # Putting the pom.xml files of forester and jcolorbrewer into their dirs. sed 's/\(VERSION_PACKAGE\)/\16.1.0+dfsg/; s/VERSION_PACKAGE\(.*\)+dfsg[0-9]*/\1/' debian/poms/pomForester.xml > biojava-forester/pom.xml sed 's/\(VERSION_PACKAGE\)/\16.1.0+dfsg/; s/VERSION_PACKAGE\(.*\)+dfsg[0-9]*/\1/' debian/poms/pomJcolorbrewer.xml > biojava-jcolorbrewer/pom.xml dh_auto_configure mh_patchpoms -plibbiojava6-java --debian-build --keep-pom-version --maven-repo=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven-repo make[1]: Leaving directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg' jh_linkjars debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg' dpkg: warning: --compare-versions used with obsolete relation operator '>' # Insert the correct JSON_SIMPLE_PACKAGE in the code. find . -type f -name \*.java -exec grep -q 'import @JSON_SIMPLE_PACKAGE@' {} \; \ -exec sed -i.json-simple \ -e 's,@JSON_SIMPLE_PACKAGE@,org.json.simple,' \ {} \; -print ./biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java dh_auto_build /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/biojava6-live-6.1.0\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf -Dproperties.file.manual=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven.properties org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/biojava6-live-6.1.0\+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... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.biojava:biojava-structure-gui:jar:6.1.0 [WARNING] 'dependencies.dependency.systemPath' for net.sourceforge.jmol:jmol:jar should use a variable instead of a hard-coded path /usr/share/java/Jmol.jar @ line 48, column 16 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] biojava [pom] [INFO] biojava-core [jar] [INFO] biojava-forester [jar] [INFO] biojava-alignment [jar] [INFO] biojava-structure [jar] [INFO] biojava-jcolorbrewer [jar] [INFO] biojava-structure-gui [jar] [INFO] biojava-genome [jar] [INFO] biojava-modfinder [jar] [INFO] biojava-ws [jar] [INFO] biojava-protein-disorder [jar] [INFO] biojava-aa-prop [jar] [INFO] biojava-survival [jar] [INFO] biojava-ontology [jar] [INFO] biojava-protein-comparison-tool [jar] [WARNING] The artifact org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 has been relocated to org.apache.maven.plugins:maven-antrun-plugin:jar:3.1.0 [WARNING] The artifact org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 has been relocated to org.apache.maven.plugins:maven-assembly-plugin:jar:3.4.2 [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] ------------------------< org.biojava:biojava >------------------------- [INFO] Building biojava 6.1.0 [1/15] [INFO] --------------------------------[ pom ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava --- [INFO] Not executing Javadoc as the project is not a Java classpath-capable package [INFO] [INFO] ----------------------< org.biojava:biojava-core >---------------------- [INFO] Building biojava-core 6.1.0 [2/15] [INFO] --------------------------------[ jar ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-core --- [INFO] Copying 24 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-core --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 188 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java: Recompile with -Xlint:removal for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-core --- [INFO] Copying 48 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-core --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 60 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/test-classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/test/java/org/biojava/nbio/core/search/io/HspTest.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/test/java/org/biojava/nbio/core/search/io/HspTest.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-core --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-core --- [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/biojava-core-6.1.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-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] Loading source files for package org.biojava.nbio.core.util... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.views... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.transcription... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.template... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.storage... 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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/AAindexFactory.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/AAIndexFileParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/AAIndexProvider.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/ABITrace.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/ABITracerCompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/AbstractCompound.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/AbstractCompoundTranslator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/AbstractFeature.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/AbstractLocation.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java:74: warning: Tag @link: reference not found: #getAllSubLocations() [WARNING] * {@link #getAllSubLocations()}. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/AbstractNucleotideCompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/AbstractReference.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/AbstractSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/AbstractSequence.AnnotationType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/AccesionedLocation.html... 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[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:68: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if sequenceIndex < 1 or sequenceIndex > [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:133: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:157: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/AlignedSequence.Step.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:41: warning: Tag @link: reference not found: Aligner [WARNING] * Defines an alignment step in order to pass alignment information from an {@link Aligner} to a constructor. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/AmbiguityDNACompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/AmbiguityDNARNAHybridCompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/AmbiguityRNACompoundSet.html... 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[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java:67: warning: invalid input: '&' [WARNING] * Class is immutable & so this is unsupported [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java:75: warning: invalid input: '&' [WARNING] * Class is immutable & so this is unsupported [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java:67: warning: invalid input: '&' [WARNING] * Class is immutable & so this is unsupported [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java:75: warning: invalid input: '&' [WARNING] * Class is immutable & so this is unsupported [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/BitSequenceReader.BitArrayWorker.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/BlastHitBuilder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/BlastHspBuilder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/BlastResult.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/BlastResultBuilder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/BlastTabularParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/BlastXMLParser.html... 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[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java:35: warning: invalid usage of tag {@link http://www.sequenceontology.org/gff3.shtml [WARNING] * to a gff3 file. {@link http://www.sequenceontology.org/gff3.shtml} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java:93: warning: invalid usage of tag {@link http://www.sequenceontology.org/gff3.shtml [WARNING] * {@link http://www.sequenceontology.org/gff3.shtml} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java:94: warning: invalid usage of tag {@link http://biowiki.org/~yam/bioe131/GFF.ppt [WARNING] * {@link http://biowiki.org/~yam/bioe131/GFF.ppt} [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/ChromosomeSequence.html... 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It can only be used in the following types of documentation: overview, module, package, class/interface. [WARNING] * @author Amr ALHOSSARY [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/FastaReaderHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/FastaSequenceParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/FastaWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/FastaWriterHelper.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriterHelper.java:99: warning: @param argument "dnaSequences" is not a parameter name. [WARNING] * @param dnaSequences [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/FeatureDbReferenceInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/FeatureInterface.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureInterface.java:72: warning: @return tag cannot be used in method with void return type. [WARNING] public void setDescription(String description); [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/FeatureRetriever.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/FeaturesKeyWordInterface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/FileDownloadUtils.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java:291: warning: invalid input: '&' [WARNING] * Recursively delete a folder & contents [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java:266: warning: invalid input: '&' [WARNING] * Recursively delete a folder & contents [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java:171: warning: Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, module, package, class/interface. [WARNING] * @author Peter Rose [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java:220: warning: Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, module, package, class/interface. [WARNING] * @author BalusC, [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java:256: warning: Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, module, package, class/interface. [WARNING] * @author Jacek Grzebyta [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java:266: warning: invalid input: '&' [WARNING] * Recursively delete a folder & contents [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java:291: warning: invalid input: '&' [WARNING] * Recursively delete a folder & contents [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.java:59: warning: @param argument "fastaFile" is not a parameter name. [WARNING] * @param fastaFile [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.java:58: warning: @param argument "fastaFile" is not a parameter name. [WARNING] * @param fastaFile [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.java:59: warning: @param argument "fastaFile" is not a parameter name. [WARNING] * @param fastaFile [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/FlatFileCache.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/FlatFileCache.java:126: warning: invalid input: '{@' [WARNING] * If the cache is {@}, returns -1 [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/FourBitSequenceReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/FourBitSequenceReader.FourBitArrayWorker.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/Frame.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/FuzzyPoint.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.java:36: warning: Tag @param cannot be used in field documentation. It can only be used in the following types of documentation: class/interface, constructor, method. [WARNING] * @param sequence [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.java:37: warning: Tag @return cannot be used in field documentation. It can only be used in the following types of documentation: method, inline text. [WARNING] * @return [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java:45: warning: invalid input: '<' [WARNING] * @author Karl Nicholas [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java:46: warning: invalid input: '<' [WARNING] * @author Jacek Grzebyta [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenbankReader.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java:142: warning: Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, module, package, class/interface. [WARNING] * @author Amr ALHOSSARY [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/GenbankReference.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenbankWriter.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriter.java:85: warning: @param argument "lineSeparator" is not a parameter name. [WARNING] * @param lineSeparator [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenbankWriterHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenericFastaHeaderFormat.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderFormat.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:185: warning: @inheritDoc used but setAccession(String) does not override or implement any method. [WARNING] public void setAccession(String accession) throws ParserException { [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:219: warning: @inheritDoc used but setComment(String) does not override or implement any method. [WARNING] public void setComment(String comment) throws ParserException { [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:193: warning: @inheritDoc used but setDescription(String) does not override or implement any method. [WARNING] public void setDescription(String description) throws ParserException { [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:201: warning: @inheritDoc used but setIdentifier(String) does not override or implement any method. [WARNING] public void setIdentifier(String identifier) throws ParserException { [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:210: warning: @inheritDoc used but setName(String) does not override or implement any method. [WARNING] public void setName(String name) throws ParserException { [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:168: warning: @inheritDoc used but setVersion(int) does not override or implement any method. [WARNING] public void setVersion(int version) throws ParserException { [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:168: warning: @inheritDoc used but setVersion(int) does not override or implement any method. [WARNING] public void setVersion(int version) throws ParserException { [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:185: warning: @inheritDoc used but setAccession(String) does not override or implement any method. [WARNING] public void setAccession(String accession) throws ParserException { [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:193: warning: @inheritDoc used but setDescription(String) does not override or implement any method. [WARNING] public void setDescription(String description) throws ParserException { [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:201: warning: @inheritDoc used but setIdentifier(String) does not override or implement any method. [WARNING] public void setIdentifier(String identifier) throws ParserException { [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:210: warning: @inheritDoc used but setName(String) does not override or implement any method. [WARNING] public void setName(String name) throws ParserException { [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:219: warning: @inheritDoc used but setComment(String) does not override or implement any method. [WARNING] public void setComment(String comment) throws ParserException { [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/GeneSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/Hashcoder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/Hit.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/Hsp.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/InputStreamProvider.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/InsdcLocations.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/InsdcLocations.BondLocation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/InsdcLocations.GroupLocation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/InsdcLocations.OneOfLocation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/InsdcLocations.OrderLocation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/InsdcParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/IntronSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/util/IOUtils.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java:181: warning: Tag @link: reference not found: IOUtils#processReader(String) [WARNING] * {@link IOUtils#processReader(String)}. Each time a line is encountered [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/util/IOUtils.ReaderProcessor.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java:181: warning: Tag @link: reference not found: IOUtils#processReader(String) [WARNING] * {@link IOUtils#processReader(String)}. Each time a line is encountered [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/IUPACParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/IUPACParser.IUPACTable.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java:264: warning: @param argument "nucleotides" is not a parameter name. [WARNING] * @param nucleotides The nucleotide set to use when building BioJava [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java:69: warning: invalid input: '<' [WARNING] * Allows creation of the store from List>. CompoundSet [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java:220: warning: invalid input: '&' [WARNING] * attempting to skip onto the next sequence as & when it is asked to [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java:69: warning: invalid input: '<' [WARNING] * Allows creation of the store from List>. CompoundSet [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java:220: warning: invalid input: '&' [WARNING] * attempting to skip onto the next sequence as & when it is asked to [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/LightweightProfile.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/LightweightProfile.java:55: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if listIndex < 1 or listIndex > number of sequences [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/LightweightProfile.java:71: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/LightweightProfile.StringFormat.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/Location.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java:74: warning: Tag @link: reference not found: #getAllSubLocations() [WARNING] * {@link #getAllSubLocations()}. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/Location.Tools.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java:169: warning: @param argument "location" is not a parameter name. [WARNING] * @param location The location which currently expresses the outer [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/LocationHelper.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java:310: warning: invalid input: '&' [WARNING] * Assumes that the first element is the start & clones it [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java:116: warning: @param argument "location" is not a parameter name. [WARNING] * @param location The location which currently expresses the outer [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java:310: warning: invalid input: '&' [WARNING] * Assumes that the first element is the start & clones it [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/Messages.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/MultipleSequenceAlignment.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/MutableAlignedSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/MutableProfile.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/MutableProfilePair.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/MutableSequencePair.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/NucleotideCompound.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/demo/ParseFastaFileDemo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/ParserException.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/PlainFastaHeaderParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/Point.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/Point.Resolver.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/PrettyXMLWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/Profile.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:61: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if listIndex < 1 or listIndex > number of sequences [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:104: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if listIndex < 1, listIndex > number of sequences, alignmentIndex < 1, or [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:104: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if listIndex < 1, listIndex > number of sequences, alignmentIndex < 1, or [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:116: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:125: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:135: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:144: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:160: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:170: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:180: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:239: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/Profile.StringFormat.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/ProfilePair.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/ProfileView.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/ProteinSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/ProteinSequenceCreator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/ProxySequenceReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/Qualifier.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/QualityFeature.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/QuantityFeature.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/ReferenceInterface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/Result.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/ResultFactory.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/ReversedSequenceView.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/RNACompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/RNASequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/RNASequenceCreator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/RnaSequenceView.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/RNAToAminoAcidTranslator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/ScaledSubstitutionMatrix.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/SearchIO.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/Sequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/SequenceAsStringHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/SequenceComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/SequenceCreatorInterface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/SequenceHeaderParserInterface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/SequenceLocation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/SequenceMixin.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:247: warning: Tag @link: reference not found: SequenceBackingStore [WARNING] * elements in a new instance of {@link SequenceBackingStore} which behaves [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:165: warning: Tag @link: reference not found: Compound#toString() [WARNING] * filled with the results of {@link Compound#toString()}. Does not [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:153: warning: @param argument "writer" is not a parameter name. [WARNING] * @param writer The writer to send data to [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:165: warning: Tag @link: reference not found: Compound#toString() [WARNING] * filled with the results of {@link Compound#toString()}. Does not [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:247: warning: Tag @link: reference not found: SequenceBackingStore [WARNING] * elements in a new instance of {@link SequenceBackingStore} which behaves [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:288: warning: invalid input: '&' [WARNING] * ATG, TGT & GTA [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:346: warning: invalid input: '&' [WARNING] * length & compound sets used. The code will also bail out the moment [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:362: warning: invalid input: '&' [WARNING] * length & compound sets used. The code will also bail out the moment [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/SequenceMixin.SequenceIterator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/SequenceOptimizationHints.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/SequenceOptimizationHints.SequenceCollection.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/SequenceOptimizationHints.SequenceUsage.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/SequencePair.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:44: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:53: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:62: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:71: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if targetIndex < 1 or targetIndex > {@link #getTarget()}.getLength() [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:80: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:89: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if queryIndex < 1 or queryIndex > {@link #getQuery()}.getLength() [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.java:35: warning: @param argument "dataInput" is not a parameter name. [WARNING] * @param dataInput [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/SequenceProxyView.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/SequenceReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/SequenceTools.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/SequenceView.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/SimpleAlignedSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/SimpleLocation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/SimplePoint.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/SimpleProfile.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/SimpleProfilePair.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/SimpleSequencePair.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/SimpleSubstitutionMatrix.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java:171: warning: Tag @link: reference not found: SequenceMixin#countCompounds(org.biojava.nbio.core.sequence.template.Sequence, C[]) [WARNING] * Delegates to {@link SequenceMixin#countCompounds(org.biojava.nbio.core.sequence.template.Sequence, C[]) } [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java:171: warning: Tag @link: reference not found: SequenceMixin#countCompounds(org.biojava.nbio.core.sequence.template.Sequence, C[]) [WARNING] * Delegates to {@link SequenceMixin#countCompounds(org.biojava.nbio.core.sequence.template.Sequence, C[]) } [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/SingleLinkageClusterer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/SoftHashMap.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/StartCodonSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/StopCodonSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/Strand.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/StringManipulationHelper.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/StringManipulationHelper.java:81: warning: Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, module, package, class/interface. [WARNING] * @author andreas [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/StringManipulationHelper.java:207: warning: invalid input: '<' [WARNING] * @throws IllegalArgumentException if n <= 0 [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/StringManipulationHelper.java:219: warning: invalid input: '<' [WARNING] * @throws IllegalArgumentException if n <= 0 [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/SubstitutionMatrix.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SubstitutionMatrix.java:106: warning: invalid input: '<' [WARNING] * @throws IllegalArgumentException if scale < 1 [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:81: warning: invalid input: '&' [WARNING] * Returns Blosum 100 matrix by Henikoff & Henikoff [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:89: warning: invalid input: '&' [WARNING] * Returns Blosum 30 matrix by Henikoff & Henikoff [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:97: warning: invalid input: '&' [WARNING] * Returns Blosum 35 matrix by Henikoff & Henikoff [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:105: warning: invalid input: '&' [WARNING] * Returns Blosum 40 matrix by Henikoff & Henikoff [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:113: warning: invalid input: '&' [WARNING] * Returns Blosum 45 matrix by Henikoff & Henikoff [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:121: warning: invalid input: '&' [WARNING] * Returns Blosum 50 matrix by Henikoff & Henikoff [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:129: warning: invalid input: '&' [WARNING] * Returns Blosum 55 matrix by Henikoff & Henikoff [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/Table.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/Table.CaseInsensitiveTriplet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/Table.Codon.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/TaxonomyID.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/TextFeature.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.html... 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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/UncompressInputStream.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/WindowedSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/XMLHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/XMLWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/demo/package-summary.html... 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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/RNASequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/ProteinSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/MultipleSequenceAlignment.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/IntronSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/GeneSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/ExonSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/ExonComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/DataSource.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/DNASequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/DNASequence.DNAType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/ChromosomeSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/CDSSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/CDSComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/BasicSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/AccessionID.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastXMLParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastTabularParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastResultBuilder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastResult.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastHspBuilder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastHitBuilder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/SearchIO.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/ResultFactory.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/Result.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/Hsp.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/Hit.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/class-use/TranslationException.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/class-use/ParserException.html... 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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/ProfilePair.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/Profile.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/Profile.StringFormat.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableSequencePair.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableProfilePair.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableProfile.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableAlignedSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/AlignedSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/AlignedSequence.Step.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/SubstitutionMatrixHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/SimpleSubstitutionMatrix.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/ScaledSubstitutionMatrix.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/DefaultAAIndexProvider.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/AAindexFactory.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/AAIndexProvider.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/AAIndexFileParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleSequencePair.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleProfilePair.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleProfile.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleAlignedSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/demo/class-use/UncompressFile.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/demo/class-use/ParseFastaFileDemo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/demo/class-use/DemoSixFrameTranslation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/demo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/util/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/deprecated-list.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/allclasses-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/index-all.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/help-doc.html... [WARNING] 100 warnings [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/biojava-core-6.1.0-javadoc.jar [INFO] [INFO] --------------------< org.biojava:biojava-forester >-------------------- [INFO] Building biojava-forester 6.1.0 [3/15] [INFO] --------------------------------[ jar ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-forester --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-forester --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 359 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/pccx/BasicExternalNodeBasedCoverageExtender.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/pccx/BasicExternalNodeBasedCoverageExtender.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/TreePanel.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/TreePanel.java: Recompile with -Xlint:removal for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-forester --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-forester --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-forester --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-forester --- [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/biojava-forester-6.1.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-forester --- [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] Loading source files for package org.forester.ws.seqdb... [WARNING] Loading source files for package org.forester.ws.wabi... [WARNING] Loading source files for package org.forester.ws.hmmer... [WARNING] Loading source files for package org.forester.archaeopteryx... [WARNING] Loading source files for package org.forester.archaeopteryx.tools... [WARNING] Loading source files for package org.forester.archaeopteryx.webservices... [WARNING] Loading source files for package org.forester.archaeopteryx.phylogeny.data... [WARNING] Loading source files for package org.forester.application... [WARNING] Loading source files for package org.forester.species... [WARNING] Loading source files for package org.forester.sequence... [WARNING] Loading source files for package org.forester.evoinference.tools... [WARNING] Loading source files for package org.forester.evoinference.parsimony... 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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmPfamOutputParser.ReturnType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmPfamOutputParser.FilterType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nhx/class-use/NHXFormatException.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nhx/class-use/NHXParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nhx/class-use/NHXParser.TAXONOMY_EXTRACTION.html... 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[WARNING] 31 warnings [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/biojava-forester-6.1.0-javadoc.jar [INFO] [INFO] -------------------< org.biojava:biojava-alignment >-------------------- [INFO] Building biojava-alignment 6.1.0 [4/15] [INFO] --------------------------------[ jar ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-alignment --- [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-alignment --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 53 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java uses or overrides a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java: Recompile with -Xlint:removal for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-alignment --- [INFO] Copying 11 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-alignment --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 24 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-alignment --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-alignment --- [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/biojava-alignment-6.1.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-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] Loading source files for package org.biojava.nbio.phylo... [WARNING] Loading source files for package org.biojava.nbio.alignment.template... 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[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityScorer.java:37: warning: Tag @link: reference not found: AlignedSequence [WARNING] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/GapPenalty.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/GapPenalty.Type.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/GuanUberbacher.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/GuanUberbacher.java:37: warning: invalid input: '<' [WARNING] * space complexity is a modest (a multiple < 2) increase in time. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/GuideTree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/GuideTree.Node.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/GuideTreeNode.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/HierarchicalClusterer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/MatrixAligner.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/MatrixAligner.java:33: warning: Tag @link: reference not found: Profile [WARNING] * @param each element of the alignment {@link Profile} is of type S [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/MatrixAligner.java:34: warning: Tag @link: reference not found: AlignedSequence [WARNING] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/NeedlemanWunsch.html... 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[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PairwiseSequenceAligner.java:35: warning: Tag @link: reference not found: AlignedSequence [WARNING] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/PairwiseSequenceScorer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/PartitionRefiner.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:34: warning: Tag @link: reference not found: Profile [WARNING] * @param each element of the alignment {@link Profile} is of type S [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:35: warning: Tag @link: reference not found: AlignedSequence [WARNING] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/ProfileProfileAligner.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:34: warning: Tag @link: reference not found: Profile [WARNING] * @param each {@link Sequence} in the pair of alignment {@link Profile}s is of type S [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:35: warning: Tag @link: reference not found: AlignedSequence [WARNING] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/ProfileProfileScorer.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileScorer.java:35: warning: Tag @link: reference not found: AlignedSequence [WARNING] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/RescoreRefiner.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:36: warning: Tag @link: reference not found: Profile [WARNING] * @param each element of the alignment {@link Profile} is of type S [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:37: warning: Tag @link: reference not found: AlignedSequence [WARNING] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: Tag @link: reference not found: Profile [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/Scorer.html... 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[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: Tag @link: reference not found: Profile [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/package-summary.html... 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[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/ProfileProfileAligner.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PartitionRefiner.html... 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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/StandardRescoreRefiner.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/SmithWaterman.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/SimpleProfileProfileAligner.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/SimpleGapPenalty.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/NeedlemanWunsch.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/GuideTree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/GuideTree.Node.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/FractionalSimilarityScorer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/FractionalSimilarityInProfileScorer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/FractionalIdentityScorer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/FractionalIdentityInProfileScorer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.RefinerType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.ProfileProfileAlignerType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.PairwiseSequenceScorerType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.PairwiseSequenceAlignerType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.PairInProfileScorerType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/demo/class-use/TestDNANeedlemanWunsch.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/demo/class-use/DemoLoadSubstMax.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/demo/class-use/DemoDistanceTree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/demo/class-use/DemoAlignProteins.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/demo/class-use/CookbookMSA.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/demo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/io/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/package-use.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: Tag @link: reference not found: Profile [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/allclasses-index.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: Tag @link: reference not found: Profile [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/index-all.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: Tag @link: reference not found: Profile [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/help-doc.html... [WARNING] 58 warnings [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/biojava-alignment-6.1.0-javadoc.jar [INFO] [INFO] -------------------< org.biojava:biojava-structure >-------------------- [INFO] Building biojava-structure 6.1.0 [5/15] [INFO] --------------------------------[ jar ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [WARNING] The artifact java3d:vecmath:jar:debian has been relocated to javax.vecmath:vecmath:jar:debian [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-structure --- [INFO] Copying 3 resources [INFO] Copying 61 resources [INFO] The encoding used to copy filtered properties files have not been set. This means that the same encoding will be used to copy filtered properties files as when copying other filtered resources. This might not be what you want! Run your build with --debug to see which files might be affected. Read more at https://maven.apache.org/plugins/maven-resources-plugin/examples/filtering-properties-files.html [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-structure --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 431 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java: Recompile with -Xlint:removal for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-structure --- [INFO] Copying 55 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-structure --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 100 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/test-classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfStructureWriter.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfStructureWriter.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityHeuristics.java: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityHeuristics.java uses or overrides a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityHeuristics.java: Recompile with -Xlint:removal for details. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-structure --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-structure --- [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/biojava-structure-6.1.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-structure --- [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] Loading source files for package org.biojava.nbio.structure.xtal.io... [WARNING] Loading source files for package org.biojava.nbio.structure.xtal... [WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.utils... [WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.misc... [WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.internal... [WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.geometry... [WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.core... [WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.axis... [WARNING] Loading source files for package org.biojava.nbio.structure.secstruc... [WARNING] Loading source files for package org.biojava.nbio.structure.scop... [WARNING] Loading source files for package org.biojava.nbio.structure.quaternary... [WARNING] Loading source files for package org.biojava.nbio.structure... [WARNING] Loading source files for package org.biojava.nbio.structure.math... [WARNING] Loading source files for package org.biojava.nbio.structure.jama... [WARNING] Loading source files for package org.biojava.nbio.structure.io.util... [WARNING] Loading source files for package org.biojava.nbio.structure.io.sifts... [WARNING] Loading source files for package org.biojava.nbio.structure.io... [WARNING] Loading source files for package org.biojava.nbio.structure.io.mmtf... [WARNING] Loading source files for package org.biojava.nbio.structure.io.cif... [WARNING] Loading source files for package org.biojava.nbio.structure.geometry... [WARNING] Loading source files for package org.biojava.nbio.structure.ecod... [WARNING] Loading source files for package org.biojava.nbio.structure.domain.pdp... [WARNING] Loading source files for package org.biojava.nbio.structure.domain... [WARNING] Loading source files for package org.biojava.nbio.structure.contact... [WARNING] Loading source files for package org.biojava.nbio.structure.cluster... [WARNING] Loading source files for package org.biojava.nbio.structure.chem... [WARNING] Loading source files for package org.biojava.nbio.structure.cath... [WARNING] Loading source files for package org.biojava.nbio.structure.basepairs... [WARNING] Loading source files for package org.biojava.nbio.structure.asa... [WARNING] Loading source files for package org.biojava.nbio.structure.align.xml... [WARNING] Loading source files for package org.biojava.nbio.structure.align.util... [WARNING] Loading source files for package org.biojava.nbio.structure.align.seq... [WARNING] Loading source files for package org.biojava.nbio.structure.align.quaternary... [WARNING] Loading source files for package org.biojava.nbio.structure.align.pairwise... [WARNING] Loading source files for package org.biojava.nbio.structure.align... [WARNING] Loading source files for package org.biojava.nbio.structure.align.multiple.util... [WARNING] Loading source files for package org.biojava.nbio.structure.align.multiple.mc... [WARNING] Loading source files for package org.biojava.nbio.structure.align.multiple... [WARNING] Loading source files for package org.biojava.nbio.structure.align.model... [WARNING] Loading source files for package org.biojava.nbio.structure.align.helper... [WARNING] Loading source files for package org.biojava.nbio.structure.align.fatcat... [WARNING] Loading source files for package org.biojava.nbio.structure.align.fatcat.calc... [WARNING] Loading source files for package org.biojava.nbio.structure.align.client... [WARNING] Loading source files for package org.biojava.nbio.structure.align.ce... [WARNING] Loading source files for package demo... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.11+9-Debian-1 [WARNING] Building tree for all the packages and classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.WrappedAtom.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/AbstractScoresCache.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/AbstractStructureAlignment.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/model/AFP.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/model/AFPChain.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java:1311: warning: Tag @link: reference not found: org.biojava.nbio.structure.gui.JMatrixPanel [WARNING] * A {@link org.biojava.nbio.structure.gui.JMatrixPanel}, which is used in [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java:56: warning: invalid input: '<' [WARNING] // AFP(k-1) < AFP(k)(refer AFP.h definition), [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java:57: warning: invalid input: '<' [WARNING] // ie i(k-1) < i(k) and j(k-1) < j(k) [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java:57: warning: invalid input: '<' [WARNING] // ie i(k-1) < i(k) and j(k-1) < j(k) [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/AFPChainFlipper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/AFPChainScorer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/model/AfpChainWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/AFPChainXMLConverter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/AFPChainXMLParser.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLParser.java:59: warning: Parameter "name1" is documented more than once. [WARNING] * @param name1 [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/AFPOptimizer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/AFPPostProcessor.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/AFPTwister.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/helper/AligMatEl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/Alignable.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/AlignmentProgressListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/AlignmentResult.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/AlignmentTools.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:506: warning: invalid input: '<' [WARNING] * A Map can be viewed as a function from K to V. This class represents [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:306: warning: invalid input: '<' [WARNING] * If none are found at n<=maxSymmetry, the alignment is reported as [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:317: warning: invalid input: '<' [WARNING] * @return The order of symmetry of alignment, or 1 if no order <= [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:474: warning: invalid input: '<' [WARNING] * List>> aln = getOptAlnAsList(AFPChain afpChain); [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:474: warning: invalid input: '<' [WARNING] * List>> aln = getOptAlnAsList(AFPChain afpChain); [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/AlignmentTools.IdentityMap.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:506: warning: invalid input: '<' [WARNING] * A Map can be viewed as a function from K to V. This class represents [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/AligNPE.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/helper/AlignUtils.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/AllChemCompProvider.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/AltAligComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/AminoAcid.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/AminoAcidImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java:48: warning: @param argument "error" is not a parameter name. [WARNING] * @param error [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java:64: warning: @param argument "error" is not a parameter name. [WARNING] * @param error [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java:85: warning: @param argument "error" is not a parameter name. [WARNING] * @param error [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/asa/AsaCalculator.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java:621: warning: invalid usage of tag {@link Element().N [WARNING] * unknown type (element) the vdw radius of {@link Element().N} is returned [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/Astral.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/Astral.AstralSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/Atom.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java:263: warning: @return tag cannot be used in method with void return type. [WARNING] public void setCharge(short charge); [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/AtomCache.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:227: warning: invalid input: '<' [WARNING] * @throws StructureException if biassemblyId < 0 or other problems while loading structure [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:251: warning: invalid input: '<' [WARNING] * @throws StructureException if biassemblyId < 0 or other problems while loading structure [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:471: warning: Tag @link: reference not found: #setStrictSCOP(boolean) [WARNING] * see {@link #setStrictSCOP(boolean)} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:677: warning: Tag @link: reference not found: #isAutoFetch() [WARNING] * if {@link #isAutoFetch()} is false. Note that an obsolete entry may still be [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:680: warning: @param argument "fetchFileEvenIfObsolete" is not a parameter name. [WARNING] * @param fetchFileEvenIfObsolete Whether to fetch obsolete records [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:681: warning: Tag @see: reference not found: #setFetchCurrent(boolean) [WARNING] * @see #setFetchCurrent(boolean) [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:691: warning: Tag @link: reference not found: #isAutoFetch() [WARNING] * such as when {@link #isAutoFetch()} is false. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:795: warning: @param argument "pdbId" is not a parameter name. [WARNING] * @param pdbId [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/AtomContact.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/AtomContactSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/AtomIdentifier.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/AtomImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/AtomIterator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/AtomPositionMap.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/AtomPositionMap.GroupMatcher.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/AugmentedResidueRange.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/Author.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/axis/AxisAligner.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/basepairs/BasePairParameters.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/BcifFileReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/BerkeleyScopInstallation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/BetaBridge.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/BioAssemblyIdentifier.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java:61: warning: @param argument "pdbCode" is not a parameter name. [WARNING] * @param pdbCode [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java:51: warning: Tag @link: reference not found: #toString() [WARNING] * It is recommended that the {@link #toString()} method also return the [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java:95: warning: Tag @see: reference not found: StructureTools#getReducedStructure(Structure, String) [WARNING] * @see StructureTools#getReducedStructure(Structure, String) [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/BioAssemblyInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/BioAssemblyTools.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java:265: warning: @param argument "structure" is not a parameter name. [WARNING] * @param structure [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/BioJavaStructureAlignment.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/utils/BlastClustReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/Block.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java:75: warning: Tag @see: reference not found: #setAlignRes() [WARNING] * @see #setAlignRes() [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java:111: warning: Tag @see: reference not found: #updateCoreLength() [WARNING] * @see #updateCoreLength() [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/BlockImpl.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java:55: warning: Tag @return cannot be used in constructor documentation. It can only be used in the following types of documentation: method, inline text. [WARNING] * @return BlockImpl a BlockImpl instance linked to its parent BlockSet. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java:72: warning: Tag @return cannot be used in constructor documentation. It can only be used in the following types of documentation: method, inline text. [WARNING] * @return BlockImpl an identical copy of the input BlockImpl object. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java:75: warning: Tag @see: reference not found: #setAlignRes() [WARNING] * @see #setAlignRes() [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java:111: warning: Tag @see: reference not found: #updateCoreLength() [WARNING] * @see #updateCoreLength() [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/BlockSet.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSet.java:114: warning: @param argument "matrices" is not a parameter name. [WARNING] * @param matrices [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/BlockSetImpl.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java:58: warning: Tag @return cannot be used in constructor documentation. It can only be used in the following types of documentation: method, inline text. [WARNING] * @return BlockSet an instance linked to the parent alignment. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java:79: warning: Tag @return cannot be used in constructor documentation. It can only be used in the following types of documentation: method, inline text. [WARNING] * @return BlockSet an identical copy of the input object. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/Bond.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/Bond.java:29: warning: invalid input: '<' [WARNING] * @author Jules Jacobsen [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/BondImpl.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java:30: warning: invalid input: '<' [WARNING] * @author Jules Jacobsen [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java:47: warning: Tag @link: reference not found: #Bond(Atom, Atom, int, boolean) [WARNING] * {@link #Bond(Atom, Atom, int, boolean)} with the [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/BondMaker.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/BondType.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/BondType.java:26: warning: invalid input: '<' [WARNING] * @author Jules Jacobsen [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/BoundingBox.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/BravaisLattice.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/BridgeType.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/BridgeType.java:25: warning: invalid input: '<' [WARNING] * (i-1,i,i+1) and (j-1,j,j+1), where i------------------ [INFO] Building biojava-jcolorbrewer 6.1.0 [6/15] [INFO] --------------------------------[ jar ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-jcolorbrewer --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-jcolorbrewer --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 7 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java uses or overrides a deprecated API. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-jcolorbrewer --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-jcolorbrewer --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-jcolorbrewer --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-jcolorbrewer --- [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/biojava-jcolorbrewer-6.1.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-jcolorbrewer --- [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] Loading source files for package org.jcolorbrewer.ui... [WARNING] Loading source files for package org.jcolorbrewer... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.11+9-Debian-1 [WARNING] Building tree for all the packages and classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ColorBrewer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/ColorPaletteChooserDialog.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java:82: warning: Tag @see: reference not found: ColorChooserDialog [WARNING] * @see ColorChooserDialog [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java:436: warning: @param argument "color" is not a parameter name. [WARNING] * @param color the new color [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/ColorPanelSelectionModel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/DivergingColorPalettePanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/PaletteIcon.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/QualitativeColorPalettePanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/SequentialColorPalettePanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/serialized-form.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/ColorPaletteChooserDialog.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/QualitativeColorPalettePanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/DivergingColorPalettePanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/SequentialColorPalettePanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/ColorPanelSelectionModel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/PaletteIcon.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/class-use/ColorBrewer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/allclasses-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/index-all.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/help-doc.html... [WARNING] 3 warnings [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/biojava-jcolorbrewer-6.1.0-javadoc.jar [INFO] [INFO] -----------------< org.biojava:biojava-structure-gui >------------------ [INFO] Building biojava-structure-gui 6.1.0 [7/15] [INFO] --------------------------------[ jar ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-structure-gui --- [INFO] Copying 49 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-structure-gui --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 131 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/SequenceDisplay.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/SequenceDisplay.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java: Recompile with -Xlint:removal for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/BiojavaJmol.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/BiojavaJmol.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-structure-gui --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-structure-gui --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 6 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-structure-gui --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-structure-gui --- [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/biojava-structure-gui-6.1.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-structure-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] Loading source files for package org.biojava.nbio.structure.symmetry.jmolScript... [WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.gui... [WARNING] Loading source files for package org.biojava.nbio.structure.gui.util... [WARNING] Loading source files for package org.biojava.nbio.structure.gui.util.color... [WARNING] Loading source files for package org.biojava.nbio.structure.gui... [WARNING] Loading source files for package org.biojava.nbio.structure.gui.events... [WARNING] Loading source files for package org.biojava.nbio.structure.align.webstart... [WARNING] Loading source files for package org.biojava.nbio.structure.align.gui.jmol... [WARNING] Loading source files for package org.biojava.nbio.structure.align.gui.autosuggest... [WARNING] Loading source files for package org.biojava.nbio.structure.align.gui.aligpanel... [WARNING] Loading source files for package org.biojava.nbio.structure.align.gui... [WARNING] Loading source files for package demo... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.11+9-Debian-1 [WARNING] Building tree for all the packages and classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/AboutDialog.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java:199: warning: @param argument "label" is not a parameter name. [WARNING] * @param label [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/AFPChainCoordManager.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/AFPFromFasta.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/AlignedPosition.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/AlignmentCalc.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/AlignmentCalc.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/AlignmentCalculationRunnable.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/AlignmentGui.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/AlignmentGuiDemo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/AlignmentPositionListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/AlignmentTextPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/AligPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/AligPanelMouseMotionListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/AligUIManager.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/AtomInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/AtomInfoParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/AutoSuggestProvider.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/BiojavaJmol.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/BrowserOpener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/ChooseDirAction.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/ColorConverter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/ColorInterpolator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/ColorUtils.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/ConfigPDBInstallPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/ConfigXMLHandler.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/ContinuousColorMapper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/ContinuousColorMapperTransform.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ContinuousColorMapperTransform.java:63: warning: @param argument "the" is not a parameter name. [WARNING] * @param the input value [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/CookBook.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/CoordManager.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/DefaultAutoSuggestProvider.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/DefaultMatrixMapper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoAlignmentFromFasta.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoCE.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoCeSymm.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoFATCAT.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoMultipleMC.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoNWALignment.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoQuatSymmetryJmol.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoRotationAxis.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoShowBiolAssembly.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoShowCATHDomain.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoShowLargeAssembly.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoStructureFromFasta.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoSW3DAligner.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/DisplayAFP.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/DotPlotPanel.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DotPlotPanel.java:59: warning: @param argument "background" is not a parameter name. [WARNING] * @param background [Optional]A matrix of 'background colors' over which to draw the alignment. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/GradientMapper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/GradientPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/HelpDialog.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/HSVColorSpace.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/HSVColorSpace.java:83: warning: @param argument "type" is not a parameter name. [WARNING] * @param type [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/HSVColorSpace.java:84: warning: @param argument "numcomponents" is not a parameter name. [WARNING] * @param numcomponents [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/JMatrixPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/JmolAlignedPositionListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.JmolLoggerAdapter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGenerator.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGenerator.java:41: warning: @param argument "rotationGroup" is not a parameter name. [WARNING] * @param rotationGroup [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorC1.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorCn.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorDn.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorI.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorO.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorT.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/JmolTools.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/JmolViewerImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/JNLPProxy.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/JPrintPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/LinearColorInterpolator.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/LinearColorInterpolator.java:145: warning: @param argument "interpDirection" is not a parameter name. [WARNING] * @param interpDirection An array of size colorSpace.getNumComponents() [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/LinearColorInterpolator.InterpolationDirection.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/LogColorMapper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MemoryMonitor.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java:54: warning: invalid input: '&' [WARNING] * Tracks Memory allocated & used, displayed in graph form. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MemoryMonitor.Surface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MenuCreator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/MenuCreator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MenuCreator.DotPlotListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MultipleAlignmentCalc.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAlignmentCoordManager.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MultipleAlignmentGUI.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MultipleAlignmentJmolDisplay.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java:157: warning: @param argument "multAln" is not a parameter name. [WARNING] * @param multAln [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java:158: warning: @param argument "colors" is not a parameter name. [WARNING] * @param colors [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanelMouseMotionListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/MultipleStatusDisplay.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MyAlignmentLoadListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MyDistMaxListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MyExportListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/MyJmolStatusListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MyOpenPdbFileListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MySaveFileListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MyTableRowSorter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/ParameterGUI.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/PDBDirPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/PDBServerPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/PDBUploadPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/RenderStyle.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/ScaleableMatrixPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/ScaleableMatrixPanel.GradientRenderer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/SCOPAutoSuggestProvider.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/ScopInstallationInstance.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/ScopSelectPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/Selection.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/SelectionImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/SelectMultiplePanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/SelectPDBPanel.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java:46: warning: invalid input: '&' [WARNING] /** A Panel that allows user to specify PDB & chain ID, as well as sub-ranges [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/SequenceDisplay.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/SequenceMouseListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/SequenceScalePanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/ShowPDBIDListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/ShowStructureInJmol.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/SqrtColorMapper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/StatusDisplay.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/StructureAlignmentDisplay.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/StructureLoaderThread.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/StructurePairSelector.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/StructureViewer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/SymmetryCalc.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java:107: warning: @param argument "msa" is not a parameter name. [WARNING] * @param msa [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/SymmetryGui.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/SymmetryListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/SystemInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/WebStartClientDemo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/WebStartMain.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/WrapLayout.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/package-summary.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java:54: warning: invalid input: '&' [WARNING] * Tracks Memory allocated & used, displayed in graph form. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java:46: warning: invalid input: '&' [WARNING] /** A Panel that allows user to specify PDB & chain ID, as well as sub-ranges [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/serialized-form.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorT.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorPointGroup.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorO.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorI.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorH.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorDn.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorCn.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorC1.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGenerator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/ColorConverter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryGui.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryDisplay.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryCalc.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/StructurePairSelector.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java:46: warning: invalid input: '&' [WARNING] /** A Panel that allows user to specify PDB & chain ID, as well as sub-ranges [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/SequenceScalePanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/SequenceMouseListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/SelectMultiplePanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/ScopSelectPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/ScopInstallationInstance.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBUploadPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBServerPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBDirPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/MenuCreator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/CoordManager.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlternativeAlignmentFrame.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlignmentCalc.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlignedPosition.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/SqrtColorMapper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LogColorMapper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LinearColorInterpolator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LinearColorInterpolator.InterpolationDirection.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/HSVColorSpace.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/GradientPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/GradientMapper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/DefaultMatrixMapper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ContinuousColorMapperTransform.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ContinuousColorMapper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ColorUtils.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ColorInterpolator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/WrapLayout.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/StructureViewer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/SequenceDisplay.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/SelectionImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/Selection.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/ScaleableMatrixPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/ScaleableMatrixPanel.GradientRenderer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/RenderStyle.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/JmolViewerImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/JMatrixPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/BiojavaJmol.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/class-use/JmolAlignedPositionListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/class-use/AlignmentPositionListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/WebStartMain.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/JNLPProxy.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/ConfigXMLHandler.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/BrowserOpener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/AligUIManager.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/StructureAlignmentJmol.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/RasmolCommandListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/MyJmolStatusListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/MultipleAlignmentJmol.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolTools.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolPanel.JmolLoggerAdapter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AtomInfoParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AtomInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AbstractAlignmentJmol.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/SCOPAutoSuggestProvider.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/JAutoSuggest.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/DefaultAutoSuggestProvider.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/AutoSuggestProvider.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/StatusDisplay.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleStatusDisplay.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAlignmentCoordManager.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAligPanelMouseMotionListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAligPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AligPanelMouseMotionListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AligPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AFPChainCoordManager.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/SystemInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/StructureLoaderThread.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/StructureAlignmentDisplay.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ShowPDBIDListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/SelectPDBPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ParameterGUI.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyTableRowSorter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MySaveFileListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyOpenPdbFileListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyExportListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyDistMaxListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyAlignmentLoadListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentJmolDisplay.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentGUI.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentCalc.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MenuCreator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MenuCreator.DotPlotListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MemoryMonitor.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MemoryMonitor.Surface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/JPrintPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/HelpDialog.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/DotPlotPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/DisplayAFP.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ConfigPDBInstallPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ChooseDirAction.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentTextPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentGui.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalculationRunnable.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalc.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AboutDialog.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoAlignmentFromFasta.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/WebStartClientDemo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/ShowStructureInJmol.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoStructureFromFasta.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoShowLargeAssembly.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoShowCATHDomain.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoShowBiolAssembly.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoSW3DAligner.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoRotationAxis.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoQuatSymmetryJmol.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoNWALignment.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoMultipleMC.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoFATCAT.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoCeSymm.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoCE.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/CookBook.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/AlignmentGuiDemo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/AFPFromFasta.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/allclasses-index.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java:54: warning: invalid input: '&' [WARNING] * Tracks Memory allocated & used, displayed in graph form. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java:46: warning: invalid input: '&' [WARNING] /** A Panel that allows user to specify PDB & chain ID, as well as sub-ranges [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/index-all.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java:54: warning: invalid input: '&' [WARNING] * Tracks Memory allocated & used, displayed in graph form. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java:46: warning: invalid input: '&' [WARNING] /** A Panel that allows user to specify PDB & chain ID, as well as sub-ranges [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/help-doc.html... [WARNING] 20 warnings [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/biojava-structure-gui-6.1.0-javadoc.jar [INFO] [INFO] ---------------------< org.biojava:biojava-genome >--------------------- [INFO] Building biojava-genome 6.1.0 [8/15] [INFO] --------------------------------[ jar ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-genome --- [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-genome --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 51 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-genome --- [INFO] Copying 83 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-genome --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 20 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-genome --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-genome --- [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/biojava-genome-6.1.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-genome --- [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] Loading source files for package org.biojava.nbio.genome.util... [WARNING] Loading source files for package org.biojava.nbio.genome.uniprot... [WARNING] Loading source files for package org.biojava.nbio.genome.query... [WARNING] Loading source files for package org.biojava.nbio.genome.parsers.twobit... [WARNING] Loading source files for package org.biojava.nbio.genome.parsers.gff... [WARNING] Loading source files for package org.biojava.nbio.genome.parsers.genename... [WARNING] Loading source files for package org.biojava.nbio.genome.parsers.geneid... [WARNING] Loading source files for package org.biojava.nbio.genome.parsers.cytoband... [WARNING] Loading source files for package org.biojava.nbio.genome.io.fastq... [WARNING] Loading source files for package org.biojava.nbio.genome.homology... [WARNING] Loading source files for package org.biojava.nbio.genome... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.11+9-Debian-1 [WARNING] Building tree for all the packages and classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/App.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/BlastHomologyHits.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/query/BlastXMLQuery.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/ChromosomeMappingTools.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java:807: warning: Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, module, package, class/interface. [WARNING] * @author Yana Valasatava [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java:854: warning: Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, module, package, class/interface. [WARNING] * @author Yana Valasatava [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/ChromPos.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/Cytoband.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/CytobandParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/Fastq.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/FastqBuilder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/FastqReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/FastqTools.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/FastqVariant.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/FastqWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/Feature.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/FeatureHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/FeatureI.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/FeatureList.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/GCStats.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/GeneChromosomePosition.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/GeneFeatureHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/GeneIDGFF2Reader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/geneid/GeneIDXMLReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/GeneMarkGTFReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/GeneName.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/GeneNamesParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/GFF3Reader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/GFF3Writer.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java:41: warning: @param argument "fileName" is not a parameter name. [WARNING] * @param fileName [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java:42: warning: @param argument "chromosomeSequence" is not a parameter name. [WARNING] * @param chromosomeSequence [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/IlluminaFastqReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/IlluminaFastqWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/Location.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java:414: warning: invalid input: '<' [WARNING] * For position < 0, return Location( start, end + position ). [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java:456: warning: invalid input: '<' [WARNING] * For position < 0, return Location( end - position, end ). [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/LocIterator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/query/OutputHitsGFF.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/ParseListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/ProteinMappingTools.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/SangerFastqReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/SangerFastqWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/SolexaFastqReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/SolexaFastqWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/SplitFasta.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/StainType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/StreamListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/TwoBitFacade.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/TwoBitParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/uniprot/UniprotToFasta.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/geneid/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/geneid/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/package-summary.html... 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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/class-use/ProteinMappingTools.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/class-use/ChromosomeMappingTools.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/uniprot/class-use/UniprotToFasta.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/query/class-use/OutputHitsGFF.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/query/class-use/BlastXMLQuery.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/TwoBitParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/TwoBitFacade.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/Location.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/LocIterator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GeneMarkGTFReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GeneIDGFF2Reader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GFF3Writer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GFF3Reader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GCStats.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureList.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureI.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/Feature.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneNamesParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneName.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneChromosomePositionParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneChromosomePosition.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/ChromPos.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/geneid/class-use/GeneIDXMLReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/StainType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/CytobandParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/Cytoband.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/StreamListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SolexaFastqWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SolexaFastqReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SangerFastqWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SangerFastqReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/ParseListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/IlluminaFastqWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/IlluminaFastqReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqVariant.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqTools.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqBuilder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/Fastq.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/class-use/GFF3FromUniprotBlastHits.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/class-use/BlastHomologyHits.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/class-use/GeneFeatureHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/class-use/App.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/geneid/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/query/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/uniprot/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/deprecated-list.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/allclasses-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/index-all.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/help-doc.html... [WARNING] 7 warnings [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/biojava-genome-6.1.0-javadoc.jar [INFO] [INFO] -------------------< org.biojava:biojava-modfinder >-------------------- [INFO] Building biojava-modfinder 6.1.0 [9/15] [INFO] --------------------------------[ jar ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-modfinder --- [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-modfinder --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 23 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java uses or overrides a deprecated API. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-modfinder --- [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-modfinder --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 5 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-modfinder --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-modfinder --- [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/biojava-modfinder-6.1.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-modfinder --- [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] Loading source files for package org.biojava.nbio.protmod.structure... [WARNING] Loading source files for package org.biojava.nbio.protmod.io... [WARNING] Loading source files for package org.biojava.nbio.protmod... [WARNING] Loading source files for package org.biojava.nbio.phosphosite... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.11+9-Debian-1 [WARNING] Building tree for all the packages and classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/Component.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java:33: warning: Tag @link: reference not found: register [WARNING] * you have to use one of the {@link register} and {@link of} methods. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java:112: warning: @param argument "pdbccIds" is not a parameter name. [WARNING] * @param pdbccIds possible Protein Data Bank ID. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/ComponentXMLConverter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/Dataset.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/ModificationCategory.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/ModificationCondition.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/ModificationConditionImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/ModificationLinkage.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationLinkage.java:57: warning: @param argument "labelOfAtomOnComponent1" is not a parameter name. [WARNING] * @param labelOfAtomOnComponent1 label of the atom on the first [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationLinkage.java:60: warning: @param argument "labelOfAtomOnComponent2" is not a parameter name. [WARNING] * @param labelOfAtomOnComponent2 label of the atom on the second [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationLinkage.java:80: warning: @param argument "labelOfAtomOnComponent1" is not a parameter name. [WARNING] * @param labelOfAtomOnComponent1 label of the atom on the first [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationLinkage.java:83: warning: @param argument "labelOfAtomOnComponent2" is not a parameter name. [WARNING] * @param labelOfAtomOnComponent2 label of the atom on the second [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/ModificationOccurrenceType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/ModifiedCompound.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java:50: warning: Tag @link: reference not found: ProteinModificationBean [WARNING] * @return {@link ProteinModificationBean} occurred on the residue. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java:76: warning: Tag @see: reference not found: #getLinkedGroupPairs [WARNING] * @see #getLinkedGroupPairs [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java:85: warning: @return tag cannot be used in method with void return type. [WARNING] public void setAtomLinkages(Set linkages); [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java:88: warning: Tag @link: reference not found: addGroup [WARNING] * Add a linkage. Add new the involved groups first using {@link addGroup}. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/ModifiedCompoundImpl.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompoundImpl.java:68: warning: Tag @return cannot be used in constructor documentation. It can only be used in the following types of documentation: method, inline text. [WARNING] * @return a {@link ModifiedCompound}. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java:50: warning: Tag @link: reference not found: ProteinModificationBean [WARNING] * @return {@link ProteinModificationBean} occurred on the residue. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java:76: warning: Tag @see: reference not found: #getLinkedGroupPairs [WARNING] * @see #getLinkedGroupPairs [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java:88: warning: Tag @link: reference not found: addGroup [WARNING] * Add a linkage. Add new the involved groups first using {@link addGroup}. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/ProteinModification.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/ProteinModificationImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/ProteinModificationImpl.Builder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/ProteinModificationRegistry.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java:209: warning: @param argument "mod" is not a parameter name. [WARNING] * @param mod [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/ProteinModificationXmlReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/Site.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/StructureAtom.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/StructureAtomLinkage.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/StructureAtomXMLConverter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/StructureGroup.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/StructureGroupXMLConverter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/StructureUtil.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/serialized-form.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureUtil.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureGroup.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureAtomLinkage.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureAtom.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/ProteinModificationIdentifier.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/ModifiedCompoundImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/ModifiedCompound.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/StructureGroupXMLConverter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/StructureAtomXMLConverter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ProteinModificationXmlReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ModifiedCompoundXMLConverter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ComponentXMLConverter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationRegistry.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationImpl.Builder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModification.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationOccurrenceType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationLinkage.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationConditionImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationCondition.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationCategory.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/Component.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/class-use/Site.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/class-use/Dataset.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/allclasses-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/index-all.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/help-doc.html... [WARNING] 16 warnings [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/biojava-modfinder-6.1.0-javadoc.jar [INFO] [INFO] -----------------------< org.biojava:biojava-ws >----------------------- [INFO] Building biojava-ws 6.1.0 [10/15] [INFO] --------------------------------[ jar ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-ws --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-ws --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 21 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-ws --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-ws --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-ws --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-ws --- [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/biojava-ws-6.1.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-ws --- [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] Loading source files for package org.biojava.nbio.ws.hmmer... [WARNING] Loading source files for package org.biojava.nbio.ws.alignment.qblast... [WARNING] Loading source files for package org.biojava.nbio.ws.alignment... [WARNING] Loading source files for package demo... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.11+9-Debian-1 [WARNING] Building tree for all the packages and classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/BlastAlignmentParameterEnum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/BlastJob.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/BlastMatrixEnum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/BlastOutputAlignmentFormatEnum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/BlastOutputFormatEnum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/BlastOutputParameterEnum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/BlastProgramEnum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/HmmerDemo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/HmmerDomain.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/HmmerResult.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/HmmerScan.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/MapToStringTransformer.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/MapToStringTransformer.java:46: warning: invalid input: '&' [WARNING] * separatorSequence = "&"; [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/MapToStringTransformer.java:79: warning: invalid input: '&' [WARNING] * {@code mappingSequence} is "=" and separator sequence is "&"; [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java:140: warning: Tag @link: reference not found: NCBIQBlastService#printRemoteBlastInfo() [WARNING] * A list of available databases can be acquired by calling {@link NCBIQBlastService#printRemoteBlastInfo()} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java:144: warning: @param argument "db" is not a parameter name. [WARNING] * @param db : a valid name to a NCBI blastable database [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastOutputProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/NCBIQBlastServiceDemo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentOutputProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentService.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/serialized-form.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/RemoteHmmerScan.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerScan.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerResult.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerDomain.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastService.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastOutputProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastAlignmentProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/MapToStringTransformer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastProgramEnum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputParameterEnum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputFormatEnum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputAlignmentFormatEnum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastMatrixEnum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastJob.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastAlignmentParameterEnum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentService.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentOutputProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/class-use/NCBIQBlastServiceDemo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/class-use/HmmerDemo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/allclasses-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/index-all.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/help-doc.html... [WARNING] 5 warnings [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/biojava-ws-6.1.0-javadoc.jar [INFO] [INFO] ----------------< org.biojava:biojava-protein-disorder >---------------- [INFO] Building biojava-protein-disorder 6.1.0 [11/15] [INFO] --------------------------------[ jar ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-protein-disorder --- [INFO] Copying 11 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-protein-disorder --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 13 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-protein-disorder --- [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-protein-disorder --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 3 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-protein-disorder --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-protein-disorder --- [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/biojava-protein-disorder-6.1.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-protein-disorder --- [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] Loading source files for package org.biojava.nbio.ronn... [WARNING] Loading source files for package org.biojava.nbio.data.sequence... [WARNING] Loading source files for package demo... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.11+9-Debian-1 [WARNING] Building tree for all the packages and classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/FastaSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/Jronn.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/Jronn.Range.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/ModelLoader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/ModelLoader.Model.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/ModelLoader.Threshold.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/NullOutputStream.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/ORonn.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/ORonnModel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/demo/PredictDisorder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/RonnConstraint.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/RonnConstraint.Threshold.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/SequenceUtil.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/Timer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/demo/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/demo/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/serialized-form.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/Timer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/RonnConstraint.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/RonnConstraint.Threshold.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ORonnModel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ORonn.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/NullOutputStream.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.Model.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.Threshold.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/Jronn.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/Jronn.Range.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/class-use/SequenceUtil.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/class-use/FastaSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/demo/class-use/PredictDisorder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/demo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/allclasses-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/index-all.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/help-doc.html... [WARNING] 1 warning [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/biojava-protein-disorder-6.1.0-javadoc.jar [INFO] [INFO] --------------------< org.biojava:biojava-aa-prop >--------------------- [INFO] Building biojava-aa-prop 6.1.0 [12/15] [INFO] --------------------------------[ jar ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-aa-prop --- [INFO] Copying 11 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-aa-prop --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 33 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-aa-prop --- [INFO] Copying 7 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-aa-prop --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 8 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/test-classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java uses or overrides a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java: Recompile with -Xlint:removal for details. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-aa-prop --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-aa-prop --- [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/biojava-aa-prop-6.1.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-aa-prop --- [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] Loading source files for package org.biojava.nbio.aaproperties.xml... [WARNING] Loading source files for package org.biojava.nbio.aaproperties.profeat... [WARNING] Loading source files for package org.biojava.nbio.aaproperties.profeat.convertor... [WARNING] Loading source files for package org.biojava.nbio.aaproperties... [WARNING] Loading source files for package demo... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.11+9-Debian-1 [WARNING] Building tree for all the packages and classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/AminoAcidComposition.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/AminoAcidProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/demo/BioJavaAADemo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/CaseFreeAminoAcidCompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/CommandPrompt.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/CommandPrompt.PropertyName.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/Constraints.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Charge.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Hydrophobicity.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/Convert2NormalizedVanDerWaalsVolume.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Polarity.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Polarizability.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/Convert2SecondaryStructure.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/Convert2SolventAccessibility.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java:40: warning: Tag @author cannot be used in field documentation. It can only be used in the following types of documentation: overview, module, package, class/interface. [WARNING] * @author kohchuanhock [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java:41: warning: Tag @version cannot be used in field documentation. It can only be used in the following types of documentation: overview, module, package, class/interface. [WARNING] * @version 2011.06.09 [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/Element.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/ElementTable.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/IPeptideProperties.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java:261: warning: invalid input: '<' [WARNING] * here [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/ProfeatPropertiesImpl.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/SchemaGenerator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/Utils.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/demo/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/demo/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/SchemaGenerator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Name2Count.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/MyValidationEventHandler.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/ModifiedAminoAcidCompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Isotope.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/ElementTable.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Element.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/CaseFreeAminoAcidCompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/AminoAcidCompositionTable.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/AminoAcidComposition.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/ProfeatPropertiesImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/ProfeatProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/IProfeatProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/IProfeatProperties.DISTRIBUTION.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/IProfeatProperties.TRANSITION.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/IProfeatProperties.GROUPING.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/IProfeatProperties.ATTRIBUTE.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convertor.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2SolventAccessibility.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2SecondaryStructure.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Polarizability.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Polarity.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2NormalizedVanDerWaalsVolume.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Hydrophobicity.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Charge.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/Utils.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/PeptidePropertiesImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/PeptideProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/PeptideProperties.SingleLetterAACode.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/IPeptideProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/Constraints.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/CommandPrompt.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/CommandPrompt.PropertyName.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/AminoAcidProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/demo/class-use/BioJavaAADemo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/demo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/allclasses-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/index-all.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/help-doc.html... [WARNING] 61 warnings [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/biojava-aa-prop-6.1.0-javadoc.jar [INFO] [INFO] --------------------< org.biojava:biojava-survival >-------------------- [INFO] Building biojava-survival 6.1.0 [13/15] [INFO] --------------------------------[ jar ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-survival --- [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-survival --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 46 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-survival --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-survival --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-survival --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-survival --- [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/biojava-survival-6.1.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-survival --- [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] Loading source files for package org.biojava.nbio.survival.kaplanmeier.metadata... [WARNING] Loading source files for package org.biojava.nbio.survival.kaplanmeier.figure... [WARNING] Loading source files for package org.biojava.nbio.survival.data... [WARNING] Loading source files for package org.biojava.nbio.survival.cox.stats... [WARNING] Loading source files for package org.biojava.nbio.survival.cox.matrix... [WARNING] Loading source files for package org.biojava.nbio.survival.cox.comparators... [WARNING] Loading source files for package org.biojava.nbio.survival.cox... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.11+9-Debian-1 [WARNING] Building tree for all the packages and classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/AgScore.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/CensorStatus.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/CensorStatusSelect.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/ChangeValue.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/ChiSq.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/Cholesky2.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/Chsolve2.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/ClinicalMetaDataOutcome.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/CompactCharSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/CoxCC.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/CoxCoefficient.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/CoxComparatorInterface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/CoxHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/CoxInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/CoxMart.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/CoxMethod.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/CoxR.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java:78: warning: invalid input: '<' [WARNING] * the percent change in loglikelihood is <= eps. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/CoxScore.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/CoxVariables.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/CoxVariablesOverallModelFitComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/CoxVariablesVariableComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/DiscreteQuantizerInterface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/GroupResults.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/HeaderInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/KMFigureInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/Matrix.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/MeanModelComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/MeanQuantizer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/MetaDataInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/ResidualsCoxph.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/ResidualsCoxph.Type.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/RiskInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/StdArrayIO.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/StrataInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/SurvFitInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.ConfLower.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.ConfType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.Error.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.Method.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/SurvivalInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/SurvivalInfoComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/SurvivalInfoHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/SurvivalInfoIndex.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/SurvivalInfoValueComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/WaldTest.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/WaldTestInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/WorkSheet.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java:1467: warning: @param argument "f" is not a parameter name. [WARNING] * @param f [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/serialized-form.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/MetaDataInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/MeanQuantizer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/DiscreteQuantizerInterface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/ClinicalMetaDataOutcome.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.ConfLower.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.ConfType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.Error.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.Method.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/NumbersAtRiskPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/KaplanMeierFigure.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/KMFigureInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/GroupResults.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/ExpressionFigure.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/CensorStatusSelect.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/CensorStatus.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/WorkSheet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/HeaderInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/CompactCharSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/ChangeValue.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/Chsolve2.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/Cholesky2.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/ChiSq.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/AgScore.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/class-use/StdArrayIO.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/class-use/Matrix.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/SurvivalInfoValueComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/SurvivalInfoComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/MeanModelComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxVariablesVariableComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxVariablesOverallModelFitComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxComparatorInterface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/WaldTestInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/WaldTest.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfoIndex.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfoHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvFitInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/StrataInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/RiskInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/ResidualsCoxph.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/ResidualsCoxph.Type.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxVariables.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxScore.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxR.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxMethod.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxMart.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxCoefficient.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxCC.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/allclasses-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/index-all.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/help-doc.html... [WARNING] 3 warnings [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/biojava-survival-6.1.0-javadoc.jar [INFO] [INFO] --------------------< org.biojava:biojava-ontology >-------------------- [INFO] Building biojava-ontology 6.1.0 [14/15] [INFO] --------------------------------[ jar ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-ontology --- [INFO] Copying 3 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-ontology --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 36 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java: Recompile with -Xlint:removal for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-ontology --- [INFO] Copying 6 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-ontology --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 3 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/test-classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestParseOBO.java: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestParseOBO.java uses unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestParseOBO.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-ontology --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-ontology --- [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/biojava-ontology-6.1.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-ontology --- [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] Loading source file /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/package-info.java... [WARNING] Loading source files for package org.biojava.nbio.ontology.utils... [WARNING] Loading source files for package org.biojava.nbio.ontology.obo... [WARNING] Loading source files for package org.biojava.nbio.ontology.io... [WARNING] Loading source files for package org.biojava.nbio.ontology... [WARNING] Loading source files for package demo... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.11+9-Debian-1 [WARNING] Building tree for all the packages and classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/AbstractAnnotation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/AbstractTerm.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/AlreadyExistsException.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/Annotatable.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotatable.java:78: warning: Tag @see: reference not found: org.biojavax.RichAnnotatable [WARNING] * @see org.biojavax.RichAnnotatable [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/Annotation.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java:56: warning: Tag @see: reference not found: org.biojavax.RichAnnotation [WARNING] * @see org.biojavax.RichAnnotation [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/App.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/AssertionFailure.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/DefaultOps.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/io/GOParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/IntegerOntology.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/IntegerOntology.IntTerm.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/InvalidTermException.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/KeyedWeakReference.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/OboFileEventListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/OboFileHandler.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/OboFileParser.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:41: 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] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/OboFileParser.SOPair.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/io/OboParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/Ontology.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java:43: warning: Tag @see: reference not found: org.biojavax.ontology.ComparableOntology [WARNING] * @see org.biojavax.ontology.ComparableOntology [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/Ontology.Impl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/OntologyException.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/OntologyFactory.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/OntologyOps.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/OntologyTerm.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/OntologyTerm.Impl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/OntoTools.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/demo/ParseGO.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/RemoteTerm.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/RemoteTerm.Impl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/SmallAnnotation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/SmallMap.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/StaticMemberPlaceHolder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/Synonym.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/io/TabDelimParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/Term.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java:35: warning: Tag @link: reference not found: org.biojava.nbio.AnnotationAnnotation [WARNING] * A term in an ontology. This has an {@link org.biojava.nbio.Annotation Annotation} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java:54: warning: Tag @see: reference not found: org.biojavax.ontology.ComparableTerm [WARNING] * @see org.biojavax.ontology.ComparableTerm [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/Term.Impl.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java:116: warning: Tag @see: reference not found: org.biojavax.ontology.SimpleComparableTermThis can be used to implement Ontology.createTerm [WARNING] * @see org.biojavax.ontology.SimpleComparableTerm [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/Triple.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java:44: warning: Tag @see: reference not found: org.biojavax.ontology.ComparableTriple [WARNING] * @see org.biojavax.ontology.ComparableTriple [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java:98: warning: invalid input: '&' [WARNING] * return to.getSubject() == getSubject() && [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java:98: warning: invalid input: '&' [WARNING] * return to.getSubject() == getSubject() && [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java:99: warning: invalid input: '&' [WARNING] * to.getObject() == getObject() && [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java:99: warning: invalid input: '&' [WARNING] * to.getObject() == getObject() && [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/Triple.Impl.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java:114: warning: Tag @see: reference not found: org.biojavax.ontology.SimpleComparableTriple [WARNING] * @see org.biojavax.ontology.SimpleComparableTriple [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/Variable.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/Variable.Impl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/WeakValueHashMap.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/demo/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/demo/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/io/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/io/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/serialized-form.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/WeakValueHashMap.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/StaticMemberPlaceHolder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/SmallMap.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/SmallAnnotation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/KeyedWeakReference.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/AssertionFailure.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/Annotation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/Annotatable.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/AbstractAnnotation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/class-use/OboFileParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/class-use/OboFileParser.SOPair.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/class-use/OboFileHandler.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/class-use/OboFileEventListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/io/class-use/TabDelimParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/io/class-use/OboParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/io/class-use/GOParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Variable.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Variable.Impl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Triple.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Triple.Impl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Term.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Term.Impl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Synonym.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/RemoteTerm.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/RemoteTerm.Impl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyTerm.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyTerm.Impl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyOps.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyFactory.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyException.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Ontology.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Ontology.Impl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntoTools.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/InvalidTermException.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/IntegerOntology.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/IntegerOntology.IntTerm.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/DefaultOps.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/App.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/AlreadyExistsException.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/AbstractTerm.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/demo/class-use/ParseGO.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/demo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/io/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/allclasses-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/index-all.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/help-doc.html... [WARNING] 14 warnings [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/biojava-ontology-6.1.0-javadoc.jar [INFO] [INFO] ------------< org.biojava:biojava-protein-comparison-tool >------------- [INFO] Building biojava-protein-comparison-tool 6.1.0 [15/15] [INFO] --------------------------------[ jar ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-protein-comparison-tool --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-protein-comparison-tool --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-protein-comparison-tool --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-protein-comparison-tool --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-protein-comparison-tool --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-protein-comparison-tool --- [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/biojava-protein-comparison-tool-6.1.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-protein-comparison-tool --- [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] Loading source files for package org.biojava.nbio.proteincomparisontool... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.11+9-Debian-1 [WARNING] Building tree for all the packages and classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/apidocs/org/biojava/nbio/proteincomparisontool/HelloWorld.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/apidocs/org/biojava/nbio/proteincomparisontool/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/apidocs/org/biojava/nbio/proteincomparisontool/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/apidocs/org/biojava/nbio/proteincomparisontool/class-use/HelloWorld.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/apidocs/org/biojava/nbio/proteincomparisontool/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/apidocs/overview-tree.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/apidocs/allclasses-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/apidocs/index-all.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/apidocs/index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/apidocs/help-doc.html... [WARNING] 1 warning [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/biojava-protein-comparison-tool-6.1.0-javadoc.jar [INFO] [INFO] ------------------------< org.biojava:biojava >------------------------- [INFO] Building biojava 6.1.0 [16/15] [INFO] --------------------------------[ pom ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] >>> maven-javadoc-plugin:3.4.1:aggregate (default-cli) > compile @ biojava >>> [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-core 6.1.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-core --- [INFO] Copying 24 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-core --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 188 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java: Recompile with -Xlint:removal for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-forester 6.1.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-forester --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-forester --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 359 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/pccx/BasicExternalNodeBasedCoverageExtender.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/pccx/BasicExternalNodeBasedCoverageExtender.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/TreePanel.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/TreePanel.java: Recompile with -Xlint:removal for details. [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-alignment 6.1.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-alignment --- [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-alignment --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 53 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java uses or overrides a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java: Recompile with -Xlint:removal for details. [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-structure 6.1.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [WARNING] The artifact java3d:vecmath:jar:debian has been relocated to javax.vecmath:vecmath:jar:debian [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-structure --- [INFO] Copying 3 resources [INFO] Copying 61 resources [INFO] The encoding used to copy filtered properties files have not been set. This means that the same encoding will be used to copy filtered properties files as when copying other filtered resources. This might not be what you want! Run your build with --debug to see which files might be affected. Read more at https://maven.apache.org/plugins/maven-resources-plugin/examples/filtering-properties-files.html [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-structure --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 431 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java: Recompile with -Xlint:removal for details. [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-jcolorbrewer 6.1.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-jcolorbrewer --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-jcolorbrewer --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 7 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java uses or overrides a deprecated API. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-structure-gui 6.1.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-structure-gui --- [INFO] Copying 49 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-structure-gui --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 131 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/SequenceDisplay.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/SequenceDisplay.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java: Recompile with -Xlint:removal for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/BiojavaJmol.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/BiojavaJmol.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-genome 6.1.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-genome --- [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-genome --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 51 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/classes [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-modfinder 6.1.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-modfinder --- [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-modfinder --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 23 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java uses or overrides a deprecated API. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-ws 6.1.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-ws --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-ws --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 21 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/classes [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-protein-disorder 6.1.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-protein-disorder --- [INFO] Copying 11 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-protein-disorder --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 13 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/classes [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-aa-prop 6.1.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-aa-prop --- [INFO] Copying 11 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-aa-prop --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 33 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/classes [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-survival 6.1.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-survival --- [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-survival --- [INFO] Changes detected - recompiling the module! 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[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java:56: warning: invalid input: '<' [WARNING] // AFP(k-1) < AFP(k)(refer AFP.h definition), [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java:57: warning: invalid input: '<' [WARNING] // ie i(k-1) < i(k) and j(k-1) < j(k) [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java:57: warning: invalid input: '<' [WARNING] // ie i(k-1) < i(k) and j(k-1) < j(k) [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/xml/AFPChainFlipper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/util/AFPChainScorer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/model/AfpChainWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/xml/AFPChainXMLConverter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/xml/AFPChainXMLParser.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLParser.java:59: warning: Parameter "name1" is documented more than once. [WARNING] * @param name1 [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/AFPFromFasta.html... 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[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:68: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if sequenceIndex < 1 or sequenceIndex > [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:133: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:157: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/template/AlignedSequence.Step.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:41: warning: Tag @link: reference not found: Aligner [WARNING] * Defines an alignment step in order to pass alignment information from an {@link Aligner} to a constructor. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/Aligner.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/Aligner.java:35: warning: Tag @link: reference not found: AlignedSequence [WARNING] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/routines/AlignerHelper.html... 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[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:125: warning: Tag @link: reference not found: AlignedSequence [WARNING] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:206: warning: Tag @link: reference not found: AlignedSequence [WARNING] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:312: warning: Tag @link: reference not found: AlignedSequence [WARNING] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:542: warning: Tag @link: reference not found: AlignedSequence [WARNING] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:615: warning: Tag @link: reference not found: AlignedSequence [WARNING] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/Alignments.PairInProfileScorerType.html... 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[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:506: warning: invalid input: '<' [WARNING] * A Map can be viewed as a function from K to V. This class represents [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:306: warning: invalid input: '<' [WARNING] * If none are found at n<=maxSymmetry, the alignment is reported as [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:317: warning: invalid input: '<' [WARNING] * @return The order of symmetry of alignment, or 1 if no order <= [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:474: warning: invalid input: '<' [WARNING] * List>> aln = getOptAlnAsList(AFPChain afpChain); [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:474: warning: invalid input: '<' [WARNING] * List>> aln = getOptAlnAsList(AFPChain afpChain); [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/util/AlignmentTools.IdentityMap.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:506: warning: invalid input: '<' [WARNING] * A Map can be viewed as a function from K to V. This class represents [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/pairwise/AligNPE.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/helper/AlignUtils.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/AligPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/AligPanelMouseMotionListener.html... 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[WARNING] * @param cutsPerSection the number of cuts added to each section during each pass [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:83: warning: @param argument "cutsPerSection" is not a parameter name. [WARNING] * @param cutsPerSection the number of cuts added to each section during each pass [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java:48: warning: @param argument "error" is not a parameter name. [WARNING] * @param error [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java:64: warning: @param argument "error" is not a parameter name. [WARNING] * @param error [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java:85: warning: @param argument "error" is not a parameter name. [WARNING] * @param error [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/utils/Annotatable.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotatable.java:78: warning: Tag @see: reference not found: org.biojavax.RichAnnotatable [WARNING] * @see org.biojavax.RichAnnotatable [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/utils/Annotation.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java:56: warning: Tag @see: reference not found: org.biojavax.RichAnnotation [WARNING] * @see org.biojavax.RichAnnotation [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/Annotation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/AnnotationParser.html... 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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/alignment/qblast/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/hmmer/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/analysis/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/phylogeny/data/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/tools/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/webservices/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/datastructures/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/development/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/distance/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/matrix/character/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/matrix/distance/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/parsimony/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/tools/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/etc/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/nexus/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/nhx/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/tol/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/util/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/writers/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa_compactor/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/factories/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/iterators/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/protein/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/rio/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sdi/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sequence/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/species/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/test/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/test/examples/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/tools/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/hmmer/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/seqdb/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/wabi/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/jcolorbrewer/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/jcolorbrewer/ui/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/deprecated-list.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/allclasses-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/index-all.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/help-doc.html... [WARNING] 100 warnings [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava 6.1.0: [INFO] [INFO] biojava ............................................ SUCCESS [ 27.469 s] [INFO] biojava-core ....................................... SUCCESS [ 25.595 s] [INFO] biojava-forester ................................... SUCCESS [ 26.667 s] [INFO] biojava-alignment .................................. SUCCESS [ 10.064 s] [INFO] biojava-structure .................................. SUCCESS [ 26.961 s] [INFO] biojava-jcolorbrewer ............................... SUCCESS [ 3.677 s] [INFO] biojava-structure-gui .............................. SUCCESS [ 8.501 s] [INFO] biojava-genome ..................................... SUCCESS [ 5.200 s] [INFO] biojava-modfinder .................................. SUCCESS [ 3.727 s] [INFO] biojava-ws ......................................... SUCCESS [ 3.052 s] [INFO] biojava-protein-disorder ........................... SUCCESS [ 2.998 s] [INFO] biojava-aa-prop .................................... SUCCESS [ 4.062 s] [INFO] biojava-survival ................................... SUCCESS [ 3.682 s] [INFO] biojava-ontology ................................... SUCCESS [ 3.269 s] [INFO] biojava-protein-comparison-tool .................... SUCCESS [ 1.729 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 02:38 min [INFO] Finished at: 2024-05-20T17:02:17+14:00 [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg' dh_auto_test /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/biojava6-live-6.1.0\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf -Dproperties.file.manual=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven.properties org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/biojava6-live-6.1.0\+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... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.biojava:biojava-structure-gui:jar:6.1.0 [WARNING] 'dependencies.dependency.systemPath' for net.sourceforge.jmol:jmol:jar should use a variable instead of a hard-coded path /usr/share/java/Jmol.jar @ line 48, column 16 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] biojava [pom] [INFO] biojava-core [jar] [INFO] biojava-forester [jar] [INFO] biojava-alignment [jar] [INFO] biojava-structure [jar] [INFO] biojava-jcolorbrewer [jar] [INFO] biojava-structure-gui [jar] [INFO] biojava-genome [jar] [INFO] biojava-modfinder [jar] [INFO] biojava-ws [jar] [INFO] biojava-protein-disorder [jar] [INFO] biojava-aa-prop [jar] [INFO] biojava-survival [jar] [INFO] biojava-ontology [jar] [INFO] biojava-protein-comparison-tool [jar] [INFO] [INFO] ------------------------< org.biojava:biojava >------------------------- [INFO] Building biojava 6.1.0 [1/15] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] ----------------------< org.biojava:biojava-core >---------------------- [INFO] Building biojava-core 6.1.0 [2/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-core --- [INFO] Copying 24 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-core --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-core --- [INFO] Copying 48 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-core --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-core --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Running org.biojava.nbio.core.TestAmbiguityCompoundSet SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.096 s - in org.biojava.nbio.core.TestAmbiguityCompoundSet [INFO] Running org.biojava.nbio.core.alignment.SimpleProfileTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.082 s - in org.biojava.nbio.core.alignment.SimpleProfileTest [INFO] Running org.biojava.nbio.core.alignment.SimpleSequencePairTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.biojava.nbio.core.alignment.SimpleSequencePairTest [INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.205 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest [INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.1 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest [INFO] Running org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.187 s - in org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest [INFO] Running org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.176 s - in org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest [INFO] Running org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 35, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.051 s - in org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest [INFO] Running org.biojava.nbio.core.fasta.TestFASTAReader SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 s - in org.biojava.nbio.core.fasta.TestFASTAReader [INFO] Running org.biojava.nbio.core.search.io.SearchIOTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.093 s - in org.biojava.nbio.core.search.io.SearchIOTest [INFO] Running org.biojava.nbio.core.search.io.HspTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. getAlignment hashCode equals [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s - in org.biojava.nbio.core.search.io.HspTest [INFO] Running org.biojava.nbio.core.search.io.blast.BlastTabularParserTest createObjects SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. getFileExtensions setFile [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.67 s - in org.biojava.nbio.core.search.io.blast.BlastTabularParserTest [INFO] Running org.biojava.nbio.core.search.io.blast.BlastXMLParserTest getFileExtensions SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. setFile [WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.028 s - in org.biojava.nbio.core.search.io.blast.BlastXMLParserTest [INFO] Running org.biojava.nbio.core.sequence.RNASequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.11 s - in org.biojava.nbio.core.sequence.RNASequenceTest [INFO] Running org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.216 s - in org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest [INFO] Running org.biojava.nbio.core.sequence.ExonSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.082 s - in org.biojava.nbio.core.sequence.ExonSequenceTest [INFO] Running org.biojava.nbio.core.sequence.JoiningSequenceReaderTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 s - in org.biojava.nbio.core.sequence.JoiningSequenceReaderTest [INFO] Running org.biojava.nbio.core.sequence.GeneSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.104 s - in org.biojava.nbio.core.sequence.GeneSequenceTest [INFO] Running org.biojava.nbio.core.sequence.ChromosomeSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.307 s - in org.biojava.nbio.core.sequence.ChromosomeSequenceTest [INFO] Running org.biojava.nbio.core.sequence.TestSequenceEquals SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 s - in org.biojava.nbio.core.sequence.TestSequenceEquals [INFO] Running org.biojava.nbio.core.sequence.TranslationTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.315 s - in org.biojava.nbio.core.sequence.TranslationTest [INFO] Running org.biojava.nbio.core.sequence.views.WindowViewTests SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 s - in org.biojava.nbio.core.sequence.views.WindowViewTests [INFO] Running org.biojava.nbio.core.sequence.DNATest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.094 s - in org.biojava.nbio.core.sequence.DNATest [INFO] Running org.biojava.nbio.core.sequence.ProteinSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 s - in org.biojava.nbio.core.sequence.ProteinSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Running org.biojava.nbio.core.sequence.location.TargetedLocationParserTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojava.nbio.core.sequence.location.TargetedLocationParserTest [INFO] Running org.biojava.nbio.core.sequence.location.LocationParserTest [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.011 s - in org.biojava.nbio.core.sequence.location.LocationParserTest [INFO] Running org.biojava.nbio.core.sequence.location.InsdcParserTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.184 s - in org.biojava.nbio.core.sequence.location.InsdcParserTest [INFO] Running org.biojava.nbio.core.sequence.location.LocationTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 s - in org.biojava.nbio.core.sequence.location.LocationTest [INFO] Running org.biojava.nbio.core.sequence.TranscriptSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.127 s - in org.biojava.nbio.core.sequence.TranscriptSequenceTest [INFO] Running org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 s - in org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest [INFO] Running org.biojava.nbio.core.sequence.EditSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 s - in org.biojava.nbio.core.sequence.EditSequenceTest [INFO] Running org.biojava.nbio.core.sequence.TaxonomyIDTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 s - in org.biojava.nbio.core.sequence.TaxonomyIDTest [INFO] Running org.biojava.nbio.core.sequence.StrandTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 s - in org.biojava.nbio.core.sequence.StrandTest [INFO] Running org.biojava.nbio.core.sequence.ExonComparatorTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 s - in org.biojava.nbio.core.sequence.ExonComparatorTest [INFO] Running org.biojava.nbio.core.sequence.SequenceViewTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 s - in org.biojava.nbio.core.sequence.SequenceViewTest [INFO] Running org.biojava.nbio.core.sequence.io.GenbankCookbookTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.216 s - in org.biojava.nbio.core.sequence.io.GenbankCookbookTest [INFO] Running org.biojava.nbio.core.sequence.io.GenbankReaderTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.357 s - in org.biojava.nbio.core.sequence.io.GenbankReaderTest [INFO] Running org.biojava.nbio.core.sequence.io.FastaWriterTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 s - in org.biojava.nbio.core.sequence.io.FastaWriterTest [INFO] Running org.biojava.nbio.core.sequence.io.GenbankWriterTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.126 s - in org.biojava.nbio.core.sequence.io.GenbankWriterTest [INFO] Running org.biojava.nbio.core.sequence.io.FastaReaderTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.09 s - in org.biojava.nbio.core.sequence.io.FastaReaderTest [INFO] Running org.biojava.nbio.core.sequence.io.embl.EmblReaderTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.108 s - in org.biojava.nbio.core.sequence.io.embl.EmblReaderTest [INFO] Running org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 s - in org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest [INFO] Running org.biojava.nbio.core.sequence.io.FastaGeneWriterTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 s - in org.biojava.nbio.core.sequence.io.FastaGeneWriterTest [INFO] Running org.biojava.nbio.core.sequence.io.ABITracerTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.451 s - in org.biojava.nbio.core.sequence.io.ABITracerTest [INFO] Running org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.078 s - in org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Running org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest [INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 s - in org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest [INFO] Running org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.242 s - in org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest [INFO] Running org.biojava.nbio.core.util.HashcoderTest [INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.131 s - in org.biojava.nbio.core.util.HashcoderTest [INFO] Running org.biojava.nbio.core.util.FlatFileCacheTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.109 s - in org.biojava.nbio.core.util.FlatFileCacheTest [INFO] Running org.biojava.nbio.core.util.EqualsTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 s - in org.biojava.nbio.core.util.EqualsTest [INFO] Running org.biojava.nbio.core.util.FileDownloadUtilsTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 18, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.321 s - in org.biojava.nbio.core.util.FileDownloadUtilsTest [INFO] Running org.biojava.nbio.core.util.SequenceToolsTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 21, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.312 s - in org.biojava.nbio.core.util.SequenceToolsTest [INFO] Running org.biojava.nbio.core.util.SingleLinkageClustererTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.106 s - in org.biojava.nbio.core.util.SingleLinkageClustererTest [INFO] Running org.biojava.nbio.core.util.XMLHelperTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.366 s - in org.biojava.nbio.core.util.XMLHelperTest [INFO] Running org.biojava.nbio.core.util.CRC64ChecksumTest [INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.131 s - in org.biojava.nbio.core.util.CRC64ChecksumTest [INFO] Running org.biojava.nbio.core.util.StringManipulationHelperTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.235 s - in org.biojava.nbio.core.util.StringManipulationHelperTest [INFO] Running org.biojava.nbio.core.util.SoftHashMapTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.108 s - in org.biojava.nbio.core.util.SoftHashMapTest [INFO] Running org.biojava.nbio.core.util.TestUncompressInputStream SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 s - in org.biojava.nbio.core.util.TestUncompressInputStream [INFO] Running org.biojava.nbio.core.util.PrettyXMLWriterTest 22 43.22 some text
2021-08-15
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.093 s - in org.biojava.nbio.core.util.PrettyXMLWriterTest [INFO] [INFO] Results: [INFO] [WARNING] Tests run: 501, Failures: 0, Errors: 0, Skipped: 15 [INFO] [INFO] [INFO] --------------------< org.biojava:biojava-forester >-------------------- [INFO] Building biojava-forester 6.1.0 [3/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-forester --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-forester --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-forester --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-forester --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-forester --- [INFO] No tests to run. [INFO] [INFO] -------------------< org.biojava:biojava-alignment >-------------------- [INFO] Building biojava-alignment 6.1.0 [4/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-alignment --- [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-alignment --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-alignment --- [INFO] Copying 11 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-alignment --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-alignment --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.phylo.TestForesterWrapper SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.112 s - in org.biojava.nbio.phylo.TestForesterWrapper [INFO] Running org.biojava.nbio.phylo.TestDistanceTreeEvaluator SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.155 s - in org.biojava.nbio.phylo.TestDistanceTreeEvaluator [INFO] Running org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.145 s - in org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest [INFO] Running org.biojava.nbio.alignment.LocalAlignmentTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.119 s - in org.biojava.nbio.alignment.LocalAlignmentTest [INFO] Running org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.152 s - in org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest [INFO] Running org.biojava.nbio.alignment.TestSubOptimalMSA SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.152 s - in org.biojava.nbio.alignment.TestSubOptimalMSA [INFO] Running org.biojava.nbio.alignment.SimpleGapPenaltyTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 s - in org.biojava.nbio.alignment.SimpleGapPenaltyTest [INFO] Running org.biojava.nbio.alignment.TestDNAAlignment SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.634 s - in org.biojava.nbio.alignment.TestDNAAlignment [INFO] Running org.biojava.nbio.alignment.NeedlemanWunschTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.244 s - in org.biojava.nbio.alignment.NeedlemanWunschTest [INFO] Running org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.411 s - in org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading [INFO] Running org.biojava.nbio.alignment.SimpleProfilePairTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.144 s - in org.biojava.nbio.alignment.SimpleProfilePairTest [INFO] Running org.biojava.nbio.alignment.FractionalIdentityScorerTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.13 s - in org.biojava.nbio.alignment.FractionalIdentityScorerTest [INFO] Running org.biojava.nbio.alignment.SmithWatermanTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.214 s - in org.biojava.nbio.alignment.SmithWatermanTest [INFO] Running org.biojava.nbio.alignment.GuideTreeTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.182 s - in org.biojava.nbio.alignment.GuideTreeTest [INFO] Running org.biojava.nbio.alignment.FractionalSimilarityScorerTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.251 s - in org.biojava.nbio.alignment.FractionalSimilarityScorerTest [INFO] Running org.biojava.nbio.alignment.routines.GuanUberbacherTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.147 s - in org.biojava.nbio.alignment.routines.GuanUberbacherTest [INFO] Running org.biojava.nbio.alignment.routines.AlignerHelperTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.12 s - in org.biojava.nbio.alignment.routines.AlignerHelperTest [INFO] Running org.biojava.nbio.alignment.io.TestStockholmParser SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.183 s - in org.biojava.nbio.alignment.io.TestStockholmParser [INFO] [INFO] Results: [INFO] [WARNING] Tests run: 127, Failures: 0, Errors: 0, Skipped: 1 [INFO] [INFO] [INFO] -------------------< org.biojava:biojava-structure >-------------------- [INFO] Building biojava-structure 6.1.0 [5/15] [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The artifact java3d:vecmath:jar:debian has been relocated to javax.vecmath:vecmath:jar:debian [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-structure --- [INFO] Copying 3 resources [INFO] Copying 61 resources [INFO] The encoding used to copy filtered properties files have not been set. This means that the same encoding will be used to copy filtered properties files as when copying other filtered resources. This might not be what you want! Run your build with --debug to see which files might be affected. Read more at https://maven.apache.org/plugins/maven-resources-plugin/examples/filtering-properties-files.html [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-structure --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-structure --- [INFO] Copying 55 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-structure --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-structure --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.structure.ResidueNumberTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.nbio.structure.ResidueNumberTest [INFO] Running org.biojava.nbio.structure.TestVeryLongFileName SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 s - in org.biojava.nbio.structure.TestVeryLongFileName [INFO] Running org.biojava.nbio.structure.TestAtomIterator [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.011 s - in org.biojava.nbio.structure.TestAtomIterator [INFO] Running org.biojava.nbio.structure.TestBioAssemblyIdentifier [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.01 s - in org.biojava.nbio.structure.TestBioAssemblyIdentifier [INFO] Running org.biojava.nbio.structure.geometry.TestSuperPosition SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.01 s - in org.biojava.nbio.structure.geometry.TestSuperPosition [INFO] Running org.biojava.nbio.structure.geometry.TestSuperPositionQCP SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.04 s - in org.biojava.nbio.structure.geometry.TestSuperPositionQCP [INFO] Running org.biojava.nbio.structure.geometry.TestUnitQuaternions [WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.021 s - in org.biojava.nbio.structure.geometry.TestUnitQuaternions [INFO] Running org.biojava.nbio.structure.redmine.Test1DARSeqAlign [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.01 s - in org.biojava.nbio.structure.redmine.Test1DARSeqAlign [INFO] Running org.biojava.nbio.structure.TestCalc SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.066 s - in org.biojava.nbio.structure.TestCalc [INFO] Running org.biojava.nbio.structure.Test2JA5 [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.01 s - in org.biojava.nbio.structure.Test2JA5 [INFO] Running org.biojava.nbio.structure.TestLoadStructureFromURL [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.011 s - in org.biojava.nbio.structure.TestLoadStructureFromURL [INFO] Running org.biojava.nbio.structure.TestPdbId [1ABC, PDB_00011ABC, 2ABC, 1ABA, 1100] [1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC] [1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC] [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.09 s - in org.biojava.nbio.structure.TestPdbId [INFO] Running org.biojava.nbio.structure.TestStructureSerialization SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.348 s - in org.biojava.nbio.structure.TestStructureSerialization [INFO] Running org.biojava.nbio.structure.TestURLIdentifier SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.264 s - in org.biojava.nbio.structure.TestURLIdentifier [INFO] Running org.biojava.nbio.structure.ChemCompTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.286 s - in org.biojava.nbio.structure.ChemCompTest [INFO] Running org.biojava.nbio.structure.TestChargeAdder [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.011 s - in org.biojava.nbio.structure.TestChargeAdder [INFO] Running org.biojava.nbio.structure.asa.TestAsaCalc SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.04 s - in org.biojava.nbio.structure.asa.TestAsaCalc [INFO] Running org.biojava.nbio.structure.TestNucleotides [WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.011 s - in org.biojava.nbio.structure.TestNucleotides [INFO] Running org.biojava.nbio.structure.PdbFileFormat30Test SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.098 s - in org.biojava.nbio.structure.PdbFileFormat30Test [INFO] Running org.biojava.nbio.structure.TestAtomCache SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.47 s - in org.biojava.nbio.structure.TestAtomCache [INFO] Running org.biojava.nbio.structure.TestEntityHeuristics SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.759 s - in org.biojava.nbio.structure.TestEntityHeuristics [INFO] Running org.biojava.nbio.structure.contact.TestInterfaceFinder SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. Interface - 4.0 Interface - 5.477225575051661 Interface - 5.477225575051661 [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.133 s - in org.biojava.nbio.structure.contact.TestInterfaceFinder [INFO] Running org.biojava.nbio.structure.contact.TestContactCalc [WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.014 s - in org.biojava.nbio.structure.contact.TestContactCalc [INFO] Running org.biojava.nbio.structure.PDBStatusTest [WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.011 s - in org.biojava.nbio.structure.PDBStatusTest [INFO] Running org.biojava.nbio.structure.Test4hhb SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.336 s - in org.biojava.nbio.structure.Test4hhb [INFO] Running org.biojava.nbio.structure.AtomPositionMapTest [WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.012 s - in org.biojava.nbio.structure.AtomPositionMapTest [INFO] Running org.biojava.nbio.structure.TestParsingCalcium [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.01 s - in org.biojava.nbio.structure.TestParsingCalcium [INFO] Running org.biojava.nbio.structure.basepairs.TestBasePairParameters [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.01 s - in org.biojava.nbio.structure.basepairs.TestBasePairParameters [INFO] Running org.biojava.nbio.structure.HetatomImplTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.065 s - in org.biojava.nbio.structure.HetatomImplTest [INFO] Running org.biojava.nbio.structure.SourceCompoundTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.474 s - in org.biojava.nbio.structure.SourceCompoundTest [INFO] Running org.biojava.nbio.structure.ElementTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojava.nbio.structure.ElementTest [INFO] Running org.biojava.nbio.structure.TestStructureImpl SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 s - in org.biojava.nbio.structure.TestStructureImpl [INFO] Running org.biojava.nbio.structure.TestExperimentalTechniques [WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.01 s - in org.biojava.nbio.structure.TestExperimentalTechniques [INFO] Running org.biojava.nbio.structure.align.ce.CeCPMainTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.059 s - in org.biojava.nbio.structure.align.ce.CeCPMainTest [INFO] Running org.biojava.nbio.structure.align.ce.TestSmallAlignment [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.011 s - in org.biojava.nbio.structure.align.ce.TestSmallAlignment [INFO] Running org.biojava.nbio.structure.align.client.TestStructureName SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.042 s - in org.biojava.nbio.structure.align.client.TestStructureName [INFO] Running org.biojava.nbio.structure.align.util.AtomCacheTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 10, Failures: 0, Errors: 0, Skipped: 8, Time elapsed: 0.068 s - in org.biojava.nbio.structure.align.util.AtomCacheTest [INFO] Running org.biojava.nbio.structure.align.util.RotationAxisTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 s - in org.biojava.nbio.structure.align.util.RotationAxisTest [INFO] Running org.biojava.nbio.structure.align.TestAlignmentConsistency [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.012 s - in org.biojava.nbio.structure.align.TestAlignmentConsistency [INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.009 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser [INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools [INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter [WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.01 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter [INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer [INFO] Running org.biojava.nbio.structure.align.multiple.TestAFPChainConversion SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 s - in org.biojava.nbio.structure.align.multiple.TestAFPChainConversion [INFO] Running org.biojava.nbio.structure.SiteTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 s - in org.biojava.nbio.structure.SiteTest [INFO] Running org.biojava.nbio.structure.xtal.TestCrystalCell [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 s - in org.biojava.nbio.structure.xtal.TestCrystalCell [INFO] Running org.biojava.nbio.structure.xtal.TestInterfaceClustering SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 2.714 s - in org.biojava.nbio.structure.xtal.TestInterfaceClustering [INFO] Running org.biojava.nbio.structure.xtal.TestCrystalInfo [WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.009 s - in org.biojava.nbio.structure.xtal.TestCrystalInfo [INFO] Running org.biojava.nbio.structure.xtal.TestSpaceGroup SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.496 s - in org.biojava.nbio.structure.xtal.TestSpaceGroup [INFO] Running org.biojava.nbio.structure.TestDNAAlignment [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.01 s - in org.biojava.nbio.structure.TestDNAAlignment [INFO] Running org.biojava.nbio.structure.TestEntityResIndexMapping SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.468 s - in org.biojava.nbio.structure.TestEntityResIndexMapping [INFO] Running org.biojava.nbio.structure.chem.TestDownloadChemCompProvider SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.27 s - in org.biojava.nbio.structure.chem.TestDownloadChemCompProvider [INFO] Running org.biojava.nbio.structure.TestAltLocs SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 11, Time elapsed: 1.04 s - in org.biojava.nbio.structure.TestAltLocs [INFO] Running org.biojava.nbio.structure.ResidueRangeTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.172 s - in org.biojava.nbio.structure.ResidueRangeTest [INFO] Running org.biojava.nbio.structure.TestKeywords SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.099 s - in org.biojava.nbio.structure.TestKeywords [INFO] Running org.biojava.nbio.structure.cluster.TestSubunitCluster SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.236 s - in org.biojava.nbio.structure.cluster.TestSubunitCluster [INFO] Running org.biojava.nbio.structure.cluster.TestSubunitExtractor [WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.028 s - in org.biojava.nbio.structure.cluster.TestSubunitExtractor [INFO] Running org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 s - in org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools [INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.061 s - in org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes [INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner [INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.036 s - in org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector [INFO] Running org.biojava.nbio.structure.symmetry.internal.TestCeSymm [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.016 s - in org.biojava.nbio.structure.symmetry.internal.TestCeSymm [INFO] Running org.biojava.nbio.structure.TestStructureCrossReferences [WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.016 s - in org.biojava.nbio.structure.TestStructureCrossReferences [INFO] Running org.biojava.nbio.structure.TestCloning [WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.012 s - in org.biojava.nbio.structure.TestCloning [INFO] Running org.biojava.nbio.structure.TestBond [WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 15, Time elapsed: 0.012 s - in org.biojava.nbio.structure.TestBond [INFO] Running org.biojava.nbio.structure.io.TestDBRefParsing SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 s - in org.biojava.nbio.structure.io.TestDBRefParsing [INFO] Running org.biojava.nbio.structure.io.TestTitleParsing [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.011 s - in org.biojava.nbio.structure.io.TestTitleParsing [INFO] Running org.biojava.nbio.structure.io.TestSiftsParsing [WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.015 s - in org.biojava.nbio.structure.io.TestSiftsParsing [INFO] Running org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.201 s - in org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest [INFO] Running org.biojava.nbio.structure.io.StructureSequenceMatcherTest [WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.032 s - in org.biojava.nbio.structure.io.StructureSequenceMatcherTest [INFO] Running org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.024 s - in org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB [INFO] Running org.biojava.nbio.structure.io.TestParseOnAsymId [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.033 s - in org.biojava.nbio.structure.io.TestParseOnAsymId [INFO] Running org.biojava.nbio.structure.io.TestShortLines SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.291 s - in org.biojava.nbio.structure.io.TestShortLines [INFO] Running org.biojava.nbio.structure.io.FastaAFPChainConverterTest [WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.012 s - in org.biojava.nbio.structure.io.FastaAFPChainConverterTest [INFO] Running org.biojava.nbio.structure.io.TestNonDepositedFiles SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 3.452 s - in org.biojava.nbio.structure.io.TestNonDepositedFiles [INFO] Running org.biojava.nbio.structure.io.TestMMCIFWriting SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.252 s - in org.biojava.nbio.structure.io.TestMMCIFWriting [INFO] Running org.biojava.nbio.structure.io.TestHardBioUnits [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.036 s - in org.biojava.nbio.structure.io.TestHardBioUnits [INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFLigands [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.024 s - in org.biojava.nbio.structure.io.TestParseMmCIFLigands [INFO] Running org.biojava.nbio.structure.io.TestQuaternaryStructureProviders [WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.016 s - in org.biojava.nbio.structure.io.TestQuaternaryStructureProviders [INFO] Running org.biojava.nbio.structure.io.TestMMcifOrganismParsing [WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.029 s - in org.biojava.nbio.structure.io.TestMMcifOrganismParsing [INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFFeatures [WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.032 s - in org.biojava.nbio.structure.io.TestParseMmCIFFeatures [INFO] Running org.biojava.nbio.structure.io.TestURLBasedFileParsing [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.014 s - in org.biojava.nbio.structure.io.TestURLBasedFileParsing [INFO] Running org.biojava.nbio.structure.io.TestDifficultMmCIFFiles SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 1.262 s - in org.biojava.nbio.structure.io.TestDifficultMmCIFFiles [INFO] Running org.biojava.nbio.structure.io.TestHeaderOnly SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 1.073 s - in org.biojava.nbio.structure.io.TestHeaderOnly [INFO] Running org.biojava.nbio.structure.io.mmcif.TestChemCompProvider SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. Using PDB_DIR=/tmp as temporary file directory [WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.44 s - in org.biojava.nbio.structure.io.mmcif.TestChemCompProvider [INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.009 s - in org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId [INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.001 s - in org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader [INFO] Running org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.009 s - in org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType [INFO] Running org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.928 s - in org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes [INFO] Running org.biojava.nbio.structure.io.mmtf.TestBondFinding [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.009 s - in org.biojava.nbio.structure.io.mmtf.TestBondFinding [INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.342 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader [INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfUtils SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 16, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.095 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfUtils [INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.012 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip [INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.017 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance [INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.156 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter [INFO] Running org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.078 s - in org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest [INFO] Running org.biojava.nbio.structure.secstruc.TestDSSPParser [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.01 s - in org.biojava.nbio.structure.secstruc.TestDSSPParser [INFO] Running org.biojava.nbio.structure.secstruc.TestSecStrucCalc [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.01 s - in org.biojava.nbio.structure.secstruc.TestSecStrucCalc [INFO] [INFO] Results: [INFO] [WARNING] Tests run: 374, Failures: 0, Errors: 0, Skipped: 188 [INFO] [INFO] [INFO] ------------------< org.biojava:biojava-jcolorbrewer >------------------ [INFO] Building biojava-jcolorbrewer 6.1.0 [6/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-jcolorbrewer --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-jcolorbrewer --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-jcolorbrewer --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-jcolorbrewer --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-jcolorbrewer --- [INFO] No tests to run. [INFO] [INFO] -----------------< org.biojava:biojava-structure-gui >------------------ [INFO] Building biojava-structure-gui 6.1.0 [7/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-structure-gui --- [INFO] Copying 49 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-structure-gui --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-structure-gui --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-structure-gui --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-structure-gui --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.structure.gui.ViewerTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 s - in org.biojava.nbio.structure.gui.ViewerTest [INFO] Running org.biojava.nbio.structure.gui.TestAtomInfo SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.093 s - in org.biojava.nbio.structure.gui.TestAtomInfo [INFO] Running org.biojava.nbio.structure.gui.RenderStyleTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 s - in org.biojava.nbio.structure.gui.RenderStyleTest [INFO] Running org.biojava.nbio.structure.gui.StructureViewerTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 s - in org.biojava.nbio.structure.gui.StructureViewerTest [INFO] Running org.biojava.nbio.structure.gui.JmolViewerImplTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.114 s - in org.biojava.nbio.structure.gui.JmolViewerImplTest [INFO] Running org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.078 s - in org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator [INFO] [INFO] Results: [INFO] [WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 1 [INFO] [INFO] [INFO] ---------------------< org.biojava:biojava-genome >--------------------- [INFO] Building biojava-genome 6.1.0 [8/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-genome --- [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-genome --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-genome --- [INFO] Copying 83 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-genome --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-genome --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.genome.TestIssue355 [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 s - in org.biojava.nbio.genome.TestIssue355 [INFO] Running org.biojava.nbio.genome.TestGenomeMapping [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.069 s - in org.biojava.nbio.genome.TestGenomeMapping [INFO] Running org.biojava.nbio.genome.TestLocation [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 s - in org.biojava.nbio.genome.TestLocation [INFO] Running org.biojava.nbio.genome.TestChromosomeMappingTools SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.096 s - in org.biojava.nbio.genome.TestChromosomeMappingTools [INFO] Running org.biojava.nbio.genome.GeneFeatureHelperTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.482 s - in org.biojava.nbio.genome.GeneFeatureHelperTest [INFO] Running org.biojava.nbio.genome.FeatureListTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 s - in org.biojava.nbio.genome.FeatureListTest [INFO] Running org.biojava.nbio.genome.io.fastq.ConvertTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.23 s - in org.biojava.nbio.genome.io.fastq.ConvertTest [INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest [INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.171 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest [INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest [INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.166 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest [INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.151 s - in org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest [INFO] Running org.biojava.nbio.genome.io.fastq.FastqVariantTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.082 s - in org.biojava.nbio.genome.io.fastq.FastqVariantTest [INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.107 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest [INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.105 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest [INFO] Running org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 s - in org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest [INFO] Running org.biojava.nbio.genome.io.fastq.FastqToolsTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.129 s - in org.biojava.nbio.genome.io.fastq.FastqToolsTest [INFO] Running org.biojava.nbio.genome.io.fastq.FastqBuilderTest [INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.112 s - in org.biojava.nbio.genome.io.fastq.FastqBuilderTest [INFO] Running org.biojava.nbio.genome.io.fastq.FastqTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 s - in org.biojava.nbio.genome.io.fastq.FastqTest [INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest [INFO] Tests run: 29, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.171 s - in org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest [INFO] [INFO] Results: [INFO] [WARNING] Tests run: 204, Failures: 0, Errors: 0, Skipped: 2 [INFO] [INFO] [INFO] -------------------< org.biojava:biojava-modfinder >-------------------- [INFO] Building biojava-modfinder 6.1.0 [9/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-modfinder --- [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-modfinder --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-modfinder --- [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-modfinder --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-modfinder --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.281 s - in org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest [INFO] Running org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.38 s - in org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest [INFO] Running org.biojava.nbio.protmod.structure.ProteinModificationParserTest [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.076 s - in org.biojava.nbio.protmod.structure.ProteinModificationParserTest [INFO] Running org.biojava.nbio.protmod.phosphosite.TestAcetylation [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.071 s - in org.biojava.nbio.protmod.phosphosite.TestAcetylation [INFO] [INFO] Results: [INFO] [WARNING] Tests run: 12, Failures: 0, Errors: 0, Skipped: 8 [INFO] [INFO] [INFO] -----------------------< org.biojava:biojava-ws >----------------------- [INFO] Building biojava-ws 6.1.0 [10/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-ws --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-ws --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-ws --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-ws --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-ws --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.124 s - in org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan [INFO] [INFO] Results: [INFO] [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1 [INFO] [INFO] [INFO] ----------------< org.biojava:biojava-protein-disorder >---------------- [INFO] Building biojava-protein-disorder 6.1.0 [11/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-protein-disorder --- [INFO] Copying 11 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-protein-disorder --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-protein-disorder --- [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-protein-disorder --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-protein-disorder --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.ronn.NonstandardProteinCompoundTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.082 s - in org.biojava.nbio.ronn.NonstandardProteinCompoundTest [INFO] Running org.biojava.nbio.ronn.JronnTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.901 s - in org.biojava.nbio.ronn.JronnTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] --------------------< org.biojava:biojava-aa-prop >--------------------- [INFO] Building biojava-aa-prop 6.1.0 [12/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-aa-prop --- [INFO] Copying 11 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-aa-prop --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-aa-prop --- [INFO] Copying 7 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-aa-prop --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-aa-prop --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.aaproperties.CookBookTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.612 s - in org.biojava.nbio.aaproperties.CookBookTest [INFO] Running org.biojava.nbio.aaproperties.PeptidePropertiesImplTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.945 s - in org.biojava.nbio.aaproperties.PeptidePropertiesImplTest [INFO] Running org.biojava.nbio.aaproperties.GenbankCommandPromptTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint NP_000257 133 aa linear PRI 27-MAR-2008,15043.5262,5960.0,6585.0,9.1715 SequenceName,A,N,MolecularWeight NP_000257 133 aa linear PRI 27-MAR-2008,0.0451,0.0075,15043.5262 SequenceName,A,N,MolecularWeight NP_000257 133 aa linear PRI 27-MAR-2008,0.0451,0.0075,15043.5262 [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.477 s - in org.biojava.nbio.aaproperties.GenbankCommandPromptTest [INFO] Running org.biojava.nbio.aaproperties.profeat.CookBookTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 s - in org.biojava.nbio.aaproperties.profeat.CookBookTest [INFO] Running org.biojava.nbio.aaproperties.CommandPromptTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint SAOV_0114,53660.5723,41370.0,41370.0,4.986 SAOV_0094,45884.0164,57760.0,57760.0,8.5193 SAA6008_00126,95002.026,55240.0,55740.0,5.7263 SequenceName,A,N,MolecularWeight SAOV_0114,0.101,0.0525,53660.5723 SAOV_0094,0.0537,0.0767,45884.0164 SAA6008_00126,0.0955,0.0414,95002.026 SequenceName,A,N,MolecularWeight SAOV_0114,0.101,0.0525,53660.5723 SAOV_0094,0.0537,0.0767,45884.0164 SAA6008_00126,0.0955,0.0414,95002.026 [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.555 s - in org.biojava.nbio.aaproperties.CommandPromptTest [INFO] Running org.biojava.nbio.aaproperties.xml.AminoAcidTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.592 s - in org.biojava.nbio.aaproperties.xml.AminoAcidTest [INFO] Running org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.105 s - in org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest [INFO] Running org.biojava.nbio.aaproperties.xml.ElementTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.468 s - in org.biojava.nbio.aaproperties.xml.ElementTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 52, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] --------------------< org.biojava:biojava-survival >-------------------- [INFO] Building biojava-survival 6.1.0 [13/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-survival --- [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-survival --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-survival --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-survival --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-survival --- [INFO] No tests to run. [INFO] [INFO] --------------------< org.biojava:biojava-ontology >-------------------- [INFO] Building biojava-ontology 6.1.0 [14/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-ontology --- [INFO] Copying 3 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-ontology --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-ontology --- [INFO] Copying 6 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-ontology --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-ontology --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.ontology.TestParseOBO SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.131 s - in org.biojava.nbio.ontology.TestParseOBO [INFO] Running org.biojava.nbio.ontology.TestOboFileParsing SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.236 s - in org.biojava.nbio.ontology.TestOboFileParsing [INFO] Running org.biojava.nbio.ontology.TestParseSBO SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.165 s - in org.biojava.nbio.ontology.TestParseSBO [INFO] [INFO] Results: [INFO] [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] ------------< org.biojava:biojava-protein-comparison-tool >------------- [INFO] Building biojava-protein-comparison-tool 6.1.0 [15/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-protein-comparison-tool --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-protein-comparison-tool --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-protein-comparison-tool --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-protein-comparison-tool --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-protein-comparison-tool --- [INFO] No tests to run. [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava 6.1.0: [INFO] [INFO] biojava ............................................ SUCCESS [ 0.006 s] [INFO] biojava-core ....................................... SUCCESS [09:50 min] [INFO] biojava-forester ................................... SUCCESS [ 0.084 s] [INFO] biojava-alignment .................................. SUCCESS [03:00 min] [INFO] biojava-structure .................................. SUCCESS [16:20 min] [INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.025 s] [INFO] biojava-structure-gui .............................. SUCCESS [01:00 min] [INFO] biojava-genome ..................................... SUCCESS [03:00 min] [INFO] biojava-modfinder .................................. SUCCESS [ 40.091 s] [INFO] biojava-ws ......................................... SUCCESS [ 10.052 s] [INFO] biojava-protein-disorder ........................... SUCCESS [ 20.054 s] [INFO] biojava-aa-prop .................................... SUCCESS [01:20 min] [INFO] biojava-survival ................................... SUCCESS [ 0.025 s] [INFO] biojava-ontology ................................... SUCCESS [ 30.040 s] [INFO] biojava-protein-comparison-tool .................... SUCCESS [ 0.071 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 36:12 min [INFO] Finished at: 2024-05-20T17:38:31+14:00 [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/reproducible-path/biojava6-live-6.1.0\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf -Dproperties.file.manual=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven.properties org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven-repo --batch-mode -Ddebian.dir=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian -Ddebian.package=libbiojava6-java -Dmaven.repo.local=/build/reproducible-path/biojava6-live-6.1.0\+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... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.biojava:biojava-structure-gui:jar:6.1.0 [WARNING] 'dependencies.dependency.systemPath' for net.sourceforge.jmol:jmol:jar should use a variable instead of a hard-coded path /usr/share/java/Jmol.jar @ line 48, column 16 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] biojava [pom] [INFO] biojava-core [jar] [INFO] biojava-forester [jar] [INFO] biojava-alignment [jar] [INFO] biojava-structure [jar] [INFO] biojava-jcolorbrewer [jar] [INFO] biojava-structure-gui [jar] [INFO] biojava-genome [jar] [INFO] biojava-modfinder [jar] [INFO] biojava-ws [jar] [INFO] biojava-protein-disorder [jar] [INFO] biojava-aa-prop [jar] [INFO] biojava-survival [jar] [INFO] biojava-ontology [jar] [INFO] biojava-protein-comparison-tool [jar] [INFO] [INFO] ------------------------< org.biojava:biojava >------------------------- [INFO] Building biojava 6.1.0 [1/15] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] --no-parent [INFO] [INFO] ----------------------< org.biojava:biojava-core >---------------------- [INFO] Building biojava-core 6.1.0 [2/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-core --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-core into /usr/share/java [INFO] [INFO] --------------------< org.biojava:biojava-forester >-------------------- [INFO] Building biojava-forester 6.1.0 [3/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-forester --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-forester into /usr/share/java [INFO] [INFO] -------------------< org.biojava:biojava-alignment >-------------------- [INFO] Building biojava-alignment 6.1.0 [4/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-alignment --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-alignment into /usr/share/java [INFO] [INFO] -------------------< org.biojava:biojava-structure >-------------------- [INFO] Building biojava-structure 6.1.0 [5/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-structure --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-structure into /usr/share/java [INFO] [INFO] ------------------< org.biojava:biojava-jcolorbrewer >------------------ [INFO] Building biojava-jcolorbrewer 6.1.0 [6/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-jcolorbrewer --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-jcolorbrewer into /usr/share/java [INFO] [INFO] -----------------< org.biojava:biojava-structure-gui >------------------ [INFO] Building biojava-structure-gui 6.1.0 [7/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-structure-gui --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-structure-gui into /usr/share/java [INFO] [INFO] ---------------------< org.biojava:biojava-genome >--------------------- [INFO] Building biojava-genome 6.1.0 [8/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-genome --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-genome into /usr/share/java [INFO] [INFO] -------------------< org.biojava:biojava-modfinder >-------------------- [INFO] Building biojava-modfinder 6.1.0 [9/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-modfinder --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-modfinder into /usr/share/java [INFO] [INFO] -----------------------< org.biojava:biojava-ws >----------------------- [INFO] Building biojava-ws 6.1.0 [10/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-ws --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-ws into /usr/share/java [INFO] [INFO] ----------------< org.biojava:biojava-protein-disorder >---------------- [INFO] Building biojava-protein-disorder 6.1.0 [11/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-protein-disorder --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-protein-disorder into /usr/share/java [INFO] [INFO] --------------------< org.biojava:biojava-aa-prop >--------------------- [INFO] Building biojava-aa-prop 6.1.0 [12/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-aa-prop --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-aa-prop into /usr/share/java [INFO] [INFO] --------------------< org.biojava:biojava-survival >-------------------- [INFO] Building biojava-survival 6.1.0 [13/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-survival --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-survival into /usr/share/java [INFO] [INFO] --------------------< org.biojava:biojava-ontology >-------------------- [INFO] Building biojava-ontology 6.1.0 [14/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-ontology --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-ontology into /usr/share/java [INFO] [INFO] ------------< org.biojava:biojava-protein-comparison-tool >------------- [INFO] Building biojava-protein-comparison-tool 6.1.0 [15/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-protein-comparison-tool --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-protein-comparison-tool into /usr/share/java [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava 6.1.0: [INFO] [INFO] biojava ............................................ SUCCESS [ 0.581 s] [INFO] biojava-core ....................................... SUCCESS [ 0.086 s] [INFO] biojava-forester ................................... SUCCESS [ 0.048 s] [INFO] biojava-alignment .................................. SUCCESS [ 0.051 s] [INFO] biojava-structure .................................. SUCCESS [ 0.051 s] [INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.038 s] [INFO] biojava-structure-gui .............................. SUCCESS [ 0.046 s] [INFO] biojava-genome ..................................... SUCCESS [ 0.054 s] [INFO] biojava-modfinder .................................. SUCCESS [ 0.045 s] [INFO] biojava-ws ......................................... SUCCESS [ 0.043 s] [INFO] biojava-protein-disorder ........................... SUCCESS [ 0.039 s] [INFO] biojava-aa-prop .................................... SUCCESS [ 0.040 s] [INFO] biojava-survival ................................... SUCCESS [ 0.043 s] [INFO] biojava-ontology ................................... SUCCESS [ 0.043 s] [INFO] biojava-protein-comparison-tool .................... SUCCESS [ 0.049 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 1.467 s [INFO] Finished at: 2024-05-20T17:38:34+14:00 [INFO] ------------------------------------------------------------------------ mh_resolve_dependencies --non-interactive --offline --build -plibbiojava6-java --javadoc --base-directory=/build/reproducible-path/biojava6-live-6.1.0\+dfsg --non-explore Analysing pom.xml... Analysing biojava-aa-prop/pom.xml... Checking the parent dependency in the sub project biojava-aa-prop/pom.xml Analysing biojava-alignment/pom.xml... Checking the parent dependency in the sub project biojava-alignment/pom.xml Analysing biojava-core/pom.xml... Checking the parent dependency in the sub project biojava-core/pom.xml Analysing biojava-forester/pom.xml... Checking the parent dependency in the sub project biojava-forester/pom.xml Analysing biojava-genome/pom.xml... Checking the parent dependency in the sub project biojava-genome/pom.xml Analysing biojava-jcolorbrewer/pom.xml... Checking the parent dependency in the sub project biojava-jcolorbrewer/pom.xml Analysing biojava-modfinder/pom.xml... Checking the parent dependency in the sub project biojava-modfinder/pom.xml Analysing biojava-ontology/pom.xml... Checking the parent dependency in the sub project biojava-ontology/pom.xml Analysing biojava-protein-comparison-tool/pom.xml... Checking the parent dependency in the sub project biojava-protein-comparison-tool/pom.xml Analysing biojava-protein-disorder/pom.xml... Checking the parent dependency in the sub project biojava-protein-disorder/pom.xml Analysing biojava-structure/pom.xml... Checking the parent dependency in the sub project biojava-structure/pom.xml Analysing biojava-structure-gui/pom.xml... Checking the parent dependency in the sub project biojava-structure-gui/pom.xml Analysing biojava-survival/pom.xml... Checking the parent dependency in the sub project biojava-survival/pom.xml Analysing biojava-ws/pom.xml... Checking the parent dependency in the sub project biojava-ws/pom.xml Checking dependencies for documentation packages... > dpkg --search /usr/share/doc/libciftools-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libciftools-java/api/index.html > dpkg --search /usr/share/doc/libciftools-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libciftools-java-doc/api/index.html > dpkg --search /usr/share/doc/libciftools-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libciftools-java/apidocs/index.html > dpkg --search /usr/share/doc/libciftools-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libciftools-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libcommons-codec-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-codec-java/api/index.html > dpkg --search /usr/share/doc/libcommons-codec-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-codec-java-doc/api/index.html > dpkg --search /usr/share/doc/libcommons-codec-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-codec-java/apidocs/index.html > dpkg --search /usr/share/doc/libcommons-codec-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-codec-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libcommons-math-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-math-java/api/index.html > dpkg --search /usr/share/doc/libcommons-math-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-math-java-doc/api/index.html > dpkg --search /usr/share/doc/libcommons-math-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-math-java/apidocs/index.html > dpkg --search /usr/share/doc/libcommons-math-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-math-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/libitext5-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libitext5-java/api/index.html > dpkg --search /usr/share/doc/libitext5-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libitext5-java-doc/api/index.html > dpkg --search /usr/share/doc/libitext5-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libitext5-java/apidocs/index.html > dpkg --search /usr/share/doc/libitext5-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libitext5-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libjackson2-databind-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjackson2-databind-java/api/index.html > dpkg --search /usr/share/doc/libjackson2-databind-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjackson2-databind-java-doc/api/index.html > dpkg --search /usr/share/doc/libjackson2-databind-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjackson2-databind-java/apidocs/index.html > dpkg --search /usr/share/doc/libjackson2-databind-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjackson2-databind-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libjaxb-api-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-api-java/api/index.html > dpkg --search /usr/share/doc/libjaxb-api-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-api-java-doc/api/index.html > dpkg --search /usr/share/doc/libjaxb-api-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-api-java/apidocs/index.html > dpkg --search /usr/share/doc/libjaxb-api-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-api-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libjaxb-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-java/api/index.html > dpkg --search /usr/share/doc/libjaxb-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-java-doc/api/index.html > dpkg --search /usr/share/doc/libjaxb-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-java/apidocs/index.html > dpkg --search /usr/share/doc/libjaxb-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libjgrapht-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjgrapht-java/api/index.html > dpkg --search /usr/share/doc/libjgrapht-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjgrapht-java-doc/api/index.html > dpkg --search /usr/share/doc/libjgrapht-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjgrapht-java/apidocs/index.html > dpkg --search /usr/share/doc/libjgrapht-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjgrapht-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libjmol-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjmol-java/api/index.html > dpkg --search /usr/share/doc/libjmol-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjmol-java-doc/api/index.html > dpkg --search /usr/share/doc/libjmol-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjmol-java/apidocs/index.html > dpkg --search /usr/share/doc/libjmol-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjmol-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libjson-simple-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjson-simple-java/api/index.html > dpkg --search /usr/share/doc/libjson-simple-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjson-simple-java-doc/api/index.html > dpkg --search /usr/share/doc/libjson-simple-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjson-simple-java/apidocs/index.html > dpkg --search /usr/share/doc/libjson-simple-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjson-simple-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libmmtf-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libmmtf-java/api/index.html > dpkg --search /usr/share/doc/libmmtf-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libmmtf-java-doc/api/index.html > dpkg --search /usr/share/doc/libmmtf-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libmmtf-java/apidocs/index.html > dpkg --search /usr/share/doc/libmmtf-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libmmtf-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libslf4j-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libslf4j-java/api/index.html > dpkg --search /usr/share/doc/libslf4j-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libslf4j-java-doc/api/index.html > dpkg --search /usr/share/doc/libslf4j-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libslf4j-java/apidocs/index.html > dpkg --search /usr/share/doc/libslf4j-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libslf4j-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libvecmath-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libvecmath-java/api/index.html > dpkg --search /usr/share/doc/libvecmath-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libvecmath-java-doc/api/index.html > dpkg --search /usr/share/doc/libvecmath-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libvecmath-java/apidocs/index.html > dpkg --search /usr/share/doc/libvecmath-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libvecmath-java-doc/apidocs/index.html bash -c "rm -f target/apidocs/*.sh target/apidocs/options" mh_unpatchpoms -plibbiojava6-java dh_install jh_installjavadoc debian/rules override_dh_installdocs make[1]: Entering directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg' dpkg: warning: --compare-versions used with obsolete relation operator '>' dh_installdocs # Deleting calls to urchinTracker to enhance privacy. for F in $(find . -name "*.html"); do \ sed -i 's/^$//' $F; \ done make[1]: Leaving directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg' dh_installchangelogs dh_lintian dh_perl dh_link jh_installlibs jh_classpath jh_manifest jh_depends dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package libbiojava6-java: substitution variable ${maven:CompileDepends} unused, but is defined dpkg-gencontrol: warning: package libbiojava6-java: substitution variable ${maven:Depends} unused, but is defined dpkg-gencontrol: warning: package libbiojava6-java: substitution variable ${maven:DocDepends} unused, but is defined dpkg-gencontrol: warning: package libbiojava6-java-doc: substitution variable ${maven:CompileDepends} unused, but is defined dpkg-gencontrol: warning: package libbiojava6-java-doc: substitution variable ${maven:Depends} unused, but is defined dpkg-gencontrol: warning: package libbiojava6-java-doc: substitution variable ${maven:DocDepends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'libbiojava6-java' in '../libbiojava6-java_6.1.0+dfsg-4_all.deb'. dpkg-deb: building package 'libbiojava6-java-doc' in '../libbiojava6-java-doc_6.1.0+dfsg-4_all.deb'. dpkg-genbuildinfo --build=binary -O../biojava6-live_6.1.0+dfsg-4_arm64.buildinfo dpkg-genchanges --build=binary -O../biojava6-live_6.1.0+dfsg-4_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3566877/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3566877/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3566877 and its subdirectories I: Current time: Mon May 20 17:44:24 +14 2024 I: pbuilder-time-stamp: 1716176664