Thu Mar 28 04:23:01 UTC 2024 I: starting to build biojava6-live/trixie/armhf on jenkins on '2024-03-28 04:22' Thu Mar 28 04:23:01 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_10/1113/console.log Thu Mar 28 04:23:01 UTC 2024 I: Downloading source for trixie/biojava6-live=6.1.0+dfsg-4 --2024-03-28 04:23:01-- http://deb.debian.org/debian/pool/main/b/biojava6-live/biojava6-live_6.1.0%2bdfsg-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 3360 (3.3K) [text/prs.lines.tag] Saving to: ‘biojava6-live_6.1.0+dfsg-4.dsc’ 0K ... 100% 404M=0s 2024-03-28 04:23:01 (404 MB/s) - ‘biojava6-live_6.1.0+dfsg-4.dsc’ saved [3360/3360] Thu Mar 28 04:23:01 UTC 2024 I: biojava6-live_6.1.0+dfsg-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: biojava6-live Binary: libbiojava6-java, libbiojava6-java-doc Architecture: all Version: 6.1.0+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Pierre Gruet Homepage: https://www.biojava.org Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/biojava6-live Vcs-Git: https://salsa.debian.org/med-team/biojava6-live.git Build-Depends: debhelper-compat (= 13), javahelper, maven-debian-helper Build-Depends-Indep: 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 Package-List: libbiojava6-java deb java optional arch=all libbiojava6-java-doc deb doc optional arch=all Checksums-Sha1: 7016114b4e93972f0011b051033c52b88f47dfa4 716817 biojava6-live_6.1.0+dfsg.orig-forester.tar.gz 8c9e87252aa79ae087f053f04169ccc519d78553 12099 biojava6-live_6.1.0+dfsg.orig-jcolorbrewer.tar.gz 3ef1b57421b0bf55e9fb18bffe0297decd30eec4 17827888 biojava6-live_6.1.0+dfsg.orig.tar.gz 26e5b5f670f1867589b21d39d1ee63279a9ed612 27320 biojava6-live_6.1.0+dfsg-4.debian.tar.xz Checksums-Sha256: c62105605104c93848056ea2726220552ac7460b5024eb98e163afe20d8247d6 716817 biojava6-live_6.1.0+dfsg.orig-forester.tar.gz d6548c423ad6202bc8f75eaa8b5839654a34591dfde51c129829ea14b3feeb8a 12099 biojava6-live_6.1.0+dfsg.orig-jcolorbrewer.tar.gz 0e544639aa1f0b7b8c265fae902c7653a5a03f379bcf8ebbc3201abb94c574e0 17827888 biojava6-live_6.1.0+dfsg.orig.tar.gz 28b5c564b2f7c9e36828f8ac1d3a2dc0567d96085f761aae5eb747922a0334e8 27320 biojava6-live_6.1.0+dfsg-4.debian.tar.xz Files: 1e9f85109426e43845585480f703addb 716817 biojava6-live_6.1.0+dfsg.orig-forester.tar.gz df2215c3446dd89de728b19bbbb02ec8 12099 biojava6-live_6.1.0+dfsg.orig-jcolorbrewer.tar.gz 57fdf02efb490c3966af01ccc9bb586b 17827888 biojava6-live_6.1.0+dfsg.orig.tar.gz 899aba4c2d3906f2570e8d8ce9eae369 27320 biojava6-live_6.1.0+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIyBAEBCgAdFiEEM8soQxPpC9J9y0UjYAMWptwndHYFAmPiKYoACgkQYAMWptwn dHa/rw/40XHhwYAhfd8K+xxNvJe8j2NEALFG+Xk2zl2uwNLWmCvwtvvXH3OjoZgK jegIK1JR2tR3pzYsR+zBnCT/q89ohGk82ldiMMXtwVWPuKzxVUoHWA03rXBsz+qy z06xX8dgIAQ7gSi/QExKAjkYuMw6rjn4EytA6vx5rck7Lba+ILYY+Rj/alpB/QRR y0wD39odzUhGveq0vMPV3ulw3D0rWPPZiTKRXtYSPjPv2VpRp2UPSwtoo4+WqBRE zzPD1Q8UPmSzwdD4QtZe2ek8Sxb5fsCMhEeGnWqmiqZEVgwOhSSosmx0F1PKsIlt KBwv6VNuGn+1r43a3zmSvyQ4D71Ebs4KQJdngpWdKHamfsCXF8GdouiMXh2QvwnH 9FrpKVbiqtj6erSdFvU/ila+5NH27E3tdRi4oJmXDmOYOFoPj5SFHhVdrOYr2Z6l v09RQvpJKR7C3AfT7ESaImp3KiqHCF/qWqNdADfbbutmX0h7ezH23EqE1jf6eZWy FmQMT3oDRA3u5pv87JAIzaqWh9vb2vCKf026VrhDR+1MRDu/4eev99ujzPJFjlrb 0BPdrU1gU1SHkeGoirMy7fhlxGGLuoQ9QIuePMLWVJCdqKlX2LXwIF3GFmBsabtT hITkMnM393bBqeqKdtRBIWH4ypJpKxRCYXPTSzgb5M3spmtkuQ== =OMCH -----END PGP SIGNATURE----- Thu Mar 28 04:23:01 UTC 2024 I: Checking whether the package is not for us Thu Mar 28 04:23:01 UTC 2024 I: Starting 1st build on remote node wbq0-armhf-rb.debian.net. Thu Mar 28 04:23:01 UTC 2024 I: Preparing to do remote build '1' on wbq0-armhf-rb.debian.net. Thu Mar 28 05:26:27 UTC 2024 I: Deleting $TMPDIR on wbq0-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Mar 27 16:23:17 -12 2024 I: pbuilder-time-stamp: 1711599797 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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/27477/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='d1f254ee6a98474b86408b4edd130a45' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='27477' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.MzdWTCiu/pbuilderrc_tSNv --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MzdWTCiu/b1 --logfile b1/build.log biojava6-live_6.1.0+dfsg-4.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux wbq0 6.1.0-18-armmp #1 SMP Debian 6.1.76-1 (2024-02-01) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 27 11:26 /bin -> usr/bin I: user script /srv/workspace/pbuilder/27477/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: armhf 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 ... 19577 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} gpg-wks-server{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{a} libasound2-data{a} libassuan0{a} libatinject-jsr330-api-java{a} libatk1.0-0{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} 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} libcups2{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} libelf1{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} libglib2.0-0{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgoogle-gson-java{a} libgraphite2-3{a} libgtk2.0-0{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} libksba8{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblightcouch-java{a} libllvm17{a} liblog4j1.2-java{a} liblog4j2-java{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1{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} libnpth0{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} libpcsclite1{a} libpicocli-java{a} libpipeline1{a} libpixman-1-0{a} libplexus-ant-factory-java{a} libplexus-archiver-java{a} libplexus-bsh-factory-java{a} libplexus-build-api-java{a} libplexus-cipher-java{a} libplexus-classworlds-java{a} libplexus-compiler-java{a} libplexus-component-annotations-java{a} libplexus-container-default-java{a} libplexus-container-default1.5-java{a} libplexus-i18n-java{a} libplexus-interactivity-api-java{a} libplexus-interpolation-java{a} libplexus-io-java{a} libplexus-languages-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libplexus-velocity-java{a} libpng16-16{a} libproc2-0{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqdox-java{a} libqdox2-java{a} libreadline8{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-override-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 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, 402 newly installed, 0 to remove and 0 not upgraded. Need to get 322 MB of archives. After unpacking 1029 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.7-1+b2 [33.4 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf binfmt-support armhf 2.2.2-6 [55.2 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf libpython3.11-minimal armhf 3.11.8-1 [802 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf libexpat1 armhf 2.5.0-2+b2 [80.2 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf python3.11-minimal armhf 3.11.8-1 [1707 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf python3-minimal armhf 3.11.6-1 [26.2 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf media-types all 10.1.0 [26.9 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf netbase all 6.4 [12.8 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf tzdata all 2024a-1 [255 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf readline-common all 8.2-3 [69.1 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf libreadline8 armhf 8.2-3+b1 [144 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf libpython3.11-stdlib armhf 3.11.8-1 [1709 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf python3.11 armhf 3.11.8-1 [597 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf libpython3-stdlib armhf 3.11.6-1 [9224 B] Get: 15 http://deb.debian.org/debian trixie/main armhf python3 armhf 3.11.6-1 [26.2 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf sgml-base all 1.31 [15.4 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf libproc2-0 armhf 2:4.0.4-4 [55.7 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf procps armhf 2:4.0.4-4 [864 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf openssl armhf 3.1.5-1 [1208 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf ca-certificates all 20240203 [158 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-2+b1 [314 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf libmagic1 armhf 1:5.45-2+b1 [97.9 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-2+b1 [42.2 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-3 [1088 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.39.3-6 [81.2 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.12.0-3 [1367 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf libgdk-pixbuf2.0-common all 2.42.10+dfsg-3 [307 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf libglib2.0-0 armhf 2.78.4-1 [1281 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b2 [599 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf shared-mime-info armhf 2.4-1 [746 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf libjpeg62-turbo armhf 1:2.1.5-2+b2 [143 kB] Get: 36 http://deb.debian.org/debian trixie/main armhf libpng16-16 armhf 1.6.43-1 [262 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf libdeflate0 armhf 1.20-1 [35.9 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf libjbig0 armhf 2.1-6.1+b1 [27.3 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf liblerc4 armhf 4.0.0+ds-4+b1 [137 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf libsharpyuv0 armhf 1.3.2-0.4 [105 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf libwebp7 armhf 1.3.2-0.4 [261 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf libtiff6 armhf 4.5.1+git230720-4 [301 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf libgdk-pixbuf-2.0-0 armhf 2.42.10+dfsg-3+b1 [124 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf gtk-update-icon-cache armhf 3.24.41-1 [44.6 kB] Get: 45 http://deb.debian.org/debian trixie/main armhf hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf adwaita-icon-theme all 46.0-1 [614 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf ca-certificates-java all 20240118 [11.6 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf java-common all 0.75 [6640 B] Get: 49 http://deb.debian.org/debian trixie/main armhf libavahi-common-data armhf 0.8-13+b1 [111 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf libavahi-common3 armhf 0.8-13+b1 [40.1 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf libdbus-1-3 armhf 1.14.10-4 [180 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf libavahi-client3 armhf 0.8-13+b1 [43.4 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf libcups2 armhf 2.4.7-1+b1 [212 kB] Get: 54 http://deb.debian.org/debian trixie/main armhf liblcms2-2 armhf 2.14-2+b1 [126 kB] Get: 55 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b3 [284 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf libfreetype6 armhf 2.13.2+dfsg-1+b1 [371 kB] Get: 57 http://deb.debian.org/debian trixie/main armhf fonts-dejavu-mono all 2.37-8 [489 kB] Get: 58 http://deb.debian.org/debian trixie/main armhf fonts-dejavu-core all 2.37-8 [840 kB] Get: 59 http://deb.debian.org/debian trixie/main armhf fontconfig-config armhf 2.15.0-1.1 [317 kB] Get: 60 http://deb.debian.org/debian trixie/main armhf libfontconfig1 armhf 2.15.0-1.1 [370 kB] Get: 61 http://deb.debian.org/debian trixie/main armhf libnspr4 armhf 2:4.35-1.1+b1 [87.2 kB] Get: 62 http://deb.debian.org/debian trixie/main armhf libnss3 armhf 2:3.99-1 [1220 kB] Get: 63 http://deb.debian.org/debian trixie/main armhf libasound2-data all 1.2.10-3 [20.7 kB] Get: 64 http://deb.debian.org/debian trixie/main armhf libasound2 armhf 1.2.10-3 [316 kB] Get: 65 http://deb.debian.org/debian trixie/main armhf libgraphite2-3 armhf 1.3.14-2 [63.2 kB] Get: 66 http://deb.debian.org/debian trixie/main armhf libharfbuzz0b armhf 8.3.0-2 [2155 kB] Get: 67 http://deb.debian.org/debian trixie/main armhf libpcsclite1 armhf 2.0.1-1+b1 [47.8 kB] Get: 68 http://deb.debian.org/debian trixie/main armhf openjdk-17-jre-headless armhf 17.0.10+7-1 [38.2 MB] Get: 69 http://deb.debian.org/debian trixie/main armhf default-jre-headless armhf 2:1.17-75 [3068 B] Get: 70 http://deb.debian.org/debian trixie/main armhf ant all 1.10.14-1 [2162 kB] Get: 71 http://deb.debian.org/debian trixie/main armhf ant-optional all 1.10.14-1 [455 kB] Get: 72 http://deb.debian.org/debian trixie/main armhf at-spi2-common all 2.50.0-1 [163 kB] Get: 73 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 74 http://deb.debian.org/debian trixie/main armhf autoconf all 2.71-3 [332 kB] Get: 75 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 76 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 77 http://deb.debian.org/debian trixie/main armhf autopoint all 0.21-14 [496 kB] Get: 78 http://deb.debian.org/debian trixie/main armhf dctrl-tools armhf 2.24-3 [96.0 kB] Get: 79 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.14.1 [85.6 kB] Get: 80 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 81 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 82 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 83 http://deb.debian.org/debian trixie/main armhf libsub-override-perl all 0.10-1 [10.6 kB] Get: 84 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 85 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 86 http://deb.debian.org/debian trixie/main armhf libelf1 armhf 0.190-1+b1 [171 kB] Get: 87 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1 [101 kB] Get: 88 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 89 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 90 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 91 http://deb.debian.org/debian trixie/main armhf debhelper all 13.14.1 [890 kB] Get: 92 http://deb.debian.org/debian trixie/main armhf libgtk2.0-common all 2.24.33-3 [2659 kB] Get: 93 http://deb.debian.org/debian trixie/main armhf libatk1.0-0 armhf 2.50.0-1+b1 [43.3 kB] Get: 94 http://deb.debian.org/debian trixie/main armhf libpixman-1-0 armhf 0.42.2-1+b1 [476 kB] Get: 95 http://deb.debian.org/debian trixie/main armhf libxau6 armhf 1:1.0.9-1 [19.0 kB] Get: 96 http://deb.debian.org/debian trixie/main armhf libbsd0 armhf 0.12.2-1 [127 kB] Get: 97 http://deb.debian.org/debian trixie/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get: 98 http://deb.debian.org/debian trixie/main armhf libxcb1 armhf 1.15-1 [140 kB] Get: 99 http://deb.debian.org/debian trixie/main armhf libx11-data all 2:1.8.7-1 [328 kB] Get: 100 http://deb.debian.org/debian trixie/main armhf libx11-6 armhf 2:1.8.7-1 [735 kB] Get: 101 http://deb.debian.org/debian trixie/main armhf libxcb-render0 armhf 1.15-1 [114 kB] Get: 102 http://deb.debian.org/debian trixie/main armhf libxcb-shm0 armhf 1.15-1 [106 kB] Get: 103 http://deb.debian.org/debian trixie/main armhf libxext6 armhf 2:1.3.4-1+b1 [47.8 kB] Get: 104 http://deb.debian.org/debian trixie/main armhf libxrender1 armhf 1:0.9.10-1.1 [30.1 kB] Get: 105 http://deb.debian.org/debian trixie/main armhf libcairo2 armhf 1.18.0-1+b1 [441 kB] Get: 106 http://deb.debian.org/debian trixie/main armhf fontconfig armhf 2.15.0-1.1 [461 kB] Get: 107 http://deb.debian.org/debian trixie/main armhf libfribidi0 armhf 1.0.13-3+b1 [69.4 kB] Get: 108 http://deb.debian.org/debian trixie/main armhf libthai-data all 0.1.29-2 [168 kB] Get: 109 http://deb.debian.org/debian trixie/main armhf libdatrie1 armhf 0.2.13-3 [34.4 kB] Get: 110 http://deb.debian.org/debian trixie/main armhf libthai0 armhf 0.1.29-2 [45.8 kB] Get: 111 http://deb.debian.org/debian trixie/main armhf libpango-1.0-0 armhf 1.52.0+ds-1 [192 kB] Get: 112 http://deb.debian.org/debian trixie/main armhf libpangoft2-1.0-0 armhf 1.52.0+ds-1 [41.8 kB] Get: 113 http://deb.debian.org/debian trixie/main armhf libpangocairo-1.0-0 armhf 1.52.0+ds-1 [31.2 kB] Get: 114 http://deb.debian.org/debian trixie/main armhf libxcomposite1 armhf 1:0.4.5-1 [16.1 kB] Get: 115 http://deb.debian.org/debian trixie/main armhf libxfixes3 armhf 1:6.0.0-2 [21.1 kB] Get: 116 http://deb.debian.org/debian trixie/main armhf libxcursor1 armhf 1:1.2.1-1 [37.9 kB] Get: 117 http://deb.debian.org/debian trixie/main armhf libxdamage1 armhf 1:1.1.6-1 [14.6 kB] Get: 118 http://deb.debian.org/debian trixie/main armhf libxi6 armhf 2:1.8.1-1 [73.8 kB] Get: 119 http://deb.debian.org/debian trixie/main armhf libxinerama1 armhf 2:1.1.4-3 [17.4 kB] Get: 120 http://deb.debian.org/debian trixie/main armhf libxrandr2 armhf 2:1.5.4-1 [33.0 kB] Get: 121 http://deb.debian.org/debian trixie/main armhf libgtk2.0-0 armhf 2.24.33-3 [1555 kB] Get: 122 http://deb.debian.org/debian trixie/main armhf libglvnd0 armhf 1.7.0-1 [52.3 kB] Get: 123 http://deb.debian.org/debian trixie/main armhf libdrm-common all 2.4.120-2 [7688 B] Get: 124 http://deb.debian.org/debian trixie/main armhf libdrm2 armhf 2.4.120-2 [33.8 kB] Get: 125 http://deb.debian.org/debian trixie/main armhf libglapi-mesa armhf 23.3.5-1 [42.5 kB] Get: 126 http://deb.debian.org/debian trixie/main armhf libx11-xcb1 armhf 2:1.8.7-1 [231 kB] Get: 127 http://deb.debian.org/debian trixie/main armhf libxcb-dri2-0 armhf 1.15-1 [107 kB] Get: 128 http://deb.debian.org/debian trixie/main armhf libxcb-dri3-0 armhf 1.15-1 [107 kB] Get: 129 http://deb.debian.org/debian trixie/main armhf libxcb-glx0 armhf 1.15-1 [120 kB] Get: 130 http://deb.debian.org/debian trixie/main armhf libxcb-present0 armhf 1.15-1 [105 kB] Get: 131 http://deb.debian.org/debian trixie/main armhf libxcb-randr0 armhf 1.15-1 [116 kB] Get: 132 http://deb.debian.org/debian trixie/main armhf libxcb-sync1 armhf 1.15-1 [108 kB] Get: 133 http://deb.debian.org/debian trixie/main armhf libxcb-xfixes0 armhf 1.15-1 [110 kB] Get: 134 http://deb.debian.org/debian trixie/main armhf libxshmfence1 armhf 1.3-1 [8592 B] Get: 135 http://deb.debian.org/debian trixie/main armhf libxxf86vm1 armhf 1:1.1.4-1+b2 [20.2 kB] Get: 136 http://deb.debian.org/debian trixie/main armhf libvulkan1 armhf 1.3.275.0-1 [109 kB] Get: 137 http://deb.debian.org/debian trixie/main armhf libdrm-amdgpu1 armhf 2.4.120-2 [20.0 kB] Get: 138 http://deb.debian.org/debian trixie/main armhf libdrm-nouveau2 armhf 2.4.120-2 [16.9 kB] Get: 139 http://deb.debian.org/debian trixie/main armhf libdrm-radeon1 armhf 2.4.120-2 [19.5 kB] Get: 140 http://deb.debian.org/debian trixie/main armhf libedit2 armhf 3.1-20230828-1 [76.8 kB] Get: 141 http://deb.debian.org/debian trixie/main armhf libz3-4 armhf 4.8.12-3.1+b2 [6324 kB] Get: 142 http://deb.debian.org/debian trixie/main armhf libllvm17 armhf 1:17.0.6-5 [21.6 MB] Get: 143 http://deb.debian.org/debian trixie/main armhf libsensors-config all 1:3.6.0-9 [14.6 kB] Get: 144 http://deb.debian.org/debian trixie/main armhf libsensors5 armhf 1:3.6.0-9 [31.9 kB] Get: 145 http://deb.debian.org/debian trixie/main armhf libgl1-mesa-dri armhf 23.3.5-1 [6405 kB] Get: 146 http://deb.debian.org/debian trixie/main armhf libglx-mesa0 armhf 23.3.5-1 [130 kB] Get: 147 http://deb.debian.org/debian trixie/main armhf libglx0 armhf 1.7.0-1 [32.2 kB] Get: 148 http://deb.debian.org/debian trixie/main armhf libgl1 armhf 1.7.0-1 [90.8 kB] Get: 149 http://deb.debian.org/debian trixie/main armhf libgif7 armhf 5.2.2-1 [41.2 kB] Get: 150 http://deb.debian.org/debian trixie/main armhf x11-common all 1:7.7+23 [252 kB] Get: 151 http://deb.debian.org/debian trixie/main armhf libxtst6 armhf 2:1.2.3-1.1 [26.2 kB] Get: 152 http://deb.debian.org/debian trixie/main armhf openjdk-17-jre armhf 17.0.10+7-1 [163 kB] Get: 153 http://deb.debian.org/debian trixie/main armhf default-jre armhf 2:1.17-75 [1056 B] Get: 154 http://deb.debian.org/debian trixie/main armhf openjdk-17-jdk-headless armhf 17.0.10+7-1 [67.4 MB] Get: 155 http://deb.debian.org/debian trixie/main armhf default-jdk-headless armhf 2:1.17-75 [1108 B] Get: 156 http://deb.debian.org/debian trixie/main armhf openjdk-17-jdk armhf 17.0.10+7-1 [2361 kB] Get: 157 http://deb.debian.org/debian trixie/main armhf default-jdk armhf 2:1.17-75 [1068 B] Get: 158 http://deb.debian.org/debian trixie/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 159 http://deb.debian.org/debian trixie/main armhf libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 160 http://deb.debian.org/debian trixie/main armhf libjs-jquery-ui-theme-base all 1.12.1+dfsg-1.1 [44.3 kB] Get: 161 http://deb.debian.org/debian trixie/main armhf openjdk-17-doc all 17.0.10+7-1 [12.8 MB] Get: 162 http://deb.debian.org/debian trixie/main armhf default-jdk-doc armhf 2:1.17-75 [3148 B] Get: 163 http://deb.debian.org/debian trixie/main armhf libassuan0 armhf 2.5.6-1 [43.3 kB] Get: 164 http://deb.debian.org/debian trixie/main armhf gpgconf armhf 2.2.40-1.1+b1 [547 kB] Get: 165 http://deb.debian.org/debian trixie/main armhf libksba8 armhf 1.6.6-1 [112 kB] Get: 166 http://deb.debian.org/debian trixie/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-4+b1 [18.2 kB] Get: 167 http://deb.debian.org/debian trixie/main armhf libsasl2-2 armhf 2.1.28+dfsg1-4+b1 [50.1 kB] Get: 168 http://deb.debian.org/debian trixie/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5+b3 [158 kB] Get: 169 http://deb.debian.org/debian trixie/main armhf libnpth0 armhf 1.6-3+b1 [16.9 kB] Get: 170 http://deb.debian.org/debian trixie/main armhf dirmngr armhf 2.2.40-1.1+b1 [750 kB] Get: 171 http://deb.debian.org/debian trixie/main armhf gnupg-l10n all 2.2.40-1.1 [1093 kB] Get: 172 http://deb.debian.org/debian trixie/main armhf gnupg-utils armhf 2.2.40-1.1+b1 [853 kB] Get: 173 http://deb.debian.org/debian trixie/main armhf gpg armhf 2.2.40-1.1+b1 [886 kB] Get: 174 http://deb.debian.org/debian trixie/main armhf pinentry-curses armhf 1.2.1-3 [73.8 kB] Get: 175 http://deb.debian.org/debian trixie/main armhf gpg-agent armhf 2.2.40-1.1+b1 [653 kB] Get: 176 http://deb.debian.org/debian trixie/main armhf gpg-wks-client armhf 2.2.40-1.1+b1 [525 kB] Get: 177 http://deb.debian.org/debian trixie/main armhf gpg-wks-server armhf 2.2.40-1.1+b1 [518 kB] Get: 178 http://deb.debian.org/debian trixie/main armhf gpgsm armhf 2.2.40-1.1+b1 [638 kB] Get: 179 http://deb.debian.org/debian trixie/main armhf gnupg all 2.2.40-1.1 [846 kB] Get: 180 http://deb.debian.org/debian trixie/main armhf libfile-dirlist-perl all 0.05-3 [7600 B] Get: 181 http://deb.debian.org/debian trixie/main armhf libfile-which-perl all 1.27-2 [15.1 kB] Get: 182 http://deb.debian.org/debian trixie/main armhf libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 183 http://deb.debian.org/debian trixie/main armhf libfile-touch-perl all 0.12-2 [8816 B] Get: 184 http://deb.debian.org/debian trixie/main armhf libio-pty-perl armhf 1:1.20-1 [33.7 kB] Get: 185 http://deb.debian.org/debian trixie/main armhf libipc-run-perl all 20231003.0-1 [102 kB] Get: 186 http://deb.debian.org/debian trixie/main armhf libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 187 http://deb.debian.org/debian trixie/main armhf libclass-xsaccessor-perl armhf 1.19-4+b2 [35.3 kB] Get: 188 http://deb.debian.org/debian trixie/main armhf libb-hooks-op-check-perl armhf 0.22-2+b2 [10.3 kB] Get: 189 http://deb.debian.org/debian trixie/main armhf libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 190 http://deb.debian.org/debian trixie/main armhf libdevel-callchecker-perl armhf 0.008-2+b1 [14.9 kB] Get: 191 http://deb.debian.org/debian trixie/main armhf libparams-classify-perl armhf 0.015-2+b2 [21.3 kB] Get: 192 http://deb.debian.org/debian trixie/main armhf libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 193 http://deb.debian.org/debian trixie/main armhf libimport-into-perl all 1.002005-2 [11.3 kB] Get: 194 http://deb.debian.org/debian trixie/main armhf librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 195 http://deb.debian.org/debian trixie/main armhf libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 196 http://deb.debian.org/debian trixie/main armhf libmoo-perl all 2.005005-1 [58.0 kB] Get: 197 http://deb.debian.org/debian trixie/main armhf libencode-locale-perl all 1.05-3 [12.9 kB] Get: 198 http://deb.debian.org/debian trixie/main armhf libtimedate-perl all 2.3300-2 [39.3 kB] Get: 199 http://deb.debian.org/debian trixie/main armhf libhttp-date-perl all 6.06-1 [10.7 kB] Get: 200 http://deb.debian.org/debian trixie/main armhf libfile-listing-perl all 6.16-1 [12.4 kB] Get: 201 http://deb.debian.org/debian trixie/main armhf libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 202 http://deb.debian.org/debian trixie/main armhf liburi-perl all 5.27-1 [98.4 kB] Get: 203 http://deb.debian.org/debian trixie/main armhf libhtml-parser-perl armhf 3.81-1+b1 [95.8 kB] Get: 204 http://deb.debian.org/debian trixie/main armhf libhtml-tree-perl all 5.07-3 [211 kB] Get: 205 http://deb.debian.org/debian trixie/main armhf libclone-perl armhf 0.46-1+b1 [13.2 kB] Get: 206 http://deb.debian.org/debian trixie/main armhf libio-html-perl all 1.004-3 [16.2 kB] Get: 207 http://deb.debian.org/debian trixie/main armhf liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 208 http://deb.debian.org/debian trixie/main armhf libhttp-message-perl all 6.45-1 [82.0 kB] Get: 209 http://deb.debian.org/debian trixie/main armhf libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 210 http://deb.debian.org/debian trixie/main armhf libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 211 http://deb.debian.org/debian trixie/main armhf perl-openssl-defaults armhf 7+b1 [7916 B] Get: 212 http://deb.debian.org/debian trixie/main armhf libnet-ssleay-perl armhf 1.94-1 [318 kB] Get: 213 http://deb.debian.org/debian trixie/main armhf libio-socket-ssl-perl all 2.085-1 [218 kB] Get: 214 http://deb.debian.org/debian trixie/main armhf libnet-http-perl all 6.23-1 [23.9 kB] Get: 215 http://deb.debian.org/debian trixie/main armhf liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 216 http://deb.debian.org/debian trixie/main armhf libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 217 http://deb.debian.org/debian trixie/main armhf libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 218 http://deb.debian.org/debian trixie/main armhf libwww-perl all 6.77-1 [183 kB] Get: 219 http://deb.debian.org/debian trixie/main armhf patchutils armhf 0.4.2-1 [72.5 kB] Get: 220 http://deb.debian.org/debian trixie/main armhf wdiff armhf 1.2.2-6 [118 kB] Get: 221 http://deb.debian.org/debian trixie/main armhf devscripts all 2.23.7 [1068 kB] Get: 222 http://deb.debian.org/debian trixie/main armhf fastjar armhf 2:0.98-7 [43.9 kB] Get: 223 http://deb.debian.org/debian trixie/main armhf jarwrapper all 0.79 [10.1 kB] Get: 224 http://deb.debian.org/debian trixie/main armhf unzip armhf 6.0-28 [152 kB] Get: 225 http://deb.debian.org/debian trixie/main armhf java-wrappers all 0.4 [8916 B] Get: 226 http://deb.debian.org/debian trixie/main armhf javahelper all 0.79 [84.6 kB] Get: 227 http://deb.debian.org/debian trixie/main armhf junit all 3.8.2-10 [108 kB] Get: 228 http://deb.debian.org/debian trixie/main armhf libhamcrest-java all 2.2-2 [121 kB] Get: 229 http://deb.debian.org/debian trixie/main armhf junit4 all 4.13.2-4 [349 kB] Get: 230 http://deb.debian.org/debian trixie/main armhf libapiguardian-java all 1.1.2-1 [4656 B] Get: 231 http://deb.debian.org/debian trixie/main armhf libopentest4j-java all 1.2.0-4 [9516 B] Get: 232 http://deb.debian.org/debian trixie/main armhf libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 233 http://deb.debian.org/debian trixie/main armhf libpicocli-java all 4.6.2-2 [390 kB] Get: 234 http://deb.debian.org/debian trixie/main armhf libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 235 http://deb.debian.org/debian trixie/main armhf junit5 all 5.10.1-1 [2458 kB] Get: 236 http://deb.debian.org/debian trixie/main armhf libactivation-java all 1.2.0-2 [84.7 kB] Get: 237 http://deb.debian.org/debian trixie/main armhf libantlr4-runtime-java all 4.9.2-2 [317 kB] Get: 238 http://deb.debian.org/debian trixie/main armhf libaopalliance-java all 20070526-7 [8572 B] Get: 239 http://deb.debian.org/debian trixie/main armhf libapache-pom-java all 29-2 [5276 B] Get: 240 http://deb.debian.org/debian trixie/main armhf libapfloat-java all 1.13.0-1 [700 kB] Get: 241 http://deb.debian.org/debian trixie/main armhf libargs4j-java all 2.33-2 [138 kB] Get: 242 http://deb.debian.org/debian trixie/main armhf libasm-java all 9.5-1 [387 kB] Get: 243 http://deb.debian.org/debian trixie/main armhf libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 244 http://deb.debian.org/debian trixie/main armhf libjaxp1.3-java all 1.3.05-6 [227 kB] Get: 245 http://deb.debian.org/debian trixie/main armhf libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 246 http://deb.debian.org/debian trixie/main armhf libcommons-parent-java all 56-1 [10.8 kB] Get: 247 http://deb.debian.org/debian trixie/main armhf libcommons-io-java all 2.11.0-2 [319 kB] Get: 248 http://deb.debian.org/debian trixie/main armhf libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 249 http://deb.debian.org/debian trixie/main armhf libxmlgraphics-commons-java all 2.8-2 [623 kB] Get: 250 http://deb.debian.org/debian trixie/main armhf libbatik-java all 1.17+dfsg-1 [3923 kB] Get: 251 http://deb.debian.org/debian trixie/main armhf libbsh-java all 2.0b4-20 [291 kB] Get: 252 http://deb.debian.org/debian trixie/main armhf libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 253 http://deb.debian.org/debian trixie/main armhf libcdi-api-java all 1.2-3 [54.3 kB] Get: 254 http://deb.debian.org/debian trixie/main armhf libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 255 http://deb.debian.org/debian trixie/main armhf libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 256 http://deb.debian.org/debian trixie/main armhf libciftools-java all 5.0.2-1 [2189 kB] Get: 257 http://deb.debian.org/debian trixie/main armhf libjaxen-java all 1.1.6-4 [214 kB] Get: 258 http://deb.debian.org/debian trixie/main armhf libdom4j-java all 2.1.4-1 [312 kB] Get: 259 http://deb.debian.org/debian trixie/main armhf libmaven-shared-utils-java all 3.3.4-1 [138 kB] Get: 260 http://deb.debian.org/debian trixie/main armhf libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 261 http://deb.debian.org/debian trixie/main armhf libcommons-lang3-java all 3.14.0-1 [621 kB] Get: 262 http://deb.debian.org/debian trixie/main armhf liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 263 http://deb.debian.org/debian trixie/main armhf libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 264 http://deb.debian.org/debian trixie/main armhf libguava-java all 32.0.1-1 [2708 kB] Get: 265 http://deb.debian.org/debian trixie/main armhf libguice-java all 4.2.3-2 [1435 kB] Get: 266 http://deb.debian.org/debian trixie/main armhf libmaven-parent-java all 35-1 [6140 B] Get: 267 http://deb.debian.org/debian trixie/main armhf libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 268 http://deb.debian.org/debian trixie/main armhf libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 269 http://deb.debian.org/debian trixie/main armhf libmaven-resolver-java all 1.6.3-1 [548 kB] Get: 270 http://deb.debian.org/debian trixie/main armhf libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 271 http://deb.debian.org/debian trixie/main armhf libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 272 http://deb.debian.org/debian trixie/main armhf libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 273 http://deb.debian.org/debian trixie/main armhf libplexus-interpolation-java all 1.26-1 [76.8 kB] Get: 274 http://deb.debian.org/debian trixie/main armhf libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 275 http://deb.debian.org/debian trixie/main armhf libslf4j-java all 1.7.32-1 [144 kB] Get: 276 http://deb.debian.org/debian trixie/main armhf libsisu-inject-java all 0.3.4-2 [347 kB] Get: 277 http://deb.debian.org/debian trixie/main armhf libsisu-plexus-java all 0.3.4-3 [181 kB] Get: 278 http://deb.debian.org/debian trixie/main armhf libmaven3-core-java all 3.8.7-2 [1573 kB] Get: 279 http://deb.debian.org/debian trixie/main armhf libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 280 http://deb.debian.org/debian trixie/main armhf libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 281 http://deb.debian.org/debian trixie/main armhf libcommons-compress-java all 1.25.0-1 [635 kB] Get: 282 http://deb.debian.org/debian trixie/main armhf libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 283 http://deb.debian.org/debian trixie/main armhf libsnappy1v5 armhf 1.1.10-1+b1 [25.2 kB] Get: 284 http://deb.debian.org/debian trixie/main armhf libsnappy-jni armhf 1.1.10.5-1 [5880 B] Get: 285 http://deb.debian.org/debian trixie/main armhf libsnappy-java all 1.1.10.5-1 [87.4 kB] Get: 286 http://deb.debian.org/debian trixie/main armhf libxz-java all 1.9-1 [143 kB] Get: 287 http://deb.debian.org/debian trixie/main armhf libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 288 http://deb.debian.org/debian trixie/main armhf libhttpcore-java all 4.4.16-1 [636 kB] Get: 289 http://deb.debian.org/debian trixie/main armhf libcommons-codec-java all 1.16.0-1 [297 kB] Get: 290 http://deb.debian.org/debian trixie/main armhf libhttpclient-java all 4.5.14-1 [1247 kB] Get: 291 http://deb.debian.org/debian trixie/main armhf libjsoup-java all 1.15.3-1 [431 kB] Get: 292 http://deb.debian.org/debian trixie/main armhf libwagon-http-java all 3.5.3-1 [49.5 kB] Get: 293 http://deb.debian.org/debian trixie/main armhf libistack-commons-java all 3.0.6-5 [145 kB] Get: 294 http://deb.debian.org/debian trixie/main armhf libcodemodel-java all 2.6+jaxb2.3.0.1-10.1 [164 kB] Get: 295 http://deb.debian.org/debian trixie/main armhf libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 296 http://deb.debian.org/debian trixie/main armhf libcommons-beanutils-java all 1.9.4-2 [233 kB] Get: 297 http://deb.debian.org/debian trixie/main armhf libcommons-collections4-java all 4.4-2 [682 kB] Get: 298 http://deb.debian.org/debian trixie/main armhf libcommons-lang-java all 2.6-10 [273 kB] Get: 299 http://deb.debian.org/debian trixie/main armhf libcommons-configuration-java all 1.10-6 [347 kB] Get: 300 http://deb.debian.org/debian trixie/main armhf libcommons-digester-java all 1.8.1-6 [137 kB] Get: 301 http://deb.debian.org/debian trixie/main armhf libcommons-exec-java all 1.3-2 [48.1 kB] Get: 302 http://deb.debian.org/debian trixie/main armhf libcommons-math-java all 2.2-8 [926 kB] Get: 303 http://deb.debian.org/debian trixie/main armhf libmaven-archiver-java all 3.6.0-1 [25.1 kB] Get: 304 http://deb.debian.org/debian trixie/main armhf libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 305 http://deb.debian.org/debian trixie/main armhf libcommons-text-java all 1.11.0-1 [217 kB] Get: 306 http://deb.debian.org/debian trixie/main armhf libcommons-validator-java all 1:1.7-1 [181 kB] Get: 307 http://deb.debian.org/debian trixie/main armhf libdoxia-core-java all 1.12.0-1 [213 kB] Get: 308 http://deb.debian.org/debian trixie/main armhf libfontbox2-java all 2.0.29-1 [1510 kB] Get: 309 http://deb.debian.org/debian trixie/main armhf libqdox-java all 1.12.1-3 [172 kB] Get: 310 http://deb.debian.org/debian trixie/main armhf libfop-java all 1:2.8-3 [10.1 MB] Get: 311 http://deb.debian.org/debian trixie/main armhf libitext1-java all 1.4-7 [1257 kB] Get: 312 http://deb.debian.org/debian trixie/main armhf libxbean-reflect-java all 4.5-8 [133 kB] Get: 313 http://deb.debian.org/debian trixie/main armhf libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 314 http://deb.debian.org/debian trixie/main armhf libdoxia-java all 1.12.0-1 [459 kB] Get: 315 http://deb.debian.org/debian trixie/main armhf libmaven-reporting-api-java all 3.1.1-1 [7240 B] Get: 316 http://deb.debian.org/debian trixie/main armhf libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB] Get: 317 http://deb.debian.org/debian trixie/main armhf velocity all 1.7-7 [431 kB] Get: 318 http://deb.debian.org/debian trixie/main armhf libplexus-velocity-java all 1.2-3.1 [10.5 kB] Get: 319 http://deb.debian.org/debian trixie/main armhf liboro-java all 2.0.8a-14 [70.5 kB] Get: 320 http://deb.debian.org/debian trixie/main armhf libvelocity-tools-java all 2.0-9 [311 kB] Get: 321 http://deb.debian.org/debian trixie/main armhf libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 322 http://deb.debian.org/debian trixie/main armhf libxerces2-java all 2.12.2-1 [1440 kB] Get: 323 http://deb.debian.org/debian trixie/main armhf libxalan2-java all 2.7.2-4 [3419 kB] Get: 324 http://deb.debian.org/debian trixie/main armhf libdoxia-sitetools-java all 1.11.1-1 [202 kB] Get: 325 http://deb.debian.org/debian trixie/main armhf libdtd-parser-java all 1.2-1 [64.9 kB] Get: 326 http://deb.debian.org/debian trixie/main armhf libel-api-java all 3.0.0-3 [64.9 kB] Get: 327 http://deb.debian.org/debian trixie/main armhf libexec-maven-plugin-java all 3.1.0-2 [66.7 kB] Get: 328 http://deb.debian.org/debian trixie/main armhf libjaxb-api-java all 2.3.1-1 [119 kB] Get: 329 http://deb.debian.org/debian trixie/main armhf libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 330 http://deb.debian.org/debian trixie/main armhf libstreambuffer-java all 1.5.4-1.1 [74.0 kB] Get: 331 http://deb.debian.org/debian trixie/main armhf librelaxng-datatype-java all 1.0+ds1-3.1 [11.7 kB] Get: 332 http://deb.debian.org/debian trixie/main armhf libxsom-java all 2.3.0.1-10.1 [400 kB] Get: 333 http://deb.debian.org/debian trixie/main armhf libfastinfoset-java all 1.2.12-3 [343 kB] Get: 334 http://deb.debian.org/debian trixie/main armhf libfastutil-java all 8.5.12+dfsg-1 [19.6 MB] Get: 335 http://deb.debian.org/debian trixie/main armhf libinchi1 armhf 1.03+dfsg-4 [352 kB] Get: 336 http://deb.debian.org/debian trixie/main armhf libitext5-java all 5.5.13.3-4 [2667 kB] Get: 337 http://deb.debian.org/debian trixie/main armhf libjackson2-annotations-java all 2.14.0-1 [68.8 kB] Get: 338 http://deb.debian.org/debian trixie/main armhf libjackson2-core-java all 2.14.1-1 [447 kB] Get: 339 http://deb.debian.org/debian trixie/main armhf libjackson2-databind-java all 2.14.0-1 [1584 kB] Get: 340 http://deb.debian.org/debian trixie/main armhf libjakarta-activation-java all 2.0.0-1 [59.8 kB] Get: 341 http://deb.debian.org/debian trixie/main armhf libjansi-java all 2.4.1-2 [100 kB] Get: 342 http://deb.debian.org/debian trixie/main armhf librngom-java all 2.3.0.1-10.1 [290 kB] Get: 343 http://deb.debian.org/debian trixie/main armhf libtxw2-java all 2.3.0.1-10.1 [134 kB] Get: 344 http://deb.debian.org/debian trixie/main armhf libjaxb-java all 2.3.0.1-10.1 [1973 kB] Get: 345 http://deb.debian.org/debian trixie/main armhf libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 346 http://deb.debian.org/debian trixie/main armhf libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 347 http://deb.debian.org/debian trixie/main armhf libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 348 http://deb.debian.org/debian trixie/main armhf libjetty9-java all 9.4.53-1 [2982 kB] Get: 349 http://deb.debian.org/debian trixie/main armhf libjheaps-java all 0.14-2 [144 kB] Get: 350 http://deb.debian.org/debian trixie/main armhf libjgraphx-java all 2.1.0.7-3 [807 kB] Get: 351 http://deb.debian.org/debian trixie/main armhf libjgrapht-java all 1.5.2-1 [1610 kB] Get: 352 http://deb.debian.org/debian trixie/main armhf libjni-inchi-jni armhf 0.8+dfsg-7 [8480 B] Get: 353 http://deb.debian.org/debian trixie/main armhf libmaven-shared-incremental-java all 1.1-4 [9924 B] Get: 354 http://deb.debian.org/debian trixie/main armhf libplexus-compiler-java all 2.12.1-2 [99.0 kB] Get: 355 http://deb.debian.org/debian trixie/main armhf libqdox2-java all 2.0.3-1 [296 kB] Get: 356 http://deb.debian.org/debian trixie/main armhf libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 357 http://deb.debian.org/debian trixie/main armhf libmaven-compiler-plugin-java all 3.10.1-2 [59.0 kB] Get: 358 http://deb.debian.org/debian trixie/main armhf liblog4j1.2-java all 1.2.17-11 [444 kB] Get: 359 http://deb.debian.org/debian trixie/main armhf libjni-inchi-java all 0.8+dfsg-7 [33.2 kB] Get: 360 http://deb.debian.org/debian trixie/main armhf libnaga-java all 3.0+svn80-5 [43.5 kB] Get: 361 http://deb.debian.org/debian trixie/main armhf libjmol-java all 14.32.83+dfsg-3 [8698 kB] Get: 362 http://deb.debian.org/debian trixie/main armhf libjson-simple-java all 2.3.0-1 [63.8 kB] Get: 363 http://deb.debian.org/debian trixie/main armhf libjtidy-java all 7+svn20110807-5 [250 kB] Get: 364 http://deb.debian.org/debian trixie/main armhf liblightcouch-java all 0.2.0-1 [75.0 kB] Get: 365 http://deb.debian.org/debian trixie/main armhf libmongodb-java all 3.6.3-2 [1901 kB] Get: 366 http://deb.debian.org/debian trixie/main armhf liblog4j2-java all 2.19.0-2 [2310 kB] Get: 367 http://deb.debian.org/debian trixie/main armhf libmaven-antrun-plugin-java all 3.1.0-1 [36.9 kB] Get: 368 http://deb.debian.org/debian trixie/main armhf libmaven-common-artifact-filters-java all 3.3.2-1 [48.2 kB] Get: 369 http://deb.debian.org/debian trixie/main armhf libmaven-artifact-transfer-java all 0.13.1-2 [158 kB] Get: 370 http://deb.debian.org/debian trixie/main armhf libplexus-build-api-java all 0.0.7-4 [10.3 kB] Get: 371 http://deb.debian.org/debian trixie/main armhf libmaven-filtering-java all 3.3.0-1 [50.2 kB] Get: 372 http://deb.debian.org/debian trixie/main armhf libmaven-assembly-plugin-java all 3.4.2-1 [242 kB] Get: 373 http://deb.debian.org/debian trixie/main armhf libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB] Get: 374 http://deb.debian.org/debian trixie/main armhf libmaven-dependency-analyzer-java all 1.13.0-1 [30.4 kB] Get: 375 http://deb.debian.org/debian trixie/main armhf libmaven-dependency-tree-java all 3.2.1-1 [34.7 kB] Get: 376 http://deb.debian.org/debian trixie/main armhf libmaven-reporting-impl-java all 3.2.0-2 [15.2 kB] Get: 377 http://deb.debian.org/debian trixie/main armhf libmaven-dependency-plugin-java all 3.5.0-1 [173 kB] Get: 378 http://deb.debian.org/debian trixie/main armhf libmaven-deploy-plugin-java all 3.1.1-1 [36.4 kB] Get: 379 http://deb.debian.org/debian trixie/main armhf libmaven-enforcer-plugin-java all 3.1.0-1 [135 kB] Get: 380 http://deb.debian.org/debian trixie/main armhf libmaven-install-plugin-java all 3.1.1-1 [28.7 kB] Get: 381 http://deb.debian.org/debian trixie/main armhf libmaven-invoker-java all 3.2.0-1 [28.1 kB] Get: 382 http://deb.debian.org/debian trixie/main armhf libplexus-interactivity-api-java all 1.1-2 [11.0 kB] Get: 383 http://deb.debian.org/debian trixie/main armhf libmaven-javadoc-plugin-java all 3.4.1-3 [454 kB] Get: 384 http://deb.debian.org/debian trixie/main armhf libplexus-container-default1.5-java all 2.1.1-1 [4476 B] Get: 385 http://deb.debian.org/debian trixie/main armhf libplexus-ant-factory-java all 1.0~alpha2.1-4 [11.4 kB] Get: 386 http://deb.debian.org/debian trixie/main armhf libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B] Get: 387 http://deb.debian.org/debian trixie/main armhf libmaven-plugin-tools-java all 3.7.1-1 [265 kB] Get: 388 http://deb.debian.org/debian trixie/main armhf libmaven-jaxb2-plugin-java all 0.15.1-1 [118 kB] Get: 389 http://deb.debian.org/debian trixie/main armhf libmaven-reporting-exec-java all 1.6.0-1 [26.8 kB] Get: 390 http://deb.debian.org/debian trixie/main armhf libmaven-resources-plugin-java all 3.3.0-1 [28.4 kB] Get: 391 http://deb.debian.org/debian trixie/main armhf libmaven-site-plugin-java all 3.12.1-2 [107 kB] Get: 392 http://deb.debian.org/debian trixie/main armhf libmsgpack-java all 0.9.6-1 [161 kB] Get: 393 http://deb.debian.org/debian trixie/main armhf libmmtf-java all 1.0.11-1 [187 kB] Get: 394 http://deb.debian.org/debian trixie/main armhf libsurefire-java all 2.22.3-2 [1169 kB] Get: 395 http://deb.debian.org/debian trixie/main armhf libvecmath-java all 1.5.2-7 [97.0 kB] Get: 396 http://deb.debian.org/debian trixie/main armhf libwagon-file-java all 3.5.3-1 [8388 B] Get: 397 http://deb.debian.org/debian trixie/main armhf libwagon-http-shaded-java all 3.5.3-1 [1341 kB] Get: 398 http://deb.debian.org/debian trixie/main armhf libxml2-utils armhf 2.9.14+dfsg-1.3+b2 [97.8 kB] Get: 399 http://deb.debian.org/debian trixie/main armhf libxmlunit-java all 1.6-2 [100 kB] Get: 400 http://deb.debian.org/debian trixie/main armhf maven all 3.8.7-2 [19.3 kB] Get: 401 http://deb.debian.org/debian trixie/main armhf maven-repo-helper all 1.11 [142 kB] Get: 402 http://deb.debian.org/debian trixie/main armhf maven-debian-helper all 2.6.4 [108 kB] Fetched 322 MB in 57s (5689 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19577 files and directories currently installed.) Preparing to unpack .../libpipeline1_1.5.7-1+b2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-1+b2) ... Selecting previously unselected package binfmt-support. Preparing to unpack .../binfmt-support_2.2.2-6_armhf.deb ... Unpacking binfmt-support (2.2.2-6) ... Selecting previously unselected package libpython3.11-minimal:armhf. 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Setting up python3-minimal (3.11.6-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20906 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.6-1_armhf.deb ... Unpacking python3 (3.11.6-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:armhf. 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Unpacking libmagic1:armhf (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../009-file_1%3a5.45-2+b1_armhf.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../010-gettext-base_0.21-14+b1_armhf.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../011-libuchardet0_0.0.8-1+b1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../012-groff-base_1.23.0-3_armhf.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../013-bsdextrautils_2.39.3-6_armhf.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package man-db. Preparing to unpack .../014-man-db_2.12.0-3_armhf.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package libgdk-pixbuf2.0-common. Preparing to unpack .../015-libgdk-pixbuf2.0-common_2.42.10+dfsg-3_all.deb ... Unpacking libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ... Selecting previously unselected package libglib2.0-0:armhf. Preparing to unpack .../016-libglib2.0-0_2.78.4-1_armhf.deb ... Unpacking libglib2.0-0:armhf (2.78.4-1) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../017-libicu72_72.1-4+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-4+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../018-libxml2_2.9.14+dfsg-1.3+b2_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.3+b2) ... Selecting previously unselected package shared-mime-info. Preparing to unpack .../019-shared-mime-info_2.4-1_armhf.deb ... Unpacking shared-mime-info (2.4-1) ... Selecting previously unselected package libjpeg62-turbo:armhf. Preparing to unpack .../020-libjpeg62-turbo_1%3a2.1.5-2+b2_armhf.deb ... Unpacking libjpeg62-turbo:armhf (1:2.1.5-2+b2) ... Selecting previously unselected package libpng16-16:armhf. Preparing to unpack .../021-libpng16-16_1.6.43-1_armhf.deb ... Unpacking libpng16-16:armhf (1.6.43-1) ... Selecting previously unselected package libdeflate0:armhf. Preparing to unpack .../022-libdeflate0_1.20-1_armhf.deb ... Unpacking libdeflate0:armhf (1.20-1) ... Selecting previously unselected package libjbig0:armhf. Preparing to unpack .../023-libjbig0_2.1-6.1+b1_armhf.deb ... Unpacking libjbig0:armhf (2.1-6.1+b1) ... Selecting previously unselected package liblerc4:armhf. Preparing to unpack .../024-liblerc4_4.0.0+ds-4+b1_armhf.deb ... Unpacking liblerc4:armhf (4.0.0+ds-4+b1) ... Selecting previously unselected package libsharpyuv0:armhf. Preparing to unpack .../025-libsharpyuv0_1.3.2-0.4_armhf.deb ... Unpacking libsharpyuv0:armhf (1.3.2-0.4) ... Selecting previously unselected package libwebp7:armhf. Preparing to unpack .../026-libwebp7_1.3.2-0.4_armhf.deb ... Unpacking libwebp7:armhf (1.3.2-0.4) ... Selecting previously unselected package libtiff6:armhf. Preparing to unpack .../027-libtiff6_4.5.1+git230720-4_armhf.deb ... Unpacking libtiff6:armhf (4.5.1+git230720-4) ... Selecting previously unselected package libgdk-pixbuf-2.0-0:armhf. Preparing to unpack .../028-libgdk-pixbuf-2.0-0_2.42.10+dfsg-3+b1_armhf.deb ... Unpacking libgdk-pixbuf-2.0-0:armhf (2.42.10+dfsg-3+b1) ... Selecting previously unselected package gtk-update-icon-cache. Preparing to unpack .../029-gtk-update-icon-cache_3.24.41-1_armhf.deb ... Unpacking gtk-update-icon-cache (3.24.41-1) ... Selecting previously unselected package hicolor-icon-theme. Preparing to unpack .../030-hicolor-icon-theme_0.17-2_all.deb ... Unpacking hicolor-icon-theme (0.17-2) ... Selecting previously unselected package adwaita-icon-theme. Preparing to unpack .../031-adwaita-icon-theme_46.0-1_all.deb ... Unpacking adwaita-icon-theme (46.0-1) ... 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Setting up libfontconfig1:armhf (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+b2) ... Setting up libcommons-codec-java (1.16.0-1) ... Setting up libllvm17:armhf (1:17.0.6-5) ... Setting up libxcomposite1:armhf (1:0.4.5-1) ... Setting up libavahi-client3:armhf (0.8-13+b1) ... Setting up libio-socket-ssl-perl (2.085-1) ... Setting up gpg (2.2.40-1.1+b1) ... Setting up gnupg-utils (2.2.40-1.1+b1) ... Setting up libhttp-message-perl (6.45-1) ... Setting up libdrm-amdgpu1:armhf (2.4.120-2) ... Setting up libxcb-dri3-0:armhf (1.15-1) ... Setting up gtk-update-icon-cache (3.24.41-1) ... Setting up libx11-xcb1:armhf (2:1.8.7-1) ... 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:armhf (2.4.120-2) ... Setting up libxdamage1:armhf (1:1.1.6-1) ... Setting up gpg-agent (2.2.40-1.1+b1) ... Setting up libxrender1:armhf (1:0.9.10-1.1) ... Setting up libcommons-compress-java (1.25.0-1) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up libcommons-io-java (2.11.0-2) ... Setting up libdrm-radeon1:armhf (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:armhf (3.11.8-1) ... Setting up libparams-classify-perl:armhf (0.015-2+b2) ... Setting up gpgsm (2.2.40-1.1+b1) ... Setting up libpango-1.0-0:armhf (1.52.0+ds-1) ... Setting up libgl1-mesa-dri:armhf (23.3.5-1) ... Setting up libxext6:armhf (2:1.3.4-1+b1) ... Setting up libxmlgraphics-commons-java (2.8-2) ... Setting up default-jdk-doc (2:1.17-75) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:armhf (1.18.0-1+b1) ... Setting up libxxf86vm1:armhf (1:1.1.4-1+b2) ... Setting up dirmngr (2.2.40-1.1+b1) ... 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:armhf (1:6.0.0-2) ... Setting up libxinerama1:armhf (2:1.1.4-3) ... Setting up libxrandr2:armhf (2:1.5.4-1) ... Setting up gpg-wks-server (2.2.40-1.1+b1) ... Setting up libcups2:armhf (2.4.7-1+b1) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up libmaven-dependency-tree-java (3.2.1-1) ... 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:armhf (1.52.0+ds-1) ... Setting up libmaven-resources-plugin-java (3.3.0-1) ... Setting up libpangocairo-1.0-0:armhf (1.52.0+ds-1) ... Setting up libpython3-stdlib:armhf (3.11.6-1) ... Setting up python3.11 (3.11.8-1) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up libglx-mesa0:armhf (23.3.5-1) ... Setting up libxi6:armhf (2:1.8.1-1) ... Setting up gpg-wks-client (2.2.40-1.1+b1) ... Setting up libglx0:armhf (1.7.0-1) ... 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:armhf (2:1.2.3-1.1) ... 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:armhf (1:1.2.1-1) ... Setting up libmaven-invoker-java (3.2.0-1) ... Setting up debhelper (13.14.1) ... Setting up python3 (3.11.6-1) ... Setting up libmaven-deploy-plugin-java (3.1.1-1) ... Setting up libgl1:armhf (1.7.0-1) ... Setting up libmaven-clean-plugin-java (3.2.0-2) ... Setting up openjdk-17-jre-headless:armhf (17.0.10+7-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up gnupg (2.2.40-1.1) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libfop-java (1:2.8-3) ... Setting up libgtk2.0-0:armhf (2.24.33-3) ... Setting up libmaven-archiver-java (3.6.0-1) ... 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 (14.32.83+dfsg-3) ... 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 (2.37-15) ... 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:armhf (17.0.10+7-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/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:armhf (17.0.10+7-1) ... Setting up default-jre (2:1.17-75) ... Setting up openjdk-17-jdk:armhf (17.0.10+7-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/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: Running cd /build/reproducible-path/biojava6-live-6.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../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 armhf 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 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 demo... [WARNING] Loading source files for package org.biojava.nbio.core.search.io... [WARNING] Loading source files for package org.biojava.nbio.core.search.io.blast... [WARNING] Loading source files for package org.biojava.nbio.core.alignment.matrices... [WARNING] Loading source files for package org.biojava.nbio.core.alignment.template... [WARNING] Loading source files for package org.biojava.nbio.core.alignment... [WARNING] Loading source files for package org.biojava.nbio.core.sequence... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.transcription... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.compound... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.template... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.views... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.loader... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.storage... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.reference... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.location.template... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.location... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.io... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.io.template... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.io.embl... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.io.util... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.edits... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.features... [WARNING] Loading source files for package org.biojava.nbio.core.exceptions... [WARNING] Loading source files for package org.biojava.nbio.core.util... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.10+7-Debian-1 [WARNING] Building tree for all the packages and classes... [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... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/Accessioned.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/AccessionID.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/AlignedSequence.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] /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... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/AminoAcidCompound.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/AminoAcidCompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/ArrayListProxySequenceReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/BasicSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/BitSequenceReader.html... [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... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.java:524: warning: invalid input: '<' [WARNING] * @exception IllegalArgumentException If readAheadLimit is < 0 [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/CaseInsensitiveCompound.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/CDSComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/CDSSequence.html... [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... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/util/ClasspathResource.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/CodonCompound.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/ComplementCompound.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/ComplementSequenceView.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/Compound.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/CompoundNotFoundException.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/CompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/CompoundTranslator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/ConcurrencyTools.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/CRC64Checksum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/DatabaseReferenceInterface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/DataSource.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/DBReferenceInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/DefaultAAIndexProvider.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/demo/DemoSixFrameTranslation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/DNACompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/DNASequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/DNASequence.DNAType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/DNASequenceCreator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/DNAToRNATranslator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/Edit.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/Edit.AbstractEdit.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/Edit.Delete.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/Edit.Insert.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/Edit.Substitute.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/EmblId.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/EmblReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/EmblRecord.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/EmblReference.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/Equals.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/ExonComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/ExonSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/FastaGeneWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/FastaHeaderFormatInterface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/FastaReader.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java:127: 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/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... 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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/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/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/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/SimpleSubstitutionMatrix.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/io/class-use/GenericFastaHeaderFormat.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericFastaHeaderParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/ABITrace.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaReaderHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/RNASequenceCreator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericGenbankHeaderFormat.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaWriterHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FileProxyRNASequenceCreator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaSequenceParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankWriterHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/ProteinSequenceCreator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankReaderHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericInsdcHeaderFormat.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/DNASequenceCreator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaGeneWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankSequenceParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/PlainFastaHeaderParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FileProxyProteinSequenceCreator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/BufferedReaderBytesRead.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/GenbankHeaderFormatInterface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/FastaHeaderFormatInterface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/SequenceParserInterface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/SequenceHeaderParserInterface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/SequenceCreatorInterface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblRecord.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblId.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblReference.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/util/class-use/ClasspathResource.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/util/class-use/IOUtils.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/util/class-use/IOUtils.ReaderProcessor.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.Substitute.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.Insert.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.Delete.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.AbstractEdit.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/DBReferenceInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/FeatureInterface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/Qualifier.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/QuantityFeature.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/FeatureRetriever.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/FeaturesKeyWordInterface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/DatabaseReferenceInterface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/FeatureDbReferenceInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/QualityFeature.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/AbstractFeature.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/TextFeature.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/class-use/CompoundNotFoundException.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/class-use/Messages.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... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/CRC64Checksum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/XMLWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/UncompressInputStream.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/InputStreamProvider.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/Hashcoder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/PrettyXMLWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/XMLHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/FileDownloadUtils.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/ConcurrencyTools.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/SoftHashMap.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/Equals.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/SequenceTools.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/FlatFileCache.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/SingleLinkageClusterer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/StringManipulationHelper.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.datastructures... [WARNING] Loading source files for package org.forester.test.examples... [WARNING] Loading source files for package org.forester.test... [WARNING] Loading source files for package org.forester.msa... [WARNING] Loading source files for package org.forester.msa_compactor... [WARNING] Loading source files for package org.forester.sdi... [WARNING] Loading source files for package org.forester.application... [WARNING] Loading source files for package org.forester.ws.hmmer... [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.protein... [WARNING] Loading source files for package org.forester.species... [WARNING] Loading source files for package org.forester.rio... [WARNING] Loading source files for package org.forester.analysis... 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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 demo... [WARNING] Loading source files for package org.biojava.nbio.alignment... 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[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityScorer.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/FractionalSimilarityInProfileScorer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/FractionalSimilarityScorer.html... [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... 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[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. 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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/class-use/MatrixAligner.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PairwiseSequenceScorer.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/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/class-use/RescoreRefiner.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/CallableProfileProfileAligner.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractPairwiseSequenceAligner.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractProfileProfileAligner.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/CallablePairwiseSequenceScorer.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... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PairInProfileScorer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/GuanUberbacher.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AnchoredPairwiseSequenceAligner.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.Subproblem.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.Anchor.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.Anchor.QueryIndexComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.Cut.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.Last.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/io/class-use/StockholmFileAnnotation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/io/class-use/StockholmFileAnnotation.StockholmFileAnnotationReference.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/io/class-use/StockholmFileParser.html... 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[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 demo... [WARNING] Loading source files for package org.biojava.nbio.structure.math... [WARNING] Loading source files for package org.biojava.nbio.structure... [WARNING] Loading source files for package org.biojava.nbio.structure.quaternary... [WARNING] Loading source files for package org.biojava.nbio.structure.ecod... [WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.axis... [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.utils... [WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.internal... [WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.misc... [WARNING] Loading source files for package org.biojava.nbio.structure.geometry... [WARNING] Loading source files for package org.biojava.nbio.structure.align... 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[WARNING] Loading source files for package org.biojava.nbio.structure.basepairs... [WARNING] Loading source files for package org.biojava.nbio.structure.io... [WARNING] Loading source files for package org.biojava.nbio.structure.io.cif... [WARNING] Loading source files for package org.biojava.nbio.structure.io.sifts... [WARNING] Loading source files for package org.biojava.nbio.structure.io.mmtf... [WARNING] Loading source files for package org.biojava.nbio.structure.io.util... [WARNING] Loading source files for package org.biojava.nbio.structure.jama... [WARNING] Loading source files for package org.biojava.nbio.structure.chem... [WARNING] Loading source files for package org.biojava.nbio.structure.contact... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.10+7-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... [WARNING] Loading source files for package org.jcolorbrewer.ui... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.10+7-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/class-use/ColorBrewer.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/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/ColorPaletteChooserDialog.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/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 demo... [WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.gui... [WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.jmolScript... [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.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.align.gui... [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.jmol... [WARNING] Loading source files for package org.biojava.nbio.structure.align.webstart... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.10+7-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/demo/class-use/DemoCE.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/DemoMultipleMC.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/DemoFATCAT.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/DemoShowBiolAssembly.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/class-use/DemoNWALignment.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/DemoSW3DAligner.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/DemoRotationAxis.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/DemoQuatSymmetryJmol.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/DemoStructureFromFasta.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/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/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/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/SymmetryCalc.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/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/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/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/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/ColorConverter.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/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/JmolSymmetryScriptGeneratorO.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/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/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/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/BiojavaJmol.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/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/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/JMatrixPanel.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/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/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/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/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/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/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/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/AlignedPosition.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/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/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/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/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/SequenceScalePanel.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/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/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/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/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/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/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/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/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/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/GradientPanel.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/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/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/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/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/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/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/AboutDialog.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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/MyTableRowSorter.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/AutoSuggestProvider.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/DefaultAutoSuggestProvider.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/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/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/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/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/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/AFPChainCoordManager.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/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/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/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/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/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/RasmolCommandListener.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/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/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/AligUIManager.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/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... [WARNING] Loading source files for package org.biojava.nbio.genome.homology... [WARNING] Loading source files for package org.biojava.nbio.genome.io.fastq... [WARNING] Loading source files for package org.biojava.nbio.genome.uniprot... [WARNING] Loading source files for package org.biojava.nbio.genome.parsers.twobit... [WARNING] Loading source files for package org.biojava.nbio.genome.parsers.cytoband... [WARNING] Loading source files for package org.biojava.nbio.genome.parsers.geneid... [WARNING] Loading source files for package org.biojava.nbio.genome.parsers.genename... [WARNING] Loading source files for package org.biojava.nbio.genome.parsers.gff... [WARNING] Loading source files for package org.biojava.nbio.genome.query... [WARNING] Loading source files for package org.biojava.nbio.genome.util... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.10+7-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/uniprot/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/serialized-form.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/class-use/GeneFeatureHelper.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/homology/class-use/GFF3FromUniprotBlastHits.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/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/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/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/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/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/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/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/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/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/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/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/Fastq.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/uniprot/class-use/UniprotToFasta.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/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/cytoband/class-use/Cytoband.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/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/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/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/ChromPos.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/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/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/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/Feature.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/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/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/FeatureHelper.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/query/class-use/OutputHitsGFF.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/class-use/SplitFasta.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/util/class-use/ProteinMappingTools.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.phosphosite... [WARNING] Loading source files for package org.biojava.nbio.protmod... [WARNING] Loading source files for package org.biojava.nbio.protmod.io... [WARNING] Loading source files for package org.biojava.nbio.protmod.structure... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.10+7-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/phosphosite/class-use/Dataset.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/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/ModificationCategory.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/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/Component.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/ModificationOccurrenceType.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/ModificationConditionImpl.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/ComponentXMLConverter.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/ModifiedCompoundXMLConverter.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/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/StructureUtil.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/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/StructureGroup.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 demo... [WARNING] Loading source files for package org.biojava.nbio.ws.alignment... [WARNING] Loading source files for package org.biojava.nbio.ws.alignment.qblast... [WARNING] Loading source files for package org.biojava.nbio.ws.hmmer... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.10+7-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/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/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentOutputProperties.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/RemotePairwiseAlignmentService.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/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/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/BlastAlignmentParameterEnum.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/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/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/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/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/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/BlastOutputFormatEnum.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/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 demo... [WARNING] Loading source files for package org.biojava.nbio.ronn... [WARNING] Loading source files for package org.biojava.nbio.data.sequence... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.10+7-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/demo/class-use/PredictDisorder.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/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/NullOutputStream.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/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/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/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 demo... [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] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.10+7-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/demo/class-use/BioJavaAADemo.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/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/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/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/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/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/AminoAcidComposition.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/ElementTable.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/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/Convert2Charge.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/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/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/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/Convert2Hydrophobicity.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/Utils.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/AminoAcidProperties.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/PeptidePropertiesImpl.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/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.figure... [WARNING] Loading source files for package org.biojava.nbio.survival.kaplanmeier.metadata... [WARNING] Loading source files for package org.biojava.nbio.survival.data... [WARNING] Loading source files for package org.biojava.nbio.survival.cox... [WARNING] Loading source files for package org.biojava.nbio.survival.cox.comparators... [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] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.10+7-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/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/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/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/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/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/CensorStatus.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/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/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/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/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/WorkSheet.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/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/SurvivalInfoHelper.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/CoxMethod.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/WaldTest.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/SurvFitInfo.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/CoxCoefficient.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/CoxMart.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/CoxInfo.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/SurvivalInfo.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/class-use/CoxVariables.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/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/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/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/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/CoxComparatorInterface.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/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/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/Chsolve2.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/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/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 demo... [WARNING] Loading source files for package org.biojava.nbio.ontology... [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] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.10+7-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/demo/class-use/ParseGO.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/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/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/OntologyException.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/InvalidTermException.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/OntologyOps.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/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/DefaultOps.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/AbstractTerm.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/OntologyFactory.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/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/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/KeyedWeakReference.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/WeakValueHashMap.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/utils/class-use/SmallMap.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/GOParser.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/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 17.0.10+7-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! 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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/survival/cox/comparators/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/matrix/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/stats/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/data/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/alignment/package-use.html... [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 [09:43 min] [INFO] biojava-core ....................................... SUCCESS [04:24 min] [INFO] biojava-forester ................................... SUCCESS [03:52 min] [INFO] biojava-alignment .................................. SUCCESS [01:21 min] [INFO] biojava-structure .................................. SUCCESS [03:40 min] [INFO] biojava-jcolorbrewer ............................... SUCCESS [ 36.286 s] [INFO] biojava-structure-gui .............................. SUCCESS [01:47 min] [INFO] biojava-genome ..................................... SUCCESS [01:08 min] [INFO] biojava-modfinder .................................. SUCCESS [ 46.247 s] [INFO] biojava-ws ......................................... SUCCESS [ 36.084 s] [INFO] biojava-protein-disorder ........................... SUCCESS [ 34.666 s] [INFO] biojava-aa-prop .................................... SUCCESS [01:26 min] [INFO] biojava-survival ................................... SUCCESS [01:43 min] [INFO] biojava-ontology ................................... SUCCESS [01:20 min] [INFO] biojava-protein-comparison-tool .................... SUCCESS [ 34.355 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 33:59 min [INFO] Finished at: 2024-03-27T17:13:07-12:00 [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 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.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: 0.472 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: 0.516 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: 13.255 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: 0.238 s - in org.biojava.nbio.core.search.io.blast.BlastXMLParserTest [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: 3.872 s - in org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest [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: 1.292 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest [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: 4.402 s - in org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest [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: 3.964 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest [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: 0.624 s - in org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest [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: 0.508 s - in org.biojava.nbio.core.alignment.SimpleSequencePairTest [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: 1.012 s - in org.biojava.nbio.core.alignment.SimpleProfileTest [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: 1.156 s - in org.biojava.nbio.core.TestAmbiguityCompoundSet [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: 0.292 s - in org.biojava.nbio.core.sequence.EditSequenceTest [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: 0.268 s - in org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest [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: 0.268 s - in org.biojava.nbio.core.sequence.SequenceViewTest [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: 1.484 s - in org.biojava.nbio.core.sequence.RNASequenceTest [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. [ERROR] Tests run: 12, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 3.64 s <<< FAILURE! - in org.biojava.nbio.core.sequence.TranslationTest [ERROR] translateBrca2 Time elapsed: 2.297 s <<< ERROR! org.junit.runners.model.TestTimedOutException: test timed out after 2000 milliseconds at app//org.biojava.nbio.core.sequence.TranslationTest.translateBrca2(TranslationTest.java:187) [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: 0.257 s - in 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] Running org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest [INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.693 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: 3.479 s - in org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest [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: 2.388 s - in org.biojava.nbio.core.sequence.ChromosomeSequenceTest [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: 1.408 s - in org.biojava.nbio.core.sequence.ProteinSequenceTest [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: 0.284 s - in org.biojava.nbio.core.sequence.JoiningSequenceReaderTest [INFO] Running org.biojava.nbio.core.sequence.TaxonomyIDTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.568 s - in org.biojava.nbio.core.sequence.TaxonomyIDTest [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: 2.33 s - in 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] Running org.biojava.nbio.core.sequence.location.TargetedLocationParserTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.221 s - in org.biojava.nbio.core.sequence.location.TargetedLocationParserTest [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: 0.324 s - in org.biojava.nbio.core.sequence.location.LocationTest [INFO] Running org.biojava.nbio.core.sequence.location.LocationParserTest [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.088 s - in org.biojava.nbio.core.sequence.location.LocationParserTest [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: 0.744 s - in org.biojava.nbio.core.sequence.ExonComparatorTest [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: 1.48 s - in org.biojava.nbio.core.sequence.TranscriptSequenceTest [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: 0.333 s - in org.biojava.nbio.core.sequence.TestSequenceEquals [INFO] Running org.biojava.nbio.core.sequence.io.embl.EmblReaderTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.208 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: 0.25 s - in org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest [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: 7.012 s - in org.biojava.nbio.core.sequence.io.ABITracerTest [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: 0.739 s - in org.biojava.nbio.core.sequence.io.FastaGeneWriterTest [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: 0.676 s - in org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest [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: 2.331 s - in org.biojava.nbio.core.sequence.io.GenbankWriterTest [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: 1.775 s - in org.biojava.nbio.core.sequence.io.GenbankReaderTest [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: 1.479 s - in org.biojava.nbio.core.sequence.io.GenbankCookbookTest [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: 1.687 s - in org.biojava.nbio.core.sequence.io.FastaReaderTest [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: 0.355 s - in org.biojava.nbio.core.sequence.io.FastaWriterTest [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: 1.832 s - in org.biojava.nbio.core.sequence.DNATest [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: 0.804 s - in org.biojava.nbio.core.sequence.ExonSequenceTest [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: 1.232 s - in org.biojava.nbio.core.sequence.GeneSequenceTest [INFO] Running org.biojava.nbio.core.sequence.StrandTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.551 s - in org.biojava.nbio.core.sequence.StrandTest [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: 2.384 s - in org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest [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: 0.403 s - in org.biojava.nbio.core.fasta.TestFASTAReader [INFO] Running org.biojava.nbio.core.util.CRC64ChecksumTest [INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.5 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: 2.868 s - in org.biojava.nbio.core.util.StringManipulationHelperTest [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: 4.16 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: 3.728 s - in org.biojava.nbio.core.util.SequenceToolsTest [INFO] Running org.biojava.nbio.core.util.HashcoderTest [INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.706 s - in org.biojava.nbio.core.util.HashcoderTest [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: 0.667 s - in org.biojava.nbio.core.util.SoftHashMapTest [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: 1.168 s - in org.biojava.nbio.core.util.FlatFileCacheTest [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: 0.724 s - in org.biojava.nbio.core.util.PrettyXMLWriterTest [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: 3.816 s - in org.biojava.nbio.core.util.XMLHelperTest [INFO] Running org.biojava.nbio.core.util.EqualsTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.128 s - in org.biojava.nbio.core.util.EqualsTest [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: 0.227 s - in org.biojava.nbio.core.util.TestUncompressInputStream [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: 0.707 s - in org.biojava.nbio.core.util.SingleLinkageClustererTest [INFO] [INFO] Results: [INFO] [ERROR] Errors: [ERROR] TranslationTest.translateBrca2:187 » TestTimedOut test timed out after 2000 mi... [INFO] [ERROR] Tests run: 501, Failures: 0, Errors: 1, Skipped: 15 [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava 6.1.0: [INFO] [INFO] biojava ............................................ SUCCESS [ 0.022 s] [INFO] biojava-core ....................................... FAILURE [12:10 min] [INFO] biojava-forester ................................... SKIPPED [INFO] biojava-alignment .................................. SKIPPED [INFO] biojava-structure .................................. SKIPPED [INFO] biojava-jcolorbrewer ............................... SKIPPED [INFO] biojava-structure-gui .............................. SKIPPED [INFO] biojava-genome ..................................... SKIPPED [INFO] biojava-modfinder .................................. SKIPPED [INFO] biojava-ws ......................................... SKIPPED [INFO] biojava-protein-disorder ........................... SKIPPED [INFO] biojava-aa-prop .................................... SKIPPED [INFO] biojava-survival ................................... SKIPPED [INFO] biojava-ontology ................................... SKIPPED [INFO] biojava-protein-comparison-tool .................... SKIPPED [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 12:13 min [INFO] Finished at: 2024-03-27T17:25:39-12:00 [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.22.3:test (default-test) on project biojava-core: There are test failures. [ERROR] [ERROR] Please refer to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/surefire-reports for the individual test results. [ERROR] Please refer to dump files (if any exist) [date].dump, [date]-jvmRun[N].dump and [date].dumpstream. [ERROR] -> [Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. [ERROR] Re-run Maven using the -X switch to enable full debug logging. [ERROR] [ERROR] For more information about the errors and possible solutions, please read the following articles: [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException [ERROR] [ERROR] After correcting the problems, you can resume the build with the command [ERROR] mvn -rf :biojava-core dh_auto_test: error: /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 returned exit code 1 make: *** [debian/rules:22: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package 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/27477 and its subdirectories Thu Mar 28 05:26:31 UTC 2024 W: No second build log, what happened?