Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/b/biojava5-live/biojava5-live_5.4.0+dfsg-4_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/biojava5-live-5.4.0+dfsg-44t_5oo6m/biojava5-live_5.4.0+dfsg-4_all.buildinfo Get source package info: biojava5-live=5.4.0+dfsg-4 Source URL: http://snapshot.notset.fr/mr/package/biojava5-live/5.4.0+dfsg-4/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.121 ant=1.10.12-1 ant-optional=1.10.12-1 autoconf=2.71-2 automake=1:1.16.5-1.3 autopoint=0.21-6 autotools-dev=20220109.1 base-files=12.2 base-passwd=3.5.52 bash=5.1-6+b1 binutils=2.38-4 binutils-common=2.38-4 binutils-x86-64-linux-gnu=2.38-4 bsdextrautils=2.38-4 bsdutils=1:2.38-4 build-essential=12.9 bzip2=1.0.8-5 ca-certificates=20211016 ca-certificates-java=20190909 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.3.0-1 dash=0.5.11+git20210903+057cd650a4ed-8 dctrl-tools=2.24-3+b1 debconf=1.5.79 debhelper=13.7.1 debianutils=5.7-0.2 default-jdk=2:1.11-72 default-jdk-doc=2:1.11-72 default-jdk-headless=2:1.11-72 default-jre=2:1.11-72 default-jre-headless=2:1.11-72 devscripts=2.22.1 dh-autoreconf=20 dh-strip-nondeterminism=1.13.0-1 diffutils=1:3.7-5 dirmngr=2.2.35-2 dpkg=1.21.7 dpkg-dev=1.21.7 dwz=0.14-1 fakeroot=1.28-1 file=1:5.41-4 findutils=4.9.0-3 fontconfig-config=2.13.1-4.4 fonts-dejavu-core=2.37-2 g++=4:11.2.0-2 g++-11=11.3.0-1 gcc=4:11.2.0-2 gcc-11=11.3.0-1 gcc-11-base=11.3.0-1 gcc-12-base=12.1.0-2 gettext=0.21-6 gettext-base=0.21-6 gnupg=2.2.35-2 gnupg-l10n=2.2.35-2 gnupg-utils=2.2.35-2 gpg=2.2.35-2 gpg-agent=2.2.35-2 gpg-wks-client=2.2.35-2 gpg-wks-server=2.2.35-2 gpgconf=2.2.35-2 gpgsm=2.2.35-2 gpgv=2.2.35-2 grep=3.7-1 groff-base=1.22.4-8 gzip=1.12-1 hostname=3.23 init-system-helpers=1.62 intltool-debian=0.35.0+20060710.5 java-common=0.72 java-wrappers=0.3 javahelper=0.78 junit=3.8.2-9 junit4=4.13.2-1 junit5=5.3.2-5 libacl1=2.3.1-1 libactivation-java=1.2.0-2 libantlr4-runtime-java=4.7.2-5 libaopalliance-java=20070526-6 libapache-pom-java=18-1 libapiguardian-java=1.1.0-3 libarchive-zip-perl=1.68-1 libargs4j-java=2.33-1.1 libasan6=11.3.0-1 libasm-java=9.3-1 libasound2=1.2.6.1-2+b1 libasound2-data=1.2.6.1-2 libassuan0=2.5.5-3 libatinject-jsr330-api-java=1.0+ds1-5 libatomic1=12.1.0-2 libattr1=1:2.5.1-1 libaudit-common=1:3.0.7-1 libaudit1=1:3.0.7-1+b1 libavahi-client3=0.8-5 libavahi-common-data=0.8-5 libavahi-common3=0.8-5 libb-hooks-op-check-perl=0.22-1+b4 libbatik-java=1.14-1 libbinutils=2.38-4 libblkid1=2.38-4 libbrotli1=1.0.9-2+b3 libbsd0=0.11.6-1 libbsh-java=2.0b4-20 libbz2-1.0=1.0.8-5 libc-bin=2.33-7 libc-dev-bin=2.33-7 libc6=2.33-7 libc6-dev=2.33-7 libcap-ng0=0.7.9-2.2+b2 libcap2=1:2.44-1 libcc1-0=12.1.0-2 libcdi-api-java=1.2-3 libciftools-java=3.0.1-1 libclass-method-modifiers-perl=2.13-1 libclass-xsaccessor-perl=1.19-3+b8 libcodemodel-java=2.6+jaxb2.3.0.1-10 libcom-err2=1.46.5-2 libcommons-beanutils-java=1.9.4-1 libcommons-cli-java=1.4-2 libcommons-codec-java=1.15-1 libcommons-collections3-java=3.2.2-2 libcommons-compress-java=1.21-1 libcommons-configuration-java=1.10-5 libcommons-digester-java=1.8.1-5 libcommons-exec-java=1.3-2 libcommons-io-java=2.11.0-2 libcommons-lang-java=2.6-9 libcommons-lang3-java=3.12.0-2 libcommons-logging-java=1.2-3 libcommons-math-java=2.2-8 libcommons-parent-java=43-1 libcommons-text-java=1.9-2 libcommons-validator-java=1:1.6-2 libcrypt-dev=1:4.4.27-1.1 libcrypt1=1:4.4.27-1.1 libctf-nobfd0=2.38-4 libctf0=2.38-4 libcups2=2.4.1op1-2 libdb5.3=5.3.28+dfsg1-0.9 libdbus-1-3=1.14.0-1 libdebconfclient0=0.262 libdebhelper-perl=13.7.1 libdevel-callchecker-perl=0.008-1+b3 libdom4j-java=2.1.3-1 libdoxia-core-java=1.7-2 libdoxia-java=1.7-2 libdoxia-sitetools-java=1.7.5-2 libdpkg-perl=1.21.7 libdrm-amdgpu1=2.4.110-1 libdrm-common=2.4.110-1 libdrm-nouveau2=2.4.110-1 libdrm-radeon1=2.4.110-1 libdrm2=2.4.110-1 libdtd-parser-java=1.2-1 libdynaloader-functions-perl=0.003-1.1 libedit2=3.1-20210910-1 libel-api-java=3.0.0-3 libelf1=0.187-1 libencode-locale-perl=1.05-1.1 libexec-maven-plugin-java=1.6.0-4.1 libexpat1=2.4.8-1 libfakeroot=1.28-1 libfastinfoset-java=1.2.12-3 libfastutil-java=8.5.8+dfsg-1 libffi8=3.4.2-4 libfile-dirlist-perl=0.05-2 libfile-homedir-perl=1.006-1 libfile-listing-perl=6.15-1 libfile-stripnondeterminism-perl=1.13.0-1 libfile-touch-perl=0.12-1 libfile-which-perl=1.27-1 libfontbox2-java=2.0.26-1 libfontconfig1=2.13.1-4.4 libfop-java=1:2.6-2 libfreetype6=2.12.1+dfsg-2 libgcc-11-dev=11.3.0-1 libgcc-s1=12.1.0-2 libgcrypt20=1.10.1-2 libgdbm-compat4=1.23-1 libgdbm6=1.23-1 libgeronimo-annotation-1.3-spec-java=1.3-1 libgeronimo-interceptor-3.0-spec-java=1.0.1-4 libgif7=5.2.1-2.4 libgl1=1.4.0-1 libgl1-mesa-dri=22.0.3-1 libglapi-mesa=22.0.3-1 libglib2.0-0=2.72.1-1 libglvnd0=1.4.0-1 libglx-mesa0=22.0.3-1 libglx0=1.4.0-1 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.4-2 libgomp1=12.1.0-2 libgoogle-gson-java=2.9.0-1 libgpg-error0=1.45-2 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.19.2-2+b2 libguava-java=29.0-6 libguice-java=4.2.3-2 libhamcrest-java=1.3-9 libharfbuzz0b=2.7.4-1+b1 libhawtjni-runtime-java=1.18-1 libhogweed6=3.7.3-1 libhtml-parser-perl=3.78-1 libhtml-tagset-perl=3.20-4 libhtml-tree-perl=5.07-2 libhttp-cookies-perl=6.10-1 libhttp-date-perl=6.05-1 libhttp-message-perl=6.36-1 libhttp-negotiate-perl=6.01-1 libhttpclient-java=4.5.13-3 libhttpcore-java=4.4.15-1 libicu71=71.1-3 libidn2-0=2.3.2-2 libimport-into-perl=1.002005-1 libinchi1=1.03+dfsg-4+b1 libio-html-perl=1.004-3 libio-pty-perl=1:1.15-2+b1 libio-socket-ssl-perl=2.074-2 libipc-run-perl=20200505.0-1 libisl23=0.24-2 libistack-commons-java=3.0.6-5 libitext1-java=1.4-7 libitext5-java=5.5.13.2-1 libitm1=12.1.0-2 libjackson2-annotations-java=2.13.0-1 libjackson2-core-java=2.13.0-2 libjackson2-databind-java=2.13.2.2-1 libjakarta-activation-java=2.0.0-1 libjansi-java=1.18-1 libjansi-native-java=1.8-1 libjaxb-api-java=2.3.1-1 libjaxb-java=2.3.0.1-10 libjaxen-java=1.1.6-4 libjaxp1.3-java=1.3.05-6 libjetty9-java=9.4.46-1 libjgrapht-java=1.5.1-3 libjgraphx-java=2.1.0.7-2 libjheaps-java=0.14-2 libjmol-java=14.32.56+dfsg-1 libjni-inchi-java=0.8+dfsg-6 libjni-inchi-jni=0.8+dfsg-6 libjpeg62-turbo=1:2.1.2-1 libjson-simple-java=2.3.0-1 libjsoup-java=1.14.3-1 libjsp-api-java=2.3.4-3 libjsr305-java=0.1~+svn49-11 libjtidy-java=7+svn20110807-5 libk5crypto3=1.19.2-2+b2 libkeyutils1=1.6.1-3 libkrb5-3=1.19.2-2+b2 libkrb5support0=1.19.2-2+b2 libksba8=1.6.0-2 liblcms2-2=2.12~rc1-2 libldap-2.5-0=2.5.12+dfsg-1 liblightcouch-java=0.0.6-1.1 libllvm14=1:14.0.3-2 liblog4j1.2-java=1.2.17-11 liblog4j2-java=2.17.2-1 liblsan0=12.1.0-2 liblwp-mediatypes-perl=6.04-1 liblwp-protocol-https-perl=6.10-1 liblz4-1=1.9.3-2 liblzma5=5.2.5-2.1 libmagic-mgc=1:5.41-4 libmagic1=1:5.41-4 libmaven-antrun-plugin-java=1.8-3 libmaven-archiver-java=3.2.0-2.1 libmaven-artifact-transfer-java=0.11.0-1 libmaven-assembly-plugin-java=3.1.0-1 libmaven-clean-plugin-java=3.1.0-1 libmaven-common-artifact-filters-java=3.1.1-1 libmaven-compiler-plugin-java=3.8.1-4 libmaven-dependency-analyzer-java=1.11.1-1 libmaven-dependency-plugin-java=3.1.1-1 libmaven-dependency-tree-java=3.0.1-1.1 libmaven-deploy-plugin-java=2.8.2-3 libmaven-enforcer-plugin-java=3.0.0~M2-1 libmaven-file-management-java=3.0.0-1 libmaven-filtering-java=3.1.1-1 libmaven-install-plugin-java=2.5.2-4.1 libmaven-invoker-java=3.0.0-1 libmaven-jar-plugin-java=3.1.2-1 libmaven-javadoc-plugin-java=3.0.1-4 libmaven-jaxb2-plugin-java=0.15.1-1 libmaven-parent-java=31-2 libmaven-plugin-tools-java=3.6.0-1 libmaven-reporting-api-java=3.0-1.1 libmaven-reporting-exec-java=1.4-3 libmaven-reporting-impl-java=3.0.0-2 libmaven-resolver-java=1.6.3-1 libmaven-resources-plugin-java=3.1.0-1 libmaven-shared-incremental-java=1.1-3 libmaven-shared-io-java=3.0.0-3 libmaven-shared-utils-java=3.3.0-1 libmaven-site-plugin-java=3.6-4 libmaven3-core-java=3.6.3-5 libmd0=1.0.4-1 libmmtf-java=1.0.11-1 libmodule-runtime-perl=0.016-1 libmongodb-java=3.6.3-2 libmoo-perl=2.005004-3 libmount1=2.38-4 libmpc3=1.2.1-2 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libmsgpack-java=0.9.1-1 libnaga-java=3.0+svn80-4 libncurses6=6.3+20220423-2 libncursesw6=6.3+20220423-2 libnet-http-perl=6.22-1 libnet-ssleay-perl=1.92-2 libnettle8=3.7.3-1 libnpth0=1.6-3 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnspr4=2:4.33-1 libnss3=2:3.77-1 libopentest4j-java=1.2.0-3 liboro-java=2.0.8a-14 libp11-kit0=0.24.1-1 libpam-modules=1.4.0-13 libpam-modules-bin=1.4.0-13 libpam-runtime=1.4.0-13 libpam0g=1.4.0-13 libparams-classify-perl=0.015-1+b4 libparboiled-java=1.1.7-2.1 libpcre2-8-0=10.40-1 libpcre3=2:8.39-14 libpcsclite1=1.9.7-1 libpegdown-java=1.6.0-1.1 libperl5.34=5.34.0-4 libpicocli-java=3.9.6-4 libpipeline1=1.5.6-1 libplexus-ant-factory-java=1.0~alpha2.1-4 libplexus-archiver-java=4.2.7-2 libplexus-bsh-factory-java=1.0~alpha7-4.1 libplexus-build-api-java=0.0.7-4 libplexus-cipher-java=2.0-1 libplexus-classworlds-java=2.6.0-1 libplexus-compiler-java=2.8.8-2 libplexus-component-annotations-java=2.1.1-1 libplexus-container-default-java=2.1.1-1 libplexus-container-default1.5-java=2.1.1-1 libplexus-i18n-java=1.0-beta-10-5 libplexus-interactivity-api-java=1.1-1 libplexus-interpolation-java=1.26-1 libplexus-io-java=3.3.1-1 libplexus-languages-java=0.9.10-2 libplexus-sec-dispatcher-java=2.0-3 libplexus-utils2-java=3.3.0-1 libplexus-velocity-java=1.2-3.1 libpng16-16=1.6.37-5 libprocps8=2:3.3.17-7+b1 libpython3-stdlib=3.10.4-1+b1 libpython3.10-minimal=3.10.4-4+b1 libpython3.10-stdlib=3.10.4-4+b1 libqdox-java=1.12.1-3 libqdox2-java=2.0.0-1 libquadmath0=12.1.0-2 libreadline8=8.1.2-1.2 librelaxng-datatype-java=1.0+ds1-3.1 librngom-java=2.3.0.1-10 librole-tiny-perl=2.002004-1 libsasl2-2=2.1.28+dfsg-6 libsasl2-modules-db=2.1.28+dfsg-6 libseccomp2=2.5.4-1 libselinux1=3.3-1+b2 libsemanage-common=3.3-1 libsemanage2=3.3-1+b2 libsensors-config=1:3.6.0-7 libsensors5=1:3.6.0-7 libsepol2=3.3-1 libservlet-api-java=4.0.1-2 libsigsegv2=2.14-1 libsisu-inject-java=0.3.4-2 libsisu-plexus-java=0.3.4-3 libslf4j-java=1.7.32-1 libsmartcols1=2.38-4 libsnappy-java=1.1.8.3-1 libsnappy-jni=1.1.8.3-1 libsnappy1v5=1.1.9-2 libsqlite3-0=3.38.5-1 libssl3=3.0.3-4 libstax-ex-java=1.7.8-3 libstdc++-11-dev=11.3.0-1 libstdc++6=12.1.0-2 libstreambuffer-java=1.5.4-1.1 libsub-override-perl=0.09-2 libsub-quote-perl=2.006006-1 libsurefire-java=2.22.3-1 libsystemd0=250.4-1 libtasn1-6=4.18.0-4 libtimedate-perl=2.3300-2 libtinfo6=6.3+20220423-2 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.7-4 libtry-tiny-perl=0.31-1 libtsan0=11.3.0-1 libtxw2-java=2.3.0.1-10 libubsan1=12.1.0-2 libuchardet0=0.0.7-1 libudev1=250.4-1 libunistring2=1.0-1 libunivocity-parsers-java=2.8.3-2 liburi-perl=5.10-1 libuuid1=2.38-4 libvecmath-java=1.5.2-7 libvelocity-tools-java=2.0-8 libvulkan1=1.3.204.1-2 libwagon-file-java=3.3.4-1 libwagon-http-java=3.3.4-1 libwagon-http-shaded-java=3.3.4-1 libwagon-provider-api-java=3.3.4-1 libwebsocket-api-java=1.1-2 libwww-perl=6.65-1 libwww-robotrules-perl=6.02-1 libx11-6=2:1.7.5-1 libx11-data=2:1.7.5-1 libx11-xcb1=2:1.7.5-1 libxalan2-java=2.7.2-4 libxau6=1:1.0.9-1 libxbean-reflect-java=4.5-8 libxcb-dri2-0=1.14-3 libxcb-dri3-0=1.14-3 libxcb-glx0=1.14-3 libxcb-present0=1.14-3 libxcb-shm0=1.14-3 libxcb-sync1=1.14-3 libxcb-xfixes0=1.14-3 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxerces2-java=2.12.2-1 libxext6=2:1.3.4-1 libxfixes3=1:6.0.0-1 libxi6=2:1.8-1 libxml-commons-external-java=1.4.01-5 libxml-commons-resolver1.1-java=1.2-11 libxml2=2.9.14+dfsg-1 libxml2-utils=2.9.14+dfsg-1 libxmlgraphics-commons-java=2.6-1 libxmlunit-java=1.6-2 libxrender1=1:0.9.10-1 libxshmfence1=1.3-1 libxsom-java=2.3.0.1-10 libxtst6=2:1.2.3-1 libxxf86vm1=1:1.1.4-1+b2 libxz-java=1.9-1 libz3-4=4.8.12-1+b1 libzstd1=1.5.2+dfsg-1 linux-libc-dev=5.17.6-1+b1 login=1:4.11.1+dfsg1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.10.2-1 maven=3.6.3-5 maven-debian-helper=2.6 maven-repo-helper=1.10 mawk=1.3.4.20200120-3+b1 media-types=8.0.0 ncurses-base=6.3+20220423-2 ncurses-bin=6.3+20220423-2 netbase=6.3 openjdk-11-doc=11.0.15+10-1 openjdk-11-jdk=11.0.15+10-1 openjdk-11-jdk-headless=11.0.15+10-1 openjdk-11-jre=11.0.15+10-1 openjdk-11-jre-headless=11.0.15+10-1 openssl=3.0.3-4 passwd=1:4.11.1+dfsg1-2 patch=2.7.6-7 patchutils=0.4.2-1 perl=5.34.0-4 perl-base=5.34.0-4 perl-modules-5.34=5.34.0-4 perl-openssl-defaults=7+b1 pinentry-curses=1.2.0-1 po-debconf=1.0.21+nmu1 procps=2:3.3.17-7+b1 python3=3.10.4-1+b1 python3-minimal=3.10.4-1+b1 python3.10=3.10.4-4+b1 python3.10-minimal=3.10.4-4+b1 readline-common=8.1.2-1.2 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sgml-base=1.30 sysvinit-utils=3.03-1 tar=1.34+dfsg-1 ucf=3.0043 unzip=6.0-26 util-linux=2.38-4 util-linux-extra=2.38-4 velocity=1.7-6 wdiff=1.2.2-2+b1 x11-common=1:7.7+23 xz-utils=5.2.5-2.1 zlib1g=1:1.2.11.dfsg-4 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20220527T032222Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220527T032222Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220531T150835Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220519T145256Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d biojava5-live=5.4.0+dfsg-4 && mkdir -p /build/biojava5-live-HFV3YZ && dpkg-source --no-check -x /*.dsc /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg && chown -R builduser:builduser /build/biojava5-live-HFV3YZ" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1653158577" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/biojava5-live-HFV3YZ /tmp/biojava5-live-5.4.0+dfsg-44t_5oo6m bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220519T145256Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.WUvppJLIBO as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.WUvppJLIBO Reading package lists... Building dependency tree... util-linux is already the newest version (2.38-4). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 135 kB of archives. After this operation, 406 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220519T145256Z unstable/main amd64 libfakeroot amd64 1.28-1 [48.2 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220519T145256Z unstable/main amd64 fakeroot amd64 1.28-1 [87.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 135 kB in 0s (1011 kB/s) Selecting previously unselected package libfakeroot:amd64. (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 ... 4629 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.28-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.28-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.28-1_amd64.deb ... Unpacking fakeroot (1.28-1) ... Setting up libfakeroot:amd64 (1.28-1) ... Setting up fakeroot (1.28-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-7) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20220527T032222Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220527T032222Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220531T150835Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220519T145256Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.WUvppJLIBO Get:1 http://snapshot.notset.fr/archive/debian/20220527T032222Z bookworm InRelease [130 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220531T150835Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20220519T145256Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20220527T032222Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220527T032222Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20220527T032222Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220527T032222Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20220527T032222Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220527T032222Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20220527T032222Z bookworm/main Sources [12.0 MB] Get:5 http://snapshot.notset.fr/archive/debian/20220527T032222Z bookworm/main amd64 Packages [11.5 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20220531T150835Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20220531T150835Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20220531T150835Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20220531T150835Z unstable/main amd64 Packages [12.5 MB] Fetched 36.2 MB in 30s (1217 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.WUvppJLIBO I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d biojava5-live=5.4.0+dfsg-4 && mkdir -p /build/biojava5-live-HFV3YZ && dpkg-source --no-check -x /*.dsc /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg && chown -R builduser:builduser /build/biojava5-live-HFV3YZ"' exec /tmp/mmdebstrap.WUvppJLIBO Reading package lists... NOTICE: 'biojava5-live' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/biojava5-live.git Please use: git clone https://salsa.debian.org/med-team/biojava5-live.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 19.3 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20220527T032222Z bookworm/main biojava5-live 5.4.0+dfsg-4 (dsc) [3311 B] Get:2 http://snapshot.notset.fr/archive/debian/20220527T032222Z bookworm/main biojava5-live 5.4.0+dfsg-4 (tar) [690 kB] Get:3 http://snapshot.notset.fr/archive/debian/20220527T032222Z bookworm/main biojava5-live 5.4.0+dfsg-4 (tar) [11.5 kB] Get:4 http://snapshot.notset.fr/archive/debian/20220527T032222Z bookworm/main biojava5-live 5.4.0+dfsg-4 (tar) [18.6 MB] Get:5 http://snapshot.notset.fr/archive/debian/20220527T032222Z bookworm/main biojava5-live 5.4.0+dfsg-4 (diff) [27.2 kB] Fetched 19.3 MB in 15s (1277 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'biojava5-live_5.4.0+dfsg-4.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting biojava5-live in /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg dpkg-source: info: unpacking biojava5-live_5.4.0+dfsg.orig.tar.gz dpkg-source: info: unpacking biojava5-live_5.4.0+dfsg.orig-forester.tar.gz dpkg-source: info: unpacking biojava5-live_5.4.0+dfsg.orig-jcolorbrewer.tar.gz dpkg-source: info: unpacking biojava5-live_5.4.0+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 faketest.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 wrong_version_in_dependency.patch dpkg-source: info: applying jmol_path_in_pom.patch dpkg-source: info: applying adapting_to_ciftools-java3.patch dpkg-source: info: applying adapting_to_jgrapht1.5.1.patch dpkg-source: info: applying remove_tests_needing_junitx.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1653158577" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.WUvppJLIBO dpkg-buildpackage: info: source package biojava5-live dpkg-buildpackage: info: source version 5.4.0+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Pierre Gruet dpkg-source --before-build . 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 -plibbiojava5-java jh_clean debian/rules override_dh_clean make[1]: Entering directory '/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg' debian/rules binary-indep dpkg: warning: --compare-versions used with obsolete relation operator '>' dh binary-indep --with javahelper dh_update_autotools_config -i dh_autoreconf -i debian/rules override_dh_auto_configure make[1]: Entering directory '/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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/\(VERSION_PACKAGE\)/\15.4.0+dfsg/; s/VERSION_PACKAGE\(.*\)+dfsg[0-9]*/\1/' debian/poms/pomForester.xml > biojava-forester/pom.xml sed 's/\(VERSION_PACKAGE\)/\15.4.0+dfsg/; s/VERSION_PACKAGE\(.*\)+dfsg[0-9]*/\1/' debian/poms/pomJcolorbrewer.xml > biojava-jcolorbrewer/pom.xml dh_auto_configure mh_patchpoms -plibbiojava5-java --debian-build --keep-pom-version --maven-repo=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0\+dfsg/debian/maven-repo make[1]: Leaving directory '/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg' jh_linkjars -i debian/rules override_dh_auto_build make[1]: Entering directory '/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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/biojava5-live-HFV3YZ/biojava5-live-5.4.0\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0\+dfsg/debian -Dmaven.repo.local=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0\+dfsg/debian/maven-repo --batch-mode package javadoc:jar javadoc:aggregate -DskipTests -Dnotimestamp=true -Dlocale=en_US [INFO] Scanning for projects... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.biojava:biojava-structure-gui:jar:5.4.0 [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] [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.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 5.4.0 [1/14] [INFO] --------------------------------[ pom ]--------------------------------- [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:3.0.1:jar (default-cli) @ biojava --- [WARNING] The POM for org.codehaus.plexus:plexus-interactivity-api:jar:debian is invalid, transitive dependencies (if any) will not be available, enable debug logging for more details [INFO] Not executing Javadoc as the project is not a Java classpath-capable package [INFO] [INFO] ----------------------< org.biojava:biojava-core >---------------------- [INFO] Building biojava-core 5.4.0 [2/14] [INFO] --------------------------------[ jar ]--------------------------------- [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:3.1.0:resources (default-resources) @ biojava-core --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 24 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-core --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 187 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/target/classes [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java: Some input files use or override a deprecated API. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java: Recompile with -Xlint:deprecation for details. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.java: Some input files use unchecked or unsafe operations. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ biojava-core --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 46 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ biojava-core --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 34 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/target/test-classes [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java: Some input files use or override a deprecated API. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java: Recompile with -Xlint:deprecation for details. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/test/java/org/biojava/nbio/core/search/io/HspTest.java: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/test/java/org/biojava/nbio/core/search/io/HspTest.java uses unchecked or unsafe operations. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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:3.1.2:jar (default-jar) @ biojava-core --- [INFO] Building jar: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/target/biojava-core-5.4.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.0.1:jar (default-cli) @ biojava-core --- [INFO] Adding the --ignore-source-errors option [INFO] Loading source files for package demo... Loading source files for package org.biojava.nbio.core.alignment... Loading source files for package org.biojava.nbio.core.alignment.matrices... Loading source files for package org.biojava.nbio.core.alignment.template... Loading source files for package org.biojava.nbio.core.exceptions... Loading source files for package org.biojava.nbio.core.search.io... Loading source files for package org.biojava.nbio.core.search.io.blast... Loading source files for package org.biojava.nbio.core.sequence... Loading source files for package org.biojava.nbio.core.sequence.compound... Loading source files for package org.biojava.nbio.core.sequence.edits... Loading source files for package org.biojava.nbio.core.sequence.features... Loading source files for package org.biojava.nbio.core.sequence.io... Loading source files for package org.biojava.nbio.core.sequence.io.embl... Loading source files for package org.biojava.nbio.core.sequence.io.template... Loading source files for package org.biojava.nbio.core.sequence.io.util... Loading source files for package org.biojava.nbio.core.sequence.loader... Loading source files for package org.biojava.nbio.core.sequence.location... Loading source files for package org.biojava.nbio.core.sequence.location.template... Loading source files for package org.biojava.nbio.core.sequence.reference... Loading source files for package org.biojava.nbio.core.sequence.storage... Loading source files for package org.biojava.nbio.core.sequence.template... Loading source files for package org.biojava.nbio.core.sequence.transcription... Loading source files for package org.biojava.nbio.core.sequence.views... Loading source files for package org.biojava.nbio.core.util... Constructing Javadoc information... Standard Doclet version 11.0.15 Building tree for all the packages and classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/demo/DemoSixFrameTranslation.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/demo/ParseFastaFileDemo.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/SimpleAlignedSequence.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/SimpleProfile.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/SimpleProfilePair.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/SimpleSequencePair.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/AAindexFactory.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/AAIndexFileParser.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/AAIndexProvider.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/DefaultAAIndexProvider.html... 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invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:101: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:109: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:117: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:125: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:133: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:141: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:149: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:157: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:165: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:173: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:181: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:189: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:197: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:77: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:85: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:93: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:101: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:109: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:117: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:125: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:133: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:141: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:149: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:157: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:165: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:173: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:181: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:189: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:197: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:41: warning - 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invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:157: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:157: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:41: warning - Tag @link: reference not found: Aligner [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:61: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:61: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:104: warning - 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invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:239: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:44: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:44: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:53: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:53: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:62: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:62: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:71: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:71: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:80: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:80: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:89: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:89: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SubstitutionMatrix.java:106: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/AccessionID.java:31: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java:34: warning - invalid usage of tag {@link http://www.sequenceontology.org/gff3.shtml [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java:85: warning - invalid usage of tag {@link http://www.sequenceontology.org/gff3.shtml [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java:86: warning - 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[WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ChromosomeSequence.java:132: warning - @param argument "end" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java:63: warning - @param argument "parentDNASequence" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TranscriptSequence.java:249: warning - @param argument "startCodonSequence" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TranscriptSequence.java:264: warning - @param argument "stopCodonSequence" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/edits/Edit.java:279: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.java:524: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java:141: 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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:98: warning - @inheritDoc used but setAccession(String) does not override or implement any method. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:133: warning - @inheritDoc used but setComment(String) does not override or implement any method. [INFO] Building jar: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/target/biojava-core-5.4.0-javadoc.jar [INFO] [INFO] --------------------< org.biojava:biojava-forester >-------------------- [INFO] Building biojava-forester 5.4.0 [3/14] [INFO] --------------------------------[ jar ]--------------------------------- [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:3.1.0:resources (default-resources) @ biojava-forester --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-forester --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 359 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/target/classes [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/MainFrame.java: Some input files use or override a deprecated API. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/MainFrame.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ biojava-forester --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1: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:3.1.2:jar (default-jar) @ biojava-forester --- [INFO] Building jar: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/target/biojava-forester-5.4.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.0.1:jar (default-cli) @ biojava-forester --- [INFO] Adding the --ignore-source-errors option [INFO] Loading source files for package org.forester.test... Loading source files for package org.forester.test.examples... Loading source files for package org.forester.evoinference... Loading source files for package org.forester.evoinference.distance... Loading source files for package org.forester.evoinference.matrix.character... Loading source files for package org.forester.evoinference.matrix.distance... Loading source files for package org.forester.evoinference.parsimony... Loading source files for package org.forester.evoinference.tools... Loading source files for package org.forester.msa... Loading source files for package org.forester.sdi... Loading source files for package org.forester.ws.hmmer... Loading source files for package org.forester.ws.wabi... Loading source files for package org.forester.ws.seqdb... Loading source files for package org.forester.applications... Loading source files for package org.forester.pccx... Loading source files for package org.forester.go... Loading source files for package org.forester.go.etc... 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Loading source files for package org.forester.io.parsers.tol... Loading source files for package org.forester.io.parsers.nhx... Loading source files for package org.forester.io.parsers... Loading source files for package org.forester.io.parsers.util... Loading source files for package org.forester.msa_compactor... Loading source files for package org.forester.archaeopteryx.webservices... Loading source files for package org.forester.archaeopteryx.tools... Loading source files for package org.forester.archaeopteryx... Loading source files for package org.forester.archaeopteryx.phylogeny.data... Loading source files for package org.forester.tools... Loading source files for package org.forester.datastructures... Loading source files for package org.forester.analysis... Constructing Javadoc information... Standard Doclet version 11.0.15 Building tree for all the packages and classes... 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Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/help-doc.html... 50 warnings [WARNING] Javadoc Warnings [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/application/support_transfer.java:55: warning - Parameter "args" is documented more than once. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/application/support_transfer.java:60: warning - Parameter "args" is documented more than once. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/application/support_transfer.java:62: warning - Parameter "args" is documented more than once. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/ArchaeopteryxE.java:544: 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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/ArchaeopteryxE.java:574: 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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/io/parsers/HmmPfamOutputParser.java:618: warning - @param argument "ignored_engulfed_domains" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/io/parsers/HmmscanPerDomainTableParser.java:604: warning - @param argument "ignored_engulfed_domains" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/io/parsers/util/PhylogenyParserException.java:48: warning - @param argument "arg0" is not a parameter name. [WARNING] javadoc: warning - invalid usage of tag < [WARNING] javadoc: warning - invalid usage of tag > [WARNING] javadoc: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/pccx/ScoringMethodForExternalNode.java:47: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/pccx/ScoringMethodForExternalNode.java:47: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/pccx/ScoringMethodForExternalNode.java:48: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/pccx/ScoringMethodForExternalNode.java:55: warning - @param argument "annotate_phylogeny" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/phylogeny/Phylogeny.java:90: warning - @param argument "n" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/phylogeny/PhylogenyNode.java:99: warning - @param argument "n" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/phylogeny/PhylogenyNode.java:292: warning - @param argument "n" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/phylogeny/PhylogenyNode.java:778: warning - @param argument "n" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/phylogeny/data/PhylogenyData.java:54: warning - @param argument "PhylogenyData" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/phylogeny/iterators/ExternalForwardIterator.java:42: warning - @param argument "tree" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/phylogeny/iterators/PostorderTreeIterator.java:45: warning - @param argument "t" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/sdi/SDI.java:85: warning - Tag @see: reference not found: #infer(boolean) [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/sdi/SDIR.java:80: warning - Tag @see: reference not found: #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean) [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/sdi/SDIR.java:101: warning - Tag @see: reference not found: #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean) [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/sdi/SDIR.java:117: warning - Tag @see: reference not found: #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean) [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/sdi/SDIR.java:130: warning - Tag @see: reference not found: #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean) [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/sdi/SDIR.java:146: warning - Tag @see: reference not found: #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean) [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/surfacing/DomainSimilarity.java:255: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/surfacing/DomainSimilarity.java:255: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/surfacing/SurfacingUtil.java:592: warning - @param argument "protein_length_stats_by_dc" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/surfacing/SurfacingUtil.java:672: warning - @param argument "consider_directedness_and_adjacency_for_bin_combinations" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/surfacing/SurfacingUtil.java:673: warning - @param argument "all_binary_domains_combination_gained" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/tools/TreeSplitMatrix.java:73: warning - @param argument "target" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/util/ForesterUtil.java:1117: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/util/ForesterUtil.java:1120: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/util/ForesterUtil.java:1123: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/util/ForesterUtil.java:1117: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/util/ForesterUtil.java:1120: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/util/ForesterUtil.java:1123: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/ws/wabi/TxSearch.java:41: warning - invalid usage of tag &mode [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/util/ForesterUtil.java:1117: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/util/ForesterUtil.java:1120: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/util/ForesterUtil.java:1123: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/util/ForesterUtil.java:1117: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/util/ForesterUtil.java:1120: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/util/ForesterUtil.java:1123: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/util/ForesterUtil.java:1117: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/util/ForesterUtil.java:1120: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/util/ForesterUtil.java:1123: warning - invalid usage of tag > [INFO] Building jar: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/target/biojava-forester-5.4.0-javadoc.jar [INFO] [INFO] -------------------< org.biojava:biojava-alignment >-------------------- [INFO] Building biojava-alignment 5.4.0 [4/14] [INFO] --------------------------------[ jar ]--------------------------------- [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:3.1.0:resources (default-resources) @ biojava-alignment --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-alignment --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 53 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/classes [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java uses or overrides a deprecated API. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ biojava-alignment --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 11 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ biojava-alignment --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 24 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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:3.1.2:jar (default-jar) @ biojava-alignment --- [INFO] Building jar: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/biojava-alignment-5.4.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.0.1:jar (default-cli) @ biojava-alignment --- [INFO] Adding the --ignore-source-errors option [ERROR] Error fetching link: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/package-list. Ignored it. [ERROR] Error fetching link: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/package-list. Ignored it. [INFO] Loading source files for package demo... Loading source files for package org.biojava.nbio.alignment... Loading source files for package org.biojava.nbio.alignment.io... Loading source files for package org.biojava.nbio.alignment.routines... Loading source files for package org.biojava.nbio.alignment.template... 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Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/CallablePairwiseSequenceScorer.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/GapPenalty.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/GapPenalty.Type.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/GuideTreeNode.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/HierarchicalClusterer.html... 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Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/ProfileProfileScorer.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/RescoreRefiner.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/Scorer.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/Comparison.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/DistanceMatrixCalculator.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/DistanceTreeEvaluator.html... 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Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/constant-values.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/serialized-form.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/demo/class-use/CookbookMSA.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/demo/class-use/DemoAlignProteins.html... 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Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/GapPenalty.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/GapPenalty.Type.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/GuideTreeNode.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/HierarchicalClusterer.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/MatrixAligner.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PairInProfileScorer.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PairwiseSequenceAligner.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PairwiseSequenceScorer.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PartitionRefiner.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/ProfileProfileAligner.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/ProfileProfileScorer.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/RescoreRefiner.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/Scorer.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/class-use/Comparison.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/class-use/DistanceMatrixCalculator.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/class-use/DistanceTreeEvaluator.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/class-use/ForesterWrapper.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/class-use/TreeConstructor.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/class-use/TreeConstructorType.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/class-use/TreeType.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/demo/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/io/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/package-use.html... Building index for all the packages and classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/overview-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/index-all.html... Building index for all classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/allclasses-index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/allpackages-index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/deprecated-list.html... Building index for all classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/allclasses.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/allclasses.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/overview-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/help-doc.html... 57 warnings [WARNING] Javadoc Warnings [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:125: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:206: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:312: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:542: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:615: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityScorer.java:37: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityScorer.java:37: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java:44: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileAnnotation.java:163: warning - @param argument "dbReference" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:45: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:70: warning - @param argument "cutsPerSection" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:83: warning - @param argument "cutsPerSection" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/GuanUberbacher.java:37: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java:49: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.java:40: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java:46: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/Aligner.java:35: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallablePairwiseSequenceAligner.java:37: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java:36: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java:37: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/MatrixAligner.java:33: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/MatrixAligner.java:34: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PairInProfileScorer.java:35: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PairwiseSequenceAligner.java:35: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:34: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:35: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:34: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:35: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileScorer.java:35: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:36: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:37: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java:41: warning - @param argument "s1" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java:43: warning - @param argument "s2" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/phylo/DistanceMatrixCalculator.java:119: warning - invalid usage of tag {@link #pamDistance(MultipleSequenceAlignment [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning - Tag @link: reference not found: Profile [INFO] Building jar: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/biojava-alignment-5.4.0-javadoc.jar [INFO] [INFO] -------------------< org.biojava:biojava-structure >-------------------- [INFO] Building biojava-structure 5.4.0 [5/14] [INFO] --------------------------------[ jar ]--------------------------------- [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 [WARNING] The artifact com.sun.xml.bind:jaxb-impl:jar:debian has been relocated to org.glassfish.jaxb:jaxb-runtime:jar:debian [WARNING] The artifact javax.activation:activation:jar:debian has been relocated to com.sun.activation:javax.activation:jar:debian [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ biojava-structure --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 3 resources [INFO] Copying 61 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-structure --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 522 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/classes [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java: Some input files use or override a deprecated API. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ biojava-structure --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 93 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ biojava-structure --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 104 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/test-classes [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityHeuristics.java: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityHeuristics.java uses or overrides a deprecated API. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityHeuristics.java: Recompile with -Xlint:deprecation for details. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/test/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImplTest.java: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/test/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImplTest.java uses unchecked or unsafe operations. 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Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/StructAsym.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/StructConn.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/StructKeywords.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/StructNcsOper.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/StructRef.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/StructRefSeq.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/StructRefSeqDif.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/StructSite.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/StructSiteGen.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/Symmetry.html... 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Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsChainToUniprotMapping.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsEntity.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsMappingProvider.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsResidue.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsSegment.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsXMLParser.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/util/class-use/PDBTemporaryStorageUtils.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/util/class-use/PDBTemporaryStorageUtils.LinkRecord.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/jama/class-use/CholeskyDecomposition.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/jama/class-use/EigenvalueDecomposition.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/jama/class-use/LUDecomposition.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/jama/class-use/Maths.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/jama/class-use/Matrix.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/jama/class-use/QRDecomposition.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/jama/class-use/SingularValueDecomposition.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/math/class-use/SparseSquareMatrix.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/math/class-use/SparseVector.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/math/class-use/SymbolTable.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/BioAssemblyInfo.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/BioAssemblyTools.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/BiologicalAssemblyBuilder.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/BiologicalAssemblyTransformation.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/CartesianProduct.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/OperatorResolver.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/OrderedPair.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/rcsb/class-use/GetRepresentatives.html... 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Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/rcsb/class-use/RCSBMacromolecule.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/rcsb/class-use/RCSBPolymer.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/rcsb/class-use/RCSBTaxonomy.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/rcsb/class-use/RCSBUpdates.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/rcsb/class-use/ReadUtils.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/Astral.html... 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Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/C2RotationSolver.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/HelicalRepeatUnit.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/Helix.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/HelixExtender.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/HelixLayers.html... 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Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/overview-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/help-doc.html... 100 warnings [WARNING] Javadoc Warnings [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/demo/DemoChangeChemCompProvider.java:39: warning - Tag @link: reference not found: FileParsingParameters#setLoadChemCompInfo(boolean) [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java:262: warning - @return tag cannot be used in method with void return type. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java:51: warning - Tag @link: reference not found: #toString() [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/Bond.java:29: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/Bond.java:29: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java:30: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java:30: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/BondType.java:26: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/BondType.java:26: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java:330: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java:438: warning - invalid usage of tag {@value #org.biojava.nbio.structure.StructureTools.RATIO_RESIDUES_TO_TOTAL [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java:265: warning - Tag @link: reference not found: #setId() [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java:265: warning - Tag @link: reference not found: #setId() [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java:288: warning - {@value org.biojava.nbio.structure.io.PDBFileReader#LOAD_CHEM_COMP_PROPERTY} (referenced by @value tag) is an unknown reference. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java:379: warning - Tag @link: reference not found: FileParsingParameters#setLoadChemCompInfo(boolean) [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java:438: warning - invalid usage of tag {@value #org.biojava.nbio.structure.StructureTools.RATIO_RESIDUES_TO_TOTAL [WARNING] javadoc: warning - invalid usage of tag {@value #org.biojava.nbio.structure.StructureTools.RATIO_RESIDUES_TO_TOTAL [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java:288: warning - {@value org.biojava.nbio.structure.io.PDBFileReader#LOAD_CHEM_COMP_PROPERTY} (referenced by @value tag) is an unknown reference. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java:379: warning - Tag @link: reference not found: FileParsingParameters#setLoadChemCompInfo(boolean) [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java:438: warning - invalid usage of tag {@value #org.biojava.nbio.structure.StructureTools.RATIO_RESIDUES_TO_TOTAL [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java:51: warning - Tag @link: reference not found: #toString() [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java:54: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java:55: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java:56: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java:68: warning - Tag @link: reference not found: #getReplacement(String, boolean)getReplacement(pdbId, true) [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java:74: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java:74: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java:95: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java:95: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java:120: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java:130: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java:143: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java:51: warning - Tag @link: reference not found: #toString() [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java:66: warning - @param argument "AtomCache" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java:86: warning - Tag @link: reference not found: #setStrictSCOP(boolean) [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java:138: warning - invalid usage of tag {@link http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java:164: warning - invalid usage of tag {@link http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java:583: warning - @param argument "g" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java:171: warning - @param argument "input" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java:285: warning - @param argument "AtomCache" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java:51: warning - Tag @link: reference not found: #toString() [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java:64: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java:64: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeParameters.java:368: warning - @param argument "maxNrIterationsForOptimization" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/OptimalCECPMain.java:461: warning - Tag @link: reference not found: #alignHeuristic(Atom[], Atom[], Object) [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/PdbPair.java:29: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java:70: warning - Tag @see: reference not found: #getNamethe name. e.g. 4hhb, 4hhb.A, d4hhba_, PDP:4HHBAa etc. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java:55: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java:56: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java:57: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java:57: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java:1310: warning - Tag @link: reference not found: org.biojava.nbio.structure.gui.JMatrixPanel [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java:75: warning - Tag @see: reference not found: #setAlignRes() [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java:111: warning - Tag @see: reference not found: #updateCoreLength() [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java:75: warning - Tag @see: reference not found: #setAlignRes() [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java:111: warning - Tag @see: reference not found: #updateCoreLength() [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java:150: warning - Tag @see: reference not found: #updateDistanceMatrix() [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java:158: warning - Tag @see: reference not found: #setMultipleAlignments() [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java:168: warning - Tag @see: reference not found: #setMultipleAlignments() [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java:70: warning - Tag @return cannot be used in constructor documentation. It can only be used in the following types of documentation: method. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java:91: warning - Tag @return cannot be used in constructor documentation. It can only be used in the following types of documentation: method. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java:105: warning - Tag @return cannot be used in constructor documentation. It can only be used in the following types of documentation: method. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java:156: warning - Tag @return cannot be used in constructor documentation. It can only be used in the following types of documentation: method. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java:150: warning - Tag @see: reference not found: #updateDistanceMatrix() [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java:158: warning - Tag @see: reference not found: #setMultipleAlignments() [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java:168: warning - Tag @see: reference not found: #setMultipleAlignments() [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java:55: warning - Tag @return cannot be used in constructor documentation. It can only be used in the following types of documentation: method. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java:67: warning - Tag @return cannot be used in constructor documentation. It can only be used in the following types of documentation: method. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java:89: warning - Tag @return cannot be used in constructor documentation. It can only be used in the following types of documentation: method. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcMain.java:94: warning - @param argument "pairwise" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/CoreSuperimposer.java:71: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java:307: warning - @param argument "reference" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java:311: warning - @param argument "alignment" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java:468: warning - @param argument "alignment" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java:481: warning - @param argument "multAln" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java:570: warning - @param argument "alignment" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java:195: warning - @param argument "afpChain" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java:290: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/ReferenceSuperimposer.java:69: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:506: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:506: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:271: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:150: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:151: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:152: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:153: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:271: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:290: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:306: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:317: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:423: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:474: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:474: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:474: warning - invalid usage of tag > [INFO] Building jar: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/biojava-structure-5.4.0-javadoc.jar [INFO] [INFO] ------------------< org.biojava:biojava-jcolorbrewer >------------------ [INFO] Building biojava-jcolorbrewer 5.4.0 [6/14] [INFO] --------------------------------[ jar ]--------------------------------- [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:3.1.0:resources (default-resources) @ biojava-jcolorbrewer --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-jcolorbrewer --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 7 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/classes [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java uses or overrides a deprecated API. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ biojava-jcolorbrewer --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1: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:3.1.2:jar (default-jar) @ biojava-jcolorbrewer --- [INFO] Building jar: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/biojava-jcolorbrewer-5.4.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.0.1:jar (default-cli) @ biojava-jcolorbrewer --- [INFO] Adding the --ignore-source-errors option [INFO] Loading source files for package org.jcolorbrewer... Loading source files for package org.jcolorbrewer.ui... Constructing Javadoc information... Standard Doclet version 11.0.15 Building tree for all the packages and classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ColorBrewer.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/ColorPaletteChooserDialog.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/ColorPanelSelectionModel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/DivergingColorPalettePanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/PaletteIcon.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/QualitativeColorPalettePanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/SequentialColorPalettePanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/package-summary.html... 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Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/DivergingColorPalettePanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/QualitativeColorPalettePanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/ColorPaletteChooserDialog.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/ColorPanelSelectionModel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/PaletteIcon.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/package-use.html... Building index for all the packages and classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/apidocs/overview-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/apidocs/index-all.html... Building index for all classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/apidocs/allclasses-index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/apidocs/allpackages-index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/apidocs/deprecated-list.html... Building index for all classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/apidocs/allclasses.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/apidocs/allclasses.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/apidocs/index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/apidocs/overview-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/apidocs/help-doc.html... 2 warnings [WARNING] Javadoc Warnings [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java:82: warning - Tag @see: reference not found: ColorChooserDialog [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java:436: warning - @param argument "color" is not a parameter name. [INFO] Building jar: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/biojava-jcolorbrewer-5.4.0-javadoc.jar [INFO] [INFO] -----------------< org.biojava:biojava-structure-gui >------------------ [INFO] Building biojava-structure-gui 5.4.0 [7/14] [INFO] --------------------------------[ jar ]--------------------------------- [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:3.1.0:resources (default-resources) @ biojava-structure-gui --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 49 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-structure-gui --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 139 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/classes [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.java: Some input files use or override a deprecated API. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.java: Recompile with -Xlint:deprecation for details. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/ScaleableMatrixPanel.java: Some input files use unchecked or unsafe operations. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/ScaleableMatrixPanel.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ biojava-structure-gui --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ biojava-structure-gui --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 5 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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:3.1.2:jar (default-jar) @ biojava-structure-gui --- [INFO] Building jar: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/biojava-structure-gui-5.4.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.0.1:jar (default-cli) @ biojava-structure-gui --- [INFO] Adding the --ignore-source-errors option [ERROR] Error fetching link: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/package-list. Ignored it. [ERROR] Error fetching link: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/package-list. Ignored it. [ERROR] Error fetching link: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/apidocs/package-list. Ignored it. [INFO] Loading source files for package demo... Loading source files for package org.biojava.nbio.structure.align.gui... Loading source files for package org.biojava.nbio.structure.align.gui.aligpanel... Loading source files for package org.biojava.nbio.structure.align.gui.autosuggest... Loading source files for package org.biojava.nbio.structure.align.gui.jmol... Loading source files for package org.biojava.nbio.structure.align.webstart... Loading source files for package org.biojava.nbio.structure.gui... Loading source files for package org.biojava.nbio.structure.gui.events... Loading source files for package org.biojava.nbio.structure.gui.util... Loading source files for package org.biojava.nbio.structure.gui.util.color... Loading source files for package org.biojava.nbio.structure.symmetry.gui... Loading source files for package org.biojava.nbio.structure.symmetry.jmolScript... Constructing Javadoc information... Standard Doclet version 11.0.15 Building tree for all the packages and classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/AFPFromFasta.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/AlignmentGuiDemo.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/CookBook.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoAlignmentFromFasta.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoCE.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoCeSymm.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoFATCAT.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoMultipleMC.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoNWALignment.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoQuatSymmetryJmol.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoRotationAxis.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoShowBiolAssembly.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoShowCATHDomain.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoShowLargeAssembly.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoShowValidationResults.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoStructureFromFasta.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoSW3DAligner.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/ShowStructureInJmol.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/WebStartClientDemo.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/AboutDialog.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/AlignmentCalc.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/AlignmentCalcDB.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/AlignmentCalculationRunnable.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/AlignmentGui.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/AlignmentTextPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/ChooseDirAction.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/ConfigPDBInstallPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/DBResultTable.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/DBSearchGUI.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/DisplayAFP.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/DotPlotPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/GUIAlignmentProgressListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/GUIFarmJobRunnable.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/HelpDialog.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/JPrintPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MemoryMonitor.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MemoryMonitor.Surface.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MenuCreator.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MenuCreator.DotPlotListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MultipleAlignmentCalc.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MultipleAlignmentGUI.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MultipleAlignmentJmolDisplay.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MyAlignmentLoadListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MyDistMaxListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MyExportListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MyOpenPdbFileListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MySaveFileListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MyTableRowSorter.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/ParameterGUI.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/SelectPDBPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/ShowPDBIDListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/StructureAlignmentDisplay.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/StructureLoaderThread.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/SystemInfo.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/AFPChainCoordManager.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/AligPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/AligPanelMouseMotionListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAlignmentCoordManager.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanelMouseMotionListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/MultipleStatusDisplay.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/StatusDisplay.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/AutoSuggestProvider.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/DefaultAutoSuggestProvider.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/SCOPAutoSuggestProvider.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/AtomInfo.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/AtomInfoParser.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.JmolLoggerAdapter.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/JmolTools.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/MyJmolStatusListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/AligUIManager.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/BrowserOpener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/ConfigXMLHandler.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/JNLPProxy.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/WebStartDBSearch.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/WebStartDBSearchResults.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/WebStartMain.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/BiojavaJmol.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/JMatrixPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/JmolViewerImpl.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/RenderStyle.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/ScaleableMatrixPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/ScaleableMatrixPanel.GradientRenderer.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/Selection.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/SelectionImpl.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/SequenceDisplay.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/StructureViewer.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/WrapLayout.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/AlignmentPositionListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/JmolAlignedPositionListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/AlignedPosition.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/AlignmentCalc.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/CoordManager.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/MenuCreator.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/PDBDirPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/PDBServerPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/PDBUploadPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/ScopInstallationInstance.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/ScopSelectPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/SelectMultiplePanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/SequenceMouseListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/SequenceScalePanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/StructurePairSelector.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/ColorInterpolator.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/ColorUtils.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/ContinuousColorMapper.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/ContinuousColorMapperTransform.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/DefaultMatrixMapper.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/GradientMapper.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/GradientPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/HSVColorSpace.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/LinearColorInterpolator.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/LinearColorInterpolator.InterpolationDirection.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/LogColorMapper.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/SqrtColorMapper.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/SymmetryCalc.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/SymmetryGui.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/SymmetryListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/ColorConverter.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGenerator.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorC1.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorCn.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorDn.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorI.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorO.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorT.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/constant-values.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/serialized-form.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/AFPFromFasta.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/AlignmentGuiDemo.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/CookBook.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoCE.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoCeSymm.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoFATCAT.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoMultipleMC.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoNWALignment.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoQuatSymmetryJmol.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoRotationAxis.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoSW3DAligner.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoShowBiolAssembly.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoShowCATHDomain.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoShowLargeAssembly.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoShowValidationResults.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoStructureFromFasta.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/ShowStructureInJmol.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/WebStartClientDemo.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoAlignmentFromFasta.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AboutDialog.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalc.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalcDB.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalculationRunnable.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentGui.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentTextPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ChooseDirAction.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ConfigPDBInstallPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/DBResultTable.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/DBSearchGUI.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/DisplayAFP.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/DotPlotPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/GUIAlignmentProgressListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/GUIFarmJobRunnable.html... 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Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MenuCreator.DotPlotListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentCalc.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentGUI.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentJmolDisplay.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyAlignmentLoadListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyDistMaxListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyExportListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyOpenPdbFileListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MySaveFileListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyTableRowSorter.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ParameterGUI.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/SelectPDBPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ShowPDBIDListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/StructureAlignmentDisplay.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/StructureLoaderThread.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/SystemInfo.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AFPChainCoordManager.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AligPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AligPanelMouseMotionListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAligPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAligPanelMouseMotionListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAlignmentCoordManager.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleStatusDisplay.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/StatusDisplay.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/AutoSuggestProvider.html... 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Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AtomInfoParser.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolPanel.JmolLoggerAdapter.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolTools.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/MultipleAlignmentJmol.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/MyJmolStatusListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/RasmolCommandListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/StructureAlignmentJmol.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/AligUIManager.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/BrowserOpener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/ConfigXMLHandler.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/JNLPProxy.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/WebStartDBSearch.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/WebStartDBSearchResults.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/WebStartMain.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/BiojavaJmol.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/JMatrixPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/JmolViewerImpl.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/RenderStyle.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/ScaleableMatrixPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/ScaleableMatrixPanel.GradientRenderer.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/Selection.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/SelectionImpl.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/SequenceDisplay.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/StructureViewer.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/WrapLayout.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/class-use/AlignmentPositionListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/class-use/JmolAlignedPositionListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlignedPosition.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlignmentCalc.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlternativeAlignmentFrame.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/CoordManager.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/MenuCreator.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBDirPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBServerPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBUploadPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/ScopInstallationInstance.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/ScopSelectPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/SelectMultiplePanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/SequenceMouseListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/SequenceScalePanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/StructurePairSelector.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ColorInterpolator.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ColorUtils.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ContinuousColorMapper.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ContinuousColorMapperTransform.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/DefaultMatrixMapper.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/GradientMapper.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/GradientPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/HSVColorSpace.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LinearColorInterpolator.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LinearColorInterpolator.InterpolationDirection.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LogColorMapper.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/SqrtColorMapper.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryCalc.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryDisplay.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryGui.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/ColorConverter.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGenerator.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorC1.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorCn.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorDn.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorH.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorI.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorO.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorPointGroup.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorT.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/package-use.html... Building index for all the packages and classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/overview-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/index-all.html... Building index for all classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/allclasses-index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/allpackages-index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/deprecated-list.html... Building index for all classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/allclasses.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/allclasses.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/overview-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/help-doc.html... 23 warnings [WARNING] Javadoc Warnings [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DotPlotPanel.java:62: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java:54: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MenuCreator.java:293: warning - @param argument "MultipleAlignment" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MenuCreator.java:754: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java:44: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGenerator.java:40: warning - @param argument "rotationGroup" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java:54: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java:44: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java:44: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java:44: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java:54: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java:44: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java:54: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java:44: warning - invalid usage of tag & [INFO] Building jar: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/biojava-structure-gui-5.4.0-javadoc.jar [INFO] [INFO] ---------------------< org.biojava:biojava-genome >--------------------- [INFO] Building biojava-genome 5.4.0 [8/14] [INFO] --------------------------------[ jar ]--------------------------------- [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:3.1.0:resources (default-resources) @ biojava-genome --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-genome --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 52 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/classes [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ biojava-genome --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 83 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ biojava-genome --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 20 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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:3.1.2:jar (default-jar) @ biojava-genome --- [INFO] Building jar: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/biojava-genome-5.4.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.0.1:jar (default-cli) @ biojava-genome --- [INFO] Adding the --ignore-source-errors option [ERROR] Error fetching link: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/package-list. Ignored it. [ERROR] Error fetching link: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/package-list. Ignored it. [INFO] Loading source files for package org.biojava.nbio.genome... Loading source files for package org.biojava.nbio.genome.homology... 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Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/class-use/GFF3FromUniprotBlastHits.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/Fastq.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqBuilder.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqReader.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqTools.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqVariant.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqWriter.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/IlluminaFastqReader.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/IlluminaFastqWriter.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/ParseListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SangerFastqReader.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SangerFastqWriter.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SolexaFastqReader.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SolexaFastqWriter.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/StreamListener.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/Cytoband.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/CytobandParser.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/StainType.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/geneid/class-use/GeneIDXMLReader.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/ChromPos.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneChromosomePosition.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneChromosomePositionParser.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneName.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneNamesParser.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/Feature.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureHelper.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureI.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureList.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GCStats.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GFF3Reader.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GFF3Writer.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GeneIDGFF2Reader.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GeneMarkGTFReader.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/LocIterator.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/Location.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/SimpleTwoBitFileProvider.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/TwoBitFacade.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/TwoBitParser.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/query/class-use/BlastXMLQuery.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/query/class-use/OutputHitsGFF.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/uniprot/class-use/UniprotToFasta.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/class-use/ChromosomeMappingTools.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/class-use/ProteinMappingTools.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/class-use/SplitFasta.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/geneid/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/query/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/uniprot/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/package-use.html... Building index for all the packages and classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/overview-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/index-all.html... Building index for all classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/allclasses-index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/allpackages-index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/deprecated-list.html... Building index for all classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/allclasses.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/allclasses.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/overview-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/help-doc.html... 8 warnings [WARNING] Javadoc Warnings [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java:412: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java:414: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java:454: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java:456: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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. [INFO] Building jar: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/biojava-genome-5.4.0-javadoc.jar [INFO] [INFO] -------------------< org.biojava:biojava-modfinder >-------------------- [INFO] Building biojava-modfinder 5.4.0 [9/14] [INFO] --------------------------------[ jar ]--------------------------------- [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:3.1.0:resources (default-resources) @ biojava-modfinder --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-modfinder --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 23 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/classes [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ biojava-modfinder --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ biojava-modfinder --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 5 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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:3.1.2:jar (default-jar) @ biojava-modfinder --- [INFO] Building jar: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/biojava-modfinder-5.4.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.0.1:jar (default-cli) @ biojava-modfinder --- [INFO] Adding the --ignore-source-errors option [ERROR] Error fetching link: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/package-list. Ignored it. [INFO] Loading source files for package org.biojava.nbio.phosphosite... Loading source files for package org.biojava.nbio.protmod... Loading source files for package org.biojava.nbio.protmod.io... Loading source files for package org.biojava.nbio.protmod.structure... Constructing Javadoc information... Standard Doclet version 11.0.15 Building tree for all the packages and classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/Dataset.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/Site.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/Component.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/ModificationCategory.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/ModificationCondition.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/ModificationConditionImpl.html... 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Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/constant-values.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/serialized-form.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/class-use/Dataset.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/class-use/Site.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/Component.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationCategory.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationCondition.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationConditionImpl.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationLinkage.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationOccurrenceType.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModification.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationImpl.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationImpl.Builder.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationRegistry.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ComponentXMLConverter.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ModifiedCompoundXMLConverter.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ProteinModificationXmlReader.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/StructureAtomXMLConverter.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/StructureGroupXMLConverter.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/ModifiedCompound.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/ModifiedCompoundImpl.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/ProteinModificationIdentifier.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureAtom.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureAtomLinkage.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureGroup.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureUtil.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/package-use.html... Building index for all the packages and classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/overview-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/index-all.html... Building index for all classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/allclasses-index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/allpackages-index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/deprecated-list.html... Building index for all classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/allclasses.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/allclasses.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/overview-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/help-doc.html... 15 warnings [WARNING] Javadoc Warnings [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java:33: warning - Tag @link: reference not found: register [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java:112: warning - @param argument "pdbccIds" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationLinkage.java:57: warning - @param argument "labelOfAtomOnComponent1" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationLinkage.java:60: warning - @param argument "labelOfAtomOnComponent2" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationLinkage.java:80: warning - @param argument "labelOfAtomOnComponent1" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationLinkage.java:83: warning - @param argument "labelOfAtomOnComponent2" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java:209: warning - @param argument "mod" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java:50: warning - Tag @link: reference not found: ProteinModificationBean [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java:76: warning - Tag @see: reference not found: #getLinkedGroupPairs [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java:88: warning - Tag @link: reference not found: addGroup [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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. [WARNING] javadoc: warning - Tag @link: reference not found: ProteinModificationBean [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java:76: warning - Tag @see: reference not found: #getLinkedGroupPairs [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java:88: warning - Tag @link: reference not found: addGroup [INFO] Building jar: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/biojava-modfinder-5.4.0-javadoc.jar [INFO] [INFO] -----------------------< org.biojava:biojava-ws >----------------------- [INFO] Building biojava-ws 5.4.0 [10/14] [INFO] --------------------------------[ jar ]--------------------------------- [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:3.1.0:resources (default-resources) @ biojava-ws --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-ws --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 21 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/classes [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ biojava-ws --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ biojava-ws --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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:3.1.2:jar (default-jar) @ biojava-ws --- [INFO] Building jar: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/biojava-ws-5.4.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.0.1:jar (default-cli) @ biojava-ws --- [INFO] Adding the --ignore-source-errors option [ERROR] Error fetching link: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/package-list. Ignored it. [INFO] Loading source files for package demo... Loading source files for package org.biojava.nbio.ws.alignment... Loading source files for package org.biojava.nbio.ws.alignment.qblast... Loading source files for package org.biojava.nbio.ws.hmmer... Constructing Javadoc information... Standard Doclet version 11.0.15 Building tree for all the packages and classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/demo/HmmerDemo.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/demo/NCBIQBlastServiceDemo.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentOutputProperties.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentProperties.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentService.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/BlastAlignmentParameterEnum.html... 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Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/HmmerScan.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/demo/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/demo/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/constant-values.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/serialized-form.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/demo/class-use/HmmerDemo.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/demo/class-use/NCBIQBlastServiceDemo.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentOutputProperties.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentProperties.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentService.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastAlignmentParameterEnum.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastJob.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastMatrixEnum.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputAlignmentFormatEnum.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputFormatEnum.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputParameterEnum.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastProgramEnum.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/MapToStringTransformer.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastAlignmentProperties.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastOutputProperties.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastService.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerDomain.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerResult.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerScan.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/RemoteHmmerScan.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/demo/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/package-use.html... Building index for all the packages and classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/overview-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/index-all.html... Building index for all classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/allclasses-index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/allpackages-index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/deprecated-list.html... Building index for all classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/allclasses.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/allclasses.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/overview-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/help-doc.html... 4 warnings [WARNING] Javadoc Warnings [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/MapToStringTransformer.java:46: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/MapToStringTransformer.java:79: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java:140: warning - Tag @link: reference not found: NCBIQBlastService#printRemoteBlastInfo() [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java:144: warning - @param argument "db" is not a parameter name. [INFO] Building jar: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/biojava-ws-5.4.0-javadoc.jar [INFO] [INFO] ----------------< org.biojava:biojava-protein-disorder >---------------- [INFO] Building biojava-protein-disorder 5.4.0 [11/14] [INFO] --------------------------------[ jar ]--------------------------------- [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:3.1.0:resources (default-resources) @ biojava-protein-disorder --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 11 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-protein-disorder --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 13 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/classes [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ biojava-protein-disorder --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ biojava-protein-disorder --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 3 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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:3.1.2:jar (default-jar) @ biojava-protein-disorder --- [INFO] Building jar: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/biojava-protein-disorder-5.4.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.0.1:jar (default-cli) @ biojava-protein-disorder --- [INFO] Adding the --ignore-source-errors option [ERROR] Error fetching link: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/package-list. Ignored it. [INFO] Loading source files for package demo... Loading source files for package org.biojava.nbio.data.sequence... Loading source files for package org.biojava.nbio.ronn... Constructing Javadoc information... Standard Doclet version 11.0.15 Building tree for all the packages and classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/demo/PredictDisorder.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/FastaSequence.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/SequenceUtil.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/Jronn.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/Jronn.Range.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/ModelLoader.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/ModelLoader.Model.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/ModelLoader.Threshold.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/NullOutputStream.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/ORonn.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/ORonnModel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/RonnConstraint.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/RonnConstraint.Threshold.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/Timer.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/demo/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/demo/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/constant-values.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/serialized-form.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/demo/class-use/PredictDisorder.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/class-use/FastaSequence.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/class-use/SequenceUtil.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/Jronn.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/Jronn.Range.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.Model.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.Threshold.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/NullOutputStream.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ORonn.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ORonnModel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/RonnConstraint.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/RonnConstraint.Threshold.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/Timer.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/demo/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/package-use.html... Building index for all the packages and classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/overview-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/index-all.html... Building index for all classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/allclasses-index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/allpackages-index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/deprecated-list.html... Building index for all classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/allclasses.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/allclasses.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/overview-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/help-doc.html... 4 warnings [WARNING] Javadoc Warnings [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java:244: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java:244: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java:269: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java:269: warning - invalid usage of tag > [INFO] Building jar: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/biojava-protein-disorder-5.4.0-javadoc.jar [INFO] [INFO] --------------------< org.biojava:biojava-aa-prop >--------------------- [INFO] Building biojava-aa-prop 5.4.0 [12/14] [INFO] --------------------------------[ jar ]--------------------------------- [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:3.1.0:resources (default-resources) @ biojava-aa-prop --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 11 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-aa-prop --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 33 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/classes [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ biojava-aa-prop --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 7 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ biojava-aa-prop --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 9 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/test-classes [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java uses or overrides a deprecated API. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java: Recompile with -Xlint:deprecation 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:3.1.2:jar (default-jar) @ biojava-aa-prop --- [INFO] Building jar: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/biojava-aa-prop-5.4.0.jar [INFO] [INFO] --- maven-assembly-plugin:3.1.0:single (assemble) @ biojava-aa-prop --- [INFO] Reading assembly descriptor: src/main/assembly/assembly.xml [WARNING] The following patterns were never triggered in this artifact inclusion filter: o 'org.biojava:biojava-core' o 'org.biojava:biojava-structure' [WARNING] The following patterns were never triggered in this artifact inclusion filter: o 'org.biojava:biojava-core' o 'org.biojava:biojava-structure' [INFO] Copying files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/AAProperties-AAProperties [WARNING] Assembly file: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/AAProperties-AAProperties is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [WARNING] Failed to build parent project for com.fasterxml.jackson:jackson-parent:pom:debian [WARNING] Failed to build parent project for com.fasterxml.jackson:jackson-bom:pom:debian [WARNING] Failed to build parent project for com.fasterxml.jackson:jackson-base:pom:debian [WARNING] Failed to build parent project for com.fasterxml.jackson.core:jackson-databind:bundle:2.x [INFO] Building jar: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/AAProperties-jar-with-dependencies.jar [INFO] [INFO] --- maven-assembly-plugin:3.1.0:single (make-assembly) @ biojava-aa-prop --- [INFO] Reading assembly descriptor: src/main/assembly/assembly.xml [WARNING] The following patterns were never triggered in this artifact inclusion filter: o 'org.biojava:biojava-core' o 'org.biojava:biojava-structure' [WARNING] The following patterns were never triggered in this artifact inclusion filter: o 'org.biojava:biojava-core' o 'org.biojava:biojava-structure' [INFO] Copying files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/AAProperties-AAProperties [WARNING] Assembly file: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/AAProperties-AAProperties is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [WARNING] Failed to build parent project for com.fasterxml.jackson:jackson-parent:pom:debian [WARNING] Failed to build parent project for com.fasterxml.jackson:jackson-bom:pom:debian [WARNING] Failed to build parent project for com.fasterxml.jackson:jackson-base:pom:debian [WARNING] Failed to build parent project for com.fasterxml.jackson.core:jackson-databind:bundle:2.x [INFO] Building jar: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/AAProperties-jar-with-dependencies.jar [INFO] [INFO] --- maven-javadoc-plugin:3.0.1:jar (default-cli) @ biojava-aa-prop --- [INFO] Adding the --ignore-source-errors option [ERROR] Error fetching link: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/package-list. Ignored it. [ERROR] Error fetching link: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/package-list. Ignored it. [INFO] Loading source files for package demo... Loading source files for package org.biojava.nbio.aaproperties... Loading source files for package org.biojava.nbio.aaproperties.profeat... Loading source files for package org.biojava.nbio.aaproperties.profeat.convertor... Loading source files for package org.biojava.nbio.aaproperties.xml... Constructing Javadoc information... Standard Doclet version 11.0.15 Building tree for all the packages and classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/demo/BioJavaAADemo.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/AminoAcidProperties.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/CommandPrompt.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/CommandPrompt.PropertyName.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/Constraints.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/IPeptideProperties.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/PeptideProperties.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/PeptideProperties.SingleLetterAACode.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/Utils.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.ATTRIBUTE.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.DISTRIBUTION.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.GROUPING.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.TRANSITION.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/ProfeatPropertiesImpl.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Charge.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Hydrophobicity.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/Convert2NormalizedVanDerWaalsVolume.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Polarity.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Polarizability.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/Convert2SecondaryStructure.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/Convert2SolventAccessibility.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/AminoAcidComposition.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/CaseFreeAminoAcidCompoundSet.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/Element.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/ElementTable.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/Isotope.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/ModifiedAminoAcidCompoundSet.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/Name2Count.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/SchemaGenerator.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/demo/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/demo/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/constant-values.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/demo/class-use/BioJavaAADemo.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/AminoAcidProperties.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/CommandPrompt.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/CommandPrompt.PropertyName.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/Constraints.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/IPeptideProperties.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/PeptideProperties.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/PeptideProperties.SingleLetterAACode.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/PeptidePropertiesImpl.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/Utils.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/IProfeatProperties.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/IProfeatProperties.DISTRIBUTION.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/IProfeatProperties.TRANSITION.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/IProfeatProperties.GROUPING.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/IProfeatProperties.ATTRIBUTE.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/ProfeatProperties.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/ProfeatPropertiesImpl.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Charge.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Hydrophobicity.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2NormalizedVanDerWaalsVolume.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Polarity.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Polarizability.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2SecondaryStructure.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2SolventAccessibility.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convertor.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/AminoAcidComposition.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/AminoAcidCompositionTable.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/CaseFreeAminoAcidCompoundSet.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Element.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/ElementTable.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Isotope.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/ModifiedAminoAcidCompoundSet.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/MyValidationEventHandler.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Name2Count.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/SchemaGenerator.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/demo/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/package-use.html... Building index for all the packages and classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/overview-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/index-all.html... Building index for all classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/allclasses-index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/allpackages-index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/deprecated-list.html... Building index for all classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/allclasses.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/allclasses.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/overview-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/help-doc.html... 62 warnings [WARNING] Javadoc Warnings [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java:261: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java:261: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java:261: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java:261: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning - invalid usage of tag & [WARNING] javadoc: warning - invalid usage of tag & [WARNING] javadoc: warning - invalid usage of tag & [WARNING] javadoc: warning - invalid usage of tag & [WARNING] javadoc: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning - invalid usage of tag & [INFO] Building jar: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/biojava-aa-prop-5.4.0-javadoc.jar [INFO] [INFO] --------------------< org.biojava:biojava-survival >-------------------- [INFO] Building biojava-survival 5.4.0 [13/14] [INFO] --------------------------------[ jar ]--------------------------------- [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:3.1.0:resources (default-resources) @ biojava-survival --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-survival --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 46 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/classes [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ biojava-survival --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1: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:3.1.2:jar (default-jar) @ biojava-survival --- [INFO] Building jar: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/biojava-survival-5.4.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.0.1:jar (default-cli) @ biojava-survival --- [INFO] Adding the --ignore-source-errors option [INFO] Loading source files for package org.biojava.nbio.survival.cox... Loading source files for package org.biojava.nbio.survival.cox.comparators... Loading source files for package org.biojava.nbio.survival.cox.matrix... Loading source files for package org.biojava.nbio.survival.cox.stats... Loading source files for package org.biojava.nbio.survival.data... Loading source files for package org.biojava.nbio.survival.kaplanmeier.figure... Loading source files for package org.biojava.nbio.survival.kaplanmeier.metadata... Constructing Javadoc information... Standard Doclet version 11.0.15 Building tree for all the packages and classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/CoxCC.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/CoxCoefficient.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/CoxHelper.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/CoxInfo.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/CoxMart.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/CoxMethod.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/CoxR.html... 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Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/CoxComparatorInterface.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/CoxVariablesOverallModelFitComparator.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/CoxVariablesVariableComparator.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/MeanModelComparator.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/SurvivalInfoComparator.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/SurvivalInfoValueComparator.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/Matrix.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/StdArrayIO.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/AgScore.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/ChiSq.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/Cholesky2.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/Chsolve2.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/ChangeValue.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/CompactCharSequence.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/HeaderInfo.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/WorkSheet.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/CensorStatus.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/CensorStatusSelect.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/GroupResults.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/KMFigureInfo.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.ConfLower.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.ConfType.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.Error.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.Method.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/ClinicalMetaDataOutcome.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/DiscreteQuantizerInterface.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/MeanQuantizer.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/MetaDataInfo.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/package-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/package-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/constant-values.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/serialized-form.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxCC.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxCoefficient.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxHelper.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxInfo.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxMart.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxMethod.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxR.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxScore.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxVariables.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/ResidualsCoxph.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/ResidualsCoxph.Type.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/RiskInfo.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/StrataInfo.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvFitInfo.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfo.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfoHelper.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfoIndex.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/WaldTest.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/WaldTestInfo.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxComparatorInterface.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxVariablesOverallModelFitComparator.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxVariablesVariableComparator.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/MeanModelComparator.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/SurvivalInfoComparator.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/SurvivalInfoValueComparator.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/class-use/Matrix.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/class-use/StdArrayIO.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/AgScore.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/ChiSq.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/Cholesky2.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/Chsolve2.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/ChangeValue.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/CompactCharSequence.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/HeaderInfo.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/WorkSheet.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/CensorStatus.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/CensorStatusSelect.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/ExpressionFigure.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/GroupResults.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/KMFigureInfo.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/KaplanMeierFigure.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/NumbersAtRiskPanel.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.ConfLower.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.ConfType.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.Error.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.Method.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/ClinicalMetaDataOutcome.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/DiscreteQuantizerInterface.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/MeanQuantizer.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/MetaDataInfo.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/package-use.html... Building index for all the packages and classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/overview-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/index-all.html... Building index for all classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/allclasses-index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/allpackages-index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/deprecated-list.html... Building index for all classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/allclasses.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/allclasses.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/overview-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/help-doc.html... 2 warnings [WARNING] Javadoc Warnings [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java:78: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java:1467: warning - @param argument "f" is not a parameter name. [INFO] Building jar: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/biojava-survival-5.4.0-javadoc.jar [INFO] [INFO] --------------------< org.biojava:biojava-ontology >-------------------- [INFO] Building biojava-ontology 5.4.0 [14/14] [INFO] --------------------------------[ jar ]--------------------------------- [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:3.1.0:resources (default-resources) @ biojava-ontology --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-ontology --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 36 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/target/classes [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileHandler.java: Some input files use or override a deprecated API. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileHandler.java: Recompile with -Xlint:deprecation for details. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/AbstractAnnotation.java: Some input files use unchecked or unsafe operations. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/AbstractAnnotation.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ biojava-ontology --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 6 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ biojava-ontology --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 3 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-ontology --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ biojava-ontology --- [INFO] Building jar: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/target/biojava-ontology-5.4.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.0.1:jar (default-cli) @ biojava-ontology --- [INFO] Adding the --ignore-source-errors option [INFO] Loading source file /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/src/main/java/package-info.java... Loading source files for package demo... Loading source files for package org.biojava.nbio.ontology... Loading source files for package org.biojava.nbio.ontology.io... Loading source files for package org.biojava.nbio.ontology.obo... Loading source files for package org.biojava.nbio.ontology.utils... Constructing Javadoc information... Standard Doclet version 11.0.15 Building tree for all the packages and classes... 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Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/class-use/OboFileParser.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/class-use/OboFileParser.SOPair.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/AbstractAnnotation.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/Annotatable.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/Annotation.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/AssertionFailure.html... 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Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/io/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/package-use.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/package-use.html... Building index for all the packages and classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/overview-tree.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/index-all.html... Building index for all classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/allclasses-index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/allpackages-index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/deprecated-list.html... Building index for all classes... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/allclasses.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/allclasses.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/index.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/overview-summary.html... Generating /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/help-doc.html... 13 warnings [WARNING] Javadoc Warnings [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java:43: warning - Tag @see: reference not found: org.biojavax.ontology.ComparableOntology [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java:35: warning - Tag @link: reference not found: org.biojava.nbio.AnnotationAnnotation [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java:54: warning - Tag @see: reference not found: org.biojavax.ontology.ComparableTerm [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java:44: warning - Tag @see: reference not found: org.biojavax.ontology.ComparableTriple [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java:98: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java:98: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java:99: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java:99: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java:114: warning - Tag @see: reference not found: org.biojavax.ontology.SimpleComparableTriple [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:41: warning - invalid usage of tag &view [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotatable.java:78: warning - Tag @see: reference not found: org.biojavax.RichAnnotatable [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java:56: warning - Tag @see: reference not found: org.biojavax.RichAnnotation [INFO] Building jar: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/target/biojava-ontology-5.4.0-javadoc.jar [INFO] [INFO] ------------------------< org.biojava:biojava >------------------------- [INFO] Building biojava 5.4.0 [15/14] [INFO] --------------------------------[ pom ]--------------------------------- [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:3.0.1:aggregate (default-cli) > compile @ biojava >>> [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-core 5.4.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ biojava-core --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 24 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-core --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 187 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/target/classes [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java: Some input files use or override a deprecated API. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java: Recompile with -Xlint:deprecation for details. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.java: Some input files use unchecked or unsafe operations. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-forester 5.4.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ biojava-forester --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-forester --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 359 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/target/classes [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/MainFrame.java: Some input files use or override a deprecated API. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/MainFrame.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-alignment 5.4.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ biojava-alignment --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-alignment --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 53 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/target/classes [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java uses or overrides a deprecated API. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-structure 5.4.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [WARNING] The artifact java3d:vecmath:jar:debian has been relocated to javax.vecmath:vecmath:jar:debian [WARNING] The artifact com.sun.xml.bind:jaxb-impl:jar:debian has been relocated to org.glassfish.jaxb:jaxb-runtime:jar:debian [WARNING] The artifact javax.activation:activation:jar:debian has been relocated to com.sun.activation:javax.activation:jar:debian [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ biojava-structure --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 3 resources [INFO] Copying 61 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-structure --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 522 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/target/classes [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java: Some input files use or override a deprecated API. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-jcolorbrewer 5.4.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ biojava-jcolorbrewer --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-jcolorbrewer --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 7 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/target/classes [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java uses or overrides a deprecated API. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-structure-gui 5.4.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ biojava-structure-gui --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 49 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-structure-gui --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 139 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/classes [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.java: Some input files use or override a deprecated API. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.java: Recompile with -Xlint:deprecation for details. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/ScaleableMatrixPanel.java: Some input files use unchecked or unsafe operations. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/ScaleableMatrixPanel.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-genome 5.4.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ biojava-genome --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-genome --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 52 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/target/classes [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-modfinder 5.4.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ biojava-modfinder --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-modfinder --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 23 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/classes [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-ws 5.4.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ biojava-ws --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-ws --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 21 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/target/classes [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-protein-disorder 5.4.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ biojava-protein-disorder --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 11 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-protein-disorder --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 13 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/classes [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-aa-prop 5.4.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ biojava-aa-prop --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 11 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-aa-prop --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 33 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/classes [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-survival 5.4.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ biojava-survival --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-survival --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 46 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/target/classes [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-ontology 5.4.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ biojava-ontology --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-ontology --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 36 source files to /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/target/classes [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileHandler.java: Some input files use or override a deprecated API. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileHandler.java: Recompile with -Xlint:deprecation for details. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/AbstractAnnotation.java: Some input files use unchecked or unsafe operations. [INFO] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/AbstractAnnotation.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] <<< maven-javadoc-plugin:3.0.1:aggregate (default-cli) < compile @ biojava <<< [INFO] [WARNING] The artifact java3d:vecmath:jar:debian has been relocated to javax.vecmath:vecmath:jar:debian [WARNING] The artifact com.sun.xml.bind:jaxb-impl:jar:debian has been relocated to org.glassfish.jaxb:jaxb-runtime:jar:debian [WARNING] The artifact javax.activation:activation:jar:debian has been relocated to com.sun.activation:javax.activation:jar:debian [INFO] [INFO] --- maven-javadoc-plugin:3.0.1:aggregate (default-cli) @ biojava --- [ERROR] no module descriptor for org.biojava:biojava [ERROR] no module descriptor for org.biojava:biojava-core [ERROR] no module descriptor for org.biojava:biojava-forester [ERROR] no module descriptor for org.biojava:biojava-alignment [ERROR] no module descriptor for org.biojava:biojava-structure [ERROR] no module descriptor for org.biojava:biojava-jcolorbrewer [ERROR] no module descriptor for org.biojava:biojava-structure-gui [ERROR] no module descriptor for org.biojava:biojava-genome [ERROR] no module descriptor for org.biojava:biojava-modfinder [ERROR] no module descriptor for org.biojava:biojava-ws [ERROR] no module descriptor for org.biojava:biojava-protein-disorder [ERROR] no module descriptor for org.biojava:biojava-aa-prop [ERROR] no module descriptor for org.biojava:biojava-survival [ERROR] no module descriptor for org.biojava:biojava-ontology [INFO] Adding the --ignore-source-errors option [INFO] Loading source file /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/src/main/java/package-info.java... 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invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning - invalid usage of tag & [WARNING] javadoc: warning - invalid usage of tag & [WARNING] javadoc: warning - invalid usage of tag & [WARNING] javadoc: warning - invalid usage of tag & [WARNING] javadoc: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+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] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:125: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:206: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:312: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:542: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:615: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityScorer.java:37: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityScorer.java:37: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java:44: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileAnnotation.java:163: warning - @param argument "dbReference" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:45: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:70: warning - @param argument "cutsPerSection" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:83: warning - @param argument "cutsPerSection" is not a parameter name. [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/GuanUberbacher.java:37: warning - invalid usage of tag < [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java:49: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.java:40: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java:46: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/Aligner.java:35: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallablePairwiseSequenceAligner.java:37: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java:36: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java:37: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/MatrixAligner.java:33: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/MatrixAligner.java:34: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PairInProfileScorer.java:35: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PairwiseSequenceAligner.java:35: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:34: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:35: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:34: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:35: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileScorer.java:35: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:36: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:37: warning - Tag @link: reference not found: AlignedSequence [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning - Tag @link: reference not found: Profile [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:121: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:146: warning - invalid usage of tag > [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:77: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:85: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:93: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:101: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:109: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:117: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:125: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:133: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:141: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:149: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:157: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:165: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:173: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:181: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:189: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:197: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:77: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:85: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:93: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:101: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:109: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:117: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:125: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:133: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:141: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:149: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:157: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:165: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:173: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:181: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:189: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:197: warning - invalid usage of tag & [WARNING] /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:41: warning - Tag @link: reference not found: Aligner [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava 5.4.0: [INFO] [INFO] biojava ............................................ SUCCESS [ 37.532 s] [INFO] biojava-core ....................................... SUCCESS [ 14.499 s] [INFO] biojava-forester ................................... SUCCESS [ 15.330 s] [INFO] biojava-alignment .................................. SUCCESS [ 4.459 s] [INFO] biojava-structure .................................. SUCCESS [ 16.923 s] [INFO] biojava-jcolorbrewer ............................... SUCCESS [ 3.016 s] [INFO] biojava-structure-gui .............................. SUCCESS [ 7.602 s] [INFO] biojava-genome ..................................... SUCCESS [ 4.789 s] [INFO] biojava-modfinder .................................. SUCCESS [ 4.034 s] [INFO] biojava-ws ......................................... SUCCESS [ 2.844 s] [INFO] biojava-protein-disorder ........................... SUCCESS [ 3.811 s] [INFO] biojava-aa-prop .................................... SUCCESS [ 9.515 s] [INFO] biojava-survival ................................... SUCCESS [ 4.165 s] [INFO] biojava-ontology ................................... SUCCESS [ 4.312 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 02:14 min [INFO] Finished at: 2022-06-30T20:33:00Z [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg' dh: command-omitted: The call to "dh_auto_test -i" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep -i dh_auto_install -i /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/biojava5-live-HFV3YZ/biojava5-live-5.4.0\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0\+dfsg/debian -Dmaven.repo.local=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0\+dfsg/debian/maven-repo --batch-mode -Ddebian.dir=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0\+dfsg/debian -Ddebian.package=libbiojava5-java -Dmaven.repo.local=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0\+dfsg/debian/maven-repo -Dinstall.to.usj=true org.debian.maven:debian-maven-plugin:2.6:install [INFO] Scanning for projects... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.biojava:biojava-structure-gui:jar:5.4.0 [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] [INFO] ------------------------< org.biojava:biojava >------------------------- [INFO] Building biojava 5.4.0 [1/14] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava --- [INFO] Cleaning pom file: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava5-java [INFO] --rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.publishedRules [INFO] --no-parent [INFO] [INFO] ----------------------< org.biojava:biojava-core >---------------------- [INFO] Building biojava-core 5.4.0 [2/14] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-core --- [INFO] Cleaning pom file: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-core/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava5-java [INFO] --rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-core into /usr/share/java [INFO] [INFO] --------------------< org.biojava:biojava-forester >-------------------- [INFO] Building biojava-forester 5.4.0 [3/14] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-forester --- [INFO] Cleaning pom file: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-forester/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava5-java [INFO] --rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-forester into /usr/share/java [INFO] [INFO] -------------------< org.biojava:biojava-alignment >-------------------- [INFO] Building biojava-alignment 5.4.0 [4/14] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-alignment --- [INFO] Cleaning pom file: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-alignment/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava5-java [INFO] --rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-alignment into /usr/share/java [INFO] [INFO] -------------------< org.biojava:biojava-structure >-------------------- [INFO] Building biojava-structure 5.4.0 [5/14] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-structure --- [INFO] Cleaning pom file: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava5-java [INFO] --rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-structure into /usr/share/java [INFO] [INFO] ------------------< org.biojava:biojava-jcolorbrewer >------------------ [INFO] Building biojava-jcolorbrewer 5.4.0 [6/14] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-jcolorbrewer --- [INFO] Cleaning pom file: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-jcolorbrewer/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava5-java [INFO] --rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-jcolorbrewer into /usr/share/java [INFO] [INFO] -----------------< org.biojava:biojava-structure-gui >------------------ [INFO] Building biojava-structure-gui 5.4.0 [7/14] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-structure-gui --- [INFO] Cleaning pom file: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava5-java [INFO] --rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-structure-gui into /usr/share/java [INFO] [INFO] ---------------------< org.biojava:biojava-genome >--------------------- [INFO] Building biojava-genome 5.4.0 [8/14] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-genome --- [INFO] Cleaning pom file: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-genome/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava5-java [INFO] --rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-genome into /usr/share/java [INFO] [INFO] -------------------< org.biojava:biojava-modfinder >-------------------- [INFO] Building biojava-modfinder 5.4.0 [9/14] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-modfinder --- [INFO] Cleaning pom file: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-modfinder/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava5-java [INFO] --rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-modfinder into /usr/share/java [INFO] [INFO] -----------------------< org.biojava:biojava-ws >----------------------- [INFO] Building biojava-ws 5.4.0 [10/14] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-ws --- [INFO] Cleaning pom file: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ws/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava5-java [INFO] --rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-ws into /usr/share/java [INFO] [INFO] ----------------< org.biojava:biojava-protein-disorder >---------------- [INFO] Building biojava-protein-disorder 5.4.0 [11/14] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-protein-disorder --- [INFO] Cleaning pom file: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava5-java [INFO] --rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-protein-disorder into /usr/share/java [INFO] [INFO] --------------------< org.biojava:biojava-aa-prop >--------------------- [INFO] Building biojava-aa-prop 5.4.0 [12/14] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-aa-prop --- [INFO] Cleaning pom file: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-aa-prop/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava5-java [INFO] --rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-aa-prop into /usr/share/java [INFO] [INFO] --------------------< org.biojava:biojava-survival >-------------------- [INFO] Building biojava-survival 5.4.0 [13/14] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-survival --- [INFO] Cleaning pom file: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-survival/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava5-java [INFO] --rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-survival into /usr/share/java [INFO] [INFO] --------------------< org.biojava:biojava-ontology >-------------------- [INFO] Building biojava-ontology 5.4.0 [14/14] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-ontology --- [INFO] Cleaning pom file: /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-ontology/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava5-java [INFO] --rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-ontology into /usr/share/java [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava 5.4.0: [INFO] [INFO] biojava ............................................ SUCCESS [ 0.753 s] [INFO] biojava-core ....................................... SUCCESS [ 0.204 s] [INFO] biojava-forester ................................... SUCCESS [ 0.060 s] [INFO] biojava-alignment .................................. SUCCESS [ 0.087 s] [INFO] biojava-structure .................................. SUCCESS [ 0.081 s] [INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.047 s] [INFO] biojava-structure-gui .............................. SUCCESS [ 0.097 s] [INFO] biojava-genome ..................................... SUCCESS [ 0.079 s] [INFO] biojava-modfinder .................................. SUCCESS [ 0.094 s] [INFO] biojava-ws ......................................... SUCCESS [ 0.037 s] [INFO] biojava-protein-disorder ........................... SUCCESS [ 0.082 s] [INFO] biojava-aa-prop .................................... SUCCESS [ 0.087 s] [INFO] biojava-survival ................................... SUCCESS [ 0.065 s] [INFO] biojava-ontology ................................... SUCCESS [ 0.073 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 2.243 s [INFO] Finished at: 2022-06-30T20:33:05Z [INFO] ------------------------------------------------------------------------ mh_resolve_dependencies --non-interactive --offline --build -plibbiojava5-java --javadoc --base-directory=/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0\+dfsg --non-explore Analysing pom.xml... Analysing biojava-aa-prop/pom.xml... Checking the parent dependency in the sub project biojava-aa-prop/pom.xml Analysing biojava-alignment/pom.xml... Checking the parent dependency in the sub project biojava-alignment/pom.xml Analysing biojava-core/pom.xml... Checking the parent dependency in the sub project biojava-core/pom.xml Analysing biojava-forester/pom.xml... Checking the parent dependency in the sub project biojava-forester/pom.xml Analysing biojava-genome/pom.xml... Checking the parent dependency in the sub project biojava-genome/pom.xml Analysing biojava-jcolorbrewer/pom.xml... Checking the parent dependency in the sub project biojava-jcolorbrewer/pom.xml Analysing biojava-modfinder/pom.xml... Checking the parent dependency in the sub project biojava-modfinder/pom.xml Analysing biojava-ontology/pom.xml... Checking the parent dependency in the sub project biojava-ontology/pom.xml Analysing biojava-protein-comparison-tool/pom.xml... Checking the parent dependency in the sub project biojava-protein-comparison-tool/pom.xml Analysing biojava-protein-disorder/pom.xml... Checking the parent dependency in the sub project biojava-protein-disorder/pom.xml Analysing biojava-structure/pom.xml... Checking the parent dependency in the sub project biojava-structure/pom.xml Analysing biojava-structure-gui/pom.xml... Checking the parent dependency in the sub project biojava-structure-gui/pom.xml Analysing biojava-survival/pom.xml... Checking the parent dependency in the sub project biojava-survival/pom.xml Analysing biojava-ws/pom.xml... Checking the parent dependency in the sub project biojava-ws/pom.xml > dpkg --search /usr/share/maven-repo/net/sourceforge/jmol/jmol/*/* dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/maven-repo/net/sourceforge/jmol/jmol Jun 30, 2022 8:33:13 PM org.debian.maven.packager.DependenciesSolver$ToResolve resolve SEVERE: Cannot resolve dependencies in /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-protein-comparison-tool/pom.xml: Dependency not found net.sourceforge.jmol:jmol:jar:debian > dpkg --search /usr/share/maven-repo/net/sourceforge/jmol/jmol/*/* dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/maven-repo/net/sourceforge/jmol/jmol Jun 30, 2022 8:33:18 PM org.debian.maven.packager.DependenciesSolver$ToResolve resolve SEVERE: Cannot resolve dependencies in /build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg/biojava-structure-gui/pom.xml: Dependency not found net.sourceforge.jmol:jmol:jar:debian ERROR: biojava-protein-comparison-tool/pom.xml: dependency is not packaged in the Maven repository for Debian: net.sourceforge.jmol:jmol:debian biojava-structure-gui/pom.xml: dependency is not packaged in the Maven repository for Debian: net.sourceforge.jmol:jmol:debian -------- Checking dependencies for documentation packages... > dpkg --search /usr/share/doc/libactivation-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libactivation-java/api/index.html > dpkg --search /usr/share/doc/libactivation-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libactivation-java-doc/api/index.html > dpkg --search /usr/share/doc/libactivation-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libactivation-java/apidocs/index.html > dpkg --search /usr/share/doc/libactivation-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libactivation-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libciftools-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libciftools-java/api/index.html > dpkg --search /usr/share/doc/libciftools-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libciftools-java-doc/api/index.html > dpkg --search /usr/share/doc/libciftools-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libciftools-java/apidocs/index.html > dpkg --search /usr/share/doc/libciftools-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libciftools-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libcommons-codec-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-codec-java/api/index.html > dpkg --search /usr/share/doc/libcommons-codec-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-codec-java-doc/api/index.html > dpkg --search /usr/share/doc/libcommons-codec-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-codec-java/apidocs/index.html > dpkg --search /usr/share/doc/libcommons-codec-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-codec-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libcommons-math-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-math-java/api/index.html > dpkg --search /usr/share/doc/libcommons-math-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-math-java-doc/api/index.html > dpkg --search /usr/share/doc/libcommons-math-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-math-java/apidocs/index.html > dpkg --search /usr/share/doc/libcommons-math-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-math-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libguava-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libguava-java/api/index.html > dpkg --search /usr/share/doc/libguava-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libguava-java-doc/api/index.html > dpkg --search /usr/share/doc/libguava-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libguava-java/apidocs/index.html > dpkg --search /usr/share/doc/libguava-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libguava-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libitext5-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libitext5-java/api/index.html > dpkg --search /usr/share/doc/libitext5-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libitext5-java-doc/api/index.html > dpkg --search /usr/share/doc/libitext5-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libitext5-java/apidocs/index.html > dpkg --search /usr/share/doc/libitext5-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libitext5-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libjaxb-api-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-api-java/api/index.html > dpkg --search /usr/share/doc/libjaxb-api-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-api-java-doc/api/index.html > dpkg --search /usr/share/doc/libjaxb-api-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-api-java/apidocs/index.html > dpkg --search /usr/share/doc/libjaxb-api-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-api-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libjaxb-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-java/api/index.html > dpkg --search /usr/share/doc/libjaxb-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-java-doc/api/index.html > dpkg --search /usr/share/doc/libjaxb-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-java/apidocs/index.html > dpkg --search /usr/share/doc/libjaxb-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libjgrapht-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjgrapht-java/api/index.html > dpkg --search /usr/share/doc/libjgrapht-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjgrapht-java-doc/api/index.html > dpkg --search /usr/share/doc/libjgrapht-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjgrapht-java/apidocs/index.html > dpkg --search /usr/share/doc/libjgrapht-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjgrapht-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libjson-simple-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjson-simple-java/api/index.html > dpkg --search /usr/share/doc/libjson-simple-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjson-simple-java-doc/api/index.html > dpkg --search /usr/share/doc/libjson-simple-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjson-simple-java/apidocs/index.html > dpkg --search /usr/share/doc/libjson-simple-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjson-simple-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/liblog4j2-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/liblog4j2-java/api/index.html > dpkg --search /usr/share/doc/liblog4j2-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/liblog4j2-java-doc/api/index.html > dpkg --search /usr/share/doc/liblog4j2-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/liblog4j2-java/apidocs/index.html > dpkg --search /usr/share/doc/liblog4j2-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/liblog4j2-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libmmtf-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libmmtf-java/api/index.html > dpkg --search /usr/share/doc/libmmtf-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libmmtf-java-doc/api/index.html > dpkg --search /usr/share/doc/libmmtf-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libmmtf-java/apidocs/index.html > dpkg --search /usr/share/doc/libmmtf-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libmmtf-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libslf4j-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libslf4j-java/api/index.html > dpkg --search /usr/share/doc/libslf4j-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libslf4j-java-doc/api/index.html > dpkg --search /usr/share/doc/libslf4j-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libslf4j-java/apidocs/index.html > dpkg --search /usr/share/doc/libslf4j-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libslf4j-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libvecmath-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libvecmath-java/api/index.html > dpkg --search /usr/share/doc/libvecmath-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libvecmath-java-doc/api/index.html > dpkg --search /usr/share/doc/libvecmath-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libvecmath-java/apidocs/index.html > dpkg --search /usr/share/doc/libvecmath-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libvecmath-java-doc/apidocs/index.html Some problems were found in this project, exiting... bash -c "rm -f target/apidocs/*.sh target/apidocs/options" mh_unpatchpoms -plibbiojava5-java dh_install -i jh_installjavadoc -i debian/rules override_dh_installdocs make[1]: Entering directory '/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg' dpkg: warning: --compare-versions used with obsolete relation operator '>' dh_installdocs # Deleting calls to urchinTracker to enhance privacy. for F in $(find . -name "*.html"); do \ sed -i 's/^$//' $F; \ done make[1]: Leaving directory '/build/biojava5-live-HFV3YZ/biojava5-live-5.4.0+dfsg' dh_installchangelogs -i dh_lintian -i dh_perl -i dh_link -i jh_installlibs -i jh_classpath -i jh_manifest -i jh_depends -i dh_strip_nondeterminism -i dh_compress -i dh_fixperms -i dh_missing -i dh_installdeb -i dh_gencontrol -i dpkg-gencontrol: warning: package libbiojava5-java: substitution variable ${java:Depends} unused, but is defined dpkg-gencontrol: warning: package libbiojava5-java: substitution variable ${maven:CompileDepends} unused, but is defined dpkg-gencontrol: warning: package libbiojava5-java: substitution variable ${maven:DocDepends} unused, but is defined dpkg-gencontrol: warning: package libbiojava5-java-doc: substitution variable ${maven:CompileDepends} unused, but is defined dpkg-gencontrol: warning: package libbiojava5-java-doc: substitution variable ${maven:Depends} unused, but is defined dpkg-gencontrol: warning: package libbiojava5-java-doc: substitution variable ${maven:DocDepends} unused, but is defined dh_md5sums -i dh_builddeb -i dpkg-deb: building package 'libbiojava5-java' in '../libbiojava5-java_5.4.0+dfsg-4_all.deb'. dpkg-deb: building package 'libbiojava5-java-doc' in '../libbiojava5-java-doc_5.4.0+dfsg-4_all.deb'. dpkg-genbuildinfo --build=all -O../biojava5-live_5.4.0+dfsg-4_all.buildinfo dpkg-genchanges --build=all -O../biojava5-live_5.4.0+dfsg-4_all.changes dpkg-genchanges: info: binary-only arch-indep upload (source code and arch-specific packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/biojava5-live-HFV3YZ /tmp/biojava5-live-5.4.0+dfsg-44t_5oo6m I: cleaning package lists and apt cache... W: deleting files in /tmp: hsperfdata_root W: deleting files in /tmp: hsperfdata_builduser I: removing tempdir /tmp/mmdebstrap.WUvppJLIBO... I: success in 1337.5563 seconds md5: libbiojava5-java-doc_5.4.0+dfsg-4_all.deb: OK md5: libbiojava5-java_5.4.0+dfsg-4_all.deb: OK sha1: libbiojava5-java-doc_5.4.0+dfsg-4_all.deb: OK sha1: libbiojava5-java_5.4.0+dfsg-4_all.deb: OK sha256: libbiojava5-java-doc_5.4.0+dfsg-4_all.deb: OK sha256: libbiojava5-java_5.4.0+dfsg-4_all.deb: OK Checksums: OK