I: pbuilder: network access will be disabled during build
I: Current time: Wed Nov  6 07:37:10 +14 2024
I: pbuilder-time-stamp: 1730828230
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [biojava6-live_6.1.0+dfsg-5.dsc]
I: copying [./biojava6-live_6.1.0+dfsg.orig-forester.tar.gz]
I: copying [./biojava6-live_6.1.0+dfsg.orig-jcolorbrewer.tar.gz]
I: copying [./biojava6-live_6.1.0+dfsg.orig.tar.gz]
I: copying [./biojava6-live_6.1.0+dfsg-5.debian.tar.xz]
I: Extracting source
gpgv: Signature made Thu Oct 31 08:00:43 2024 
gpgv:                using RSA key 33CB284313E90BD27DCB4523600316A6DC277476
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./biojava6-live_6.1.0+dfsg-5.dsc: no acceptable signature found
dpkg-source: info: extracting biojava6-live in biojava6-live-6.1.0+dfsg
dpkg-source: info: unpacking biojava6-live_6.1.0+dfsg.orig.tar.gz
dpkg-source: info: unpacking biojava6-live_6.1.0+dfsg.orig-forester.tar.gz
dpkg-source: info: unpacking biojava6-live_6.1.0+dfsg.orig-jcolorbrewer.tar.gz
dpkg-source: info: unpacking biojava6-live_6.1.0+dfsg-5.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying fix_itext_class_updates.patch
dpkg-source: info: applying use_simple_json.patch
dpkg-source: info: applying fix_import.patch
dpkg-source: info: applying fix_ascii_characters_mapping.patch
dpkg-source: info: applying skip_network_related_tests.patch
dpkg-source: info: applying remove_openchart_use.patch
dpkg-source: info: applying ignore_fake_tests.patch
dpkg-source: info: applying poms.patch
dpkg-source: info: applying jmol_path_in_pom.patch
dpkg-source: info: applying remove_tests_needing_junitx.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/2957838/tmp/hooks/D01_modify_environment starting
debug: Running on codethink02-arm64.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Nov  5 17:37 /bin/sh -> /bin/bash
I: Setting pbuilder2's login shell to /bin/bash
I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
I: user script /srv/workspace/pbuilder/2957838/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/2957838/tmp/hooks/D02_print_environment starting
I: set
  BASH=/bin/sh
  BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
  BASH_ALIASES=()
  BASH_ARGC=()
  BASH_ARGV=()
  BASH_CMDS=()
  BASH_LINENO=([0]="12" [1]="0")
  BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
  BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
  BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu")
  BASH_VERSION='5.2.32(1)-release'
  BUILDDIR=/build/reproducible-path
  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
  BUILDUSERNAME=pbuilder2
  BUILD_ARCH=arm64
  DEBIAN_FRONTEND=noninteractive
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
  DIRSTACK=()
  DISTRIBUTION=unstable
  EUID=0
  FUNCNAME=([0]="Echo" [1]="main")
  GROUPS=()
  HOME=/root
  HOSTNAME=i-capture-the-hostname
  HOSTTYPE=aarch64
  HOST_ARCH=arm64
  IFS=' 	
  '
  INVOCATION_ID=0f21f3a912f7473ca487d84c895d34be
  LANG=C
  LANGUAGE=nl_BE:nl
  LC_ALL=C
  MACHTYPE=aarch64-unknown-linux-gnu
  MAIL=/var/mail/root
  OPTERR=1
  OPTIND=1
  OSTYPE=linux-gnu
  PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
  PBCURRENTCOMMANDLINEOPERATION=build
  PBUILDER_OPERATION=build
  PBUILDER_PKGDATADIR=/usr/share/pbuilder
  PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
  PBUILDER_SYSCONFDIR=/etc
  PIPESTATUS=([0]="0")
  POSIXLY_CORRECT=y
  PPID=2957838
  PS4='+ '
  PWD=/
  SHELL=/bin/bash
  SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
  SHLVL=3
  SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.lShG5mJh/pbuilderrc_3iH1 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.lShG5mJh/b2 --logfile b2/build.log biojava6-live_6.1.0+dfsg-5.dsc'
  SUDO_GID=109
  SUDO_UID=104
  SUDO_USER=jenkins
  TERM=unknown
  TZ=/usr/share/zoneinfo/Etc/GMT-14
  UID=0
  USER=root
  _='I: set'
  http_proxy=http://192.168.101.4:3128
I: uname -a
  Linux i-capture-the-hostname 6.1.0-26-cloud-arm64 #1 SMP Debian 6.1.112-1 (2024-09-30) aarch64 GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 Aug  4 21:30 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/2957838/tmp/hooks/D02_print_environment finished
 -> Attempting to satisfy build-dependencies
 -> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: arm64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
 This package was created automatically by pbuilder to satisfy the
 build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), javahelper, maven-debian-helper, default-jdk, default-jdk-doc, junit4, libactivation-java, libciftools-java, libcommons-codec-java, libcommons-math-java, libguava-java, libitext5-java, libjackson2-databind-java, libjaxb-api-java, libjaxb-java, libjgrapht-java, libjmol-java (>= 14.32.77+dfsg-1~), libjson-simple-java, liblog4j2-java, libmaven-antrun-plugin-java, libmaven-assembly-plugin-java, libmaven-dependency-plugin-java, libmaven-deploy-plugin-java, libmaven-enforcer-plugin-java, libmaven-install-plugin-java, libmaven-javadoc-plugin-java, libmaven-jaxb2-plugin-java, libmmtf-java, libslf4j-java, libvecmath-java, libxmlunit-java
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 20087 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
 pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
  Package debhelper-compat is not installed.
 pbuilder-satisfydepends-dummy depends on javahelper; however:
  Package javahelper is not installed.
 pbuilder-satisfydepends-dummy depends on maven-debian-helper; however:
  Package maven-debian-helper is not installed.
 pbuilder-satisfydepends-dummy depends on default-jdk; however:
  Package default-jdk is not installed.
 pbuilder-satisfydepends-dummy depends on default-jdk-doc; however:
  Package default-jdk-doc is not installed.
 pbuilder-satisfydepends-dummy depends on junit4; however:
  Package junit4 is not installed.
 pbuilder-satisfydepends-dummy depends on libactivation-java; however:
  Package libactivation-java is not installed.
 pbuilder-satisfydepends-dummy depends on libciftools-java; however:
  Package libciftools-java is not installed.
 pbuilder-satisfydepends-dummy depends on libcommons-codec-java; however:
  Package libcommons-codec-java is not installed.
 pbuilder-satisfydepends-dummy depends on libcommons-math-java; however:
  Package libcommons-math-java is not installed.
 pbuilder-satisfydepends-dummy depends on libguava-java; however:
  Package libguava-java is not installed.
 pbuilder-satisfydepends-dummy depends on libitext5-java; however:
  Package libitext5-java is not installed.
 pbuilder-satisfydepends-dummy depends on libjackson2-databind-java; however:
  Package libjackson2-databind-java is not installed.
 pbuilder-satisfydepends-dummy depends on libjaxb-api-java; however:
  Package libjaxb-api-java is not installed.
 pbuilder-satisfydepends-dummy depends on libjaxb-java; however:
  Package libjaxb-java is not installed.
 pbuilder-satisfydepends-dummy depends on libjgrapht-java; however:
  Package libjgrapht-java is not installed.
 pbuilder-satisfydepends-dummy depends on libjmol-java (>= 14.32.77+dfsg-1~); however:
  Package libjmol-java is not installed.
 pbuilder-satisfydepends-dummy depends on libjson-simple-java; however:
  Package libjson-simple-java is not installed.
 pbuilder-satisfydepends-dummy depends on liblog4j2-java; however:
  Package liblog4j2-java is not installed.
 pbuilder-satisfydepends-dummy depends on libmaven-antrun-plugin-java; however:
  Package libmaven-antrun-plugin-java is not installed.
 pbuilder-satisfydepends-dummy depends on libmaven-assembly-plugin-java; however:
  Package libmaven-assembly-plugin-java is not installed.
 pbuilder-satisfydepends-dummy depends on libmaven-dependency-plugin-java; however:
  Package libmaven-dependency-plugin-java is not installed.
 pbuilder-satisfydepends-dummy depends on libmaven-deploy-plugin-java; however:
  Package libmaven-deploy-plugin-java is not installed.
 pbuilder-satisfydepends-dummy depends on libmaven-enforcer-plugin-java; however:
  Package libmaven-enforcer-plugin-java is not installed.
 pbuilder-satisfydepends-dummy depends on libmaven-install-plugin-java; however:
  Package libmaven-install-plugin-java is not installed.
 pbuilder-satisfydepends-dummy depends on libmaven-javadoc-plugin-java; however:
  Package libmaven-javadoc-plugin-java is not installed.
 pbuilder-satisfydepends-dummy depends on libmaven-jaxb2-plugin-java; however:
  Package libmaven-jaxb2-plugin-java is not installed.
 pbuilder-satisfydepends-dummy depends on libmmtf-java; however:
  Package libmmtf-java is not installed.
 pbuilder-satisfydepends-dummy depends on libslf4j-java; however:
  Package libslf4j-java is not installed.
 pbuilder-satisfydepends-dummy depends on libvecmath-java; however:
  Package libvecmath-java is not installed.
 pbuilder-satisfydepends-dummy depends on libxmlunit-java; however:
  Package libxmlunit-java is not installed.

Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
  adwaita-icon-theme{a} ant{a} ant-optional{a} at-spi2-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} binfmt-support{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} dbus{a} dbus-bin{a} dbus-daemon{a} dbus-session-bus-common{a} dbus-system-bus-common{a} dbus-user-session{a} dconf-gsettings-backend{a} dconf-service{a} dctrl-tools{a} debhelper{a} default-jdk{a} default-jdk-doc{a} default-jdk-headless{a} default-jre{a} default-jre-headless{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} dwz{a} fastjar{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gpg{a} gpg-agent{a} gpgconf{a} gpgsm{a} groff-base{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} intltool-debian{a} jarwrapper{a} java-common{a} javahelper{a} junit{a} junit4{a} junit5{a} libactivation-java{a} libantlr4-runtime-java{a} libaopalliance-java{a} libapache-pom-java{a} libapfloat-java{a} libapiguardian-java{a} libapparmor1{a} libarchive-zip-perl{a} libargs4j-java{a} libasm-java{a} libasound2-data{a} libasound2t64{a} libassuan9{a} libatinject-jsr330-api-java{a} libatk-bridge2.0-0t64{a} libatk1.0-0t64{a} libatspi2.0-0t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libb-hooks-op-check-perl{a} libbrotli1{a} libbsh-java{a} libcairo-gobject2{a} libcairo2{a} libcdi-api-java{a} libciftools-java{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcloudproviders0{a} libcodemodel-java{a} libcolord2{a} libcom-err2{a} libcommons-beanutils-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-compress-java{a} libcommons-digester-java{a} libcommons-exec-java{a} libcommons-io-java{a} libcommons-lang-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-math-java{a} libcommons-parent-java{a} libcommons-text-java{a} libcommons-validator-java{a} libcups2t64{a} libdatrie1{a} libdbus-1-3{a} libdconf1{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdom4j-java{a} libdoxia-core-java{a} libdoxia-java{a} libdoxia-sitetools-java{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-radeon1{a} libdrm2{a} libdtd-parser-java{a} libdynaloader-functions-perl{a} libedit2{a} libel-api-java{a} libelf1t64{a} libencode-locale-perl{a} libepoxy0{a} liberror-prone-java{a} libexec-maven-plugin-java{a} libexpat1{a} libfastinfoset-java{a} libfastutil-java{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgbm1{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libgif7{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0t64{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgoogle-gson-java{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgtk-3-0t64{a} libgtk-3-common{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libhttpclient-java{a} libhttpcore-java{a} libicu72{a} libimport-into-perl{a} libinchi1.07{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libistack-commons-java{a} libitext5-java{a} libjackson2-annotations-java{a} libjackson2-core-java{a} libjackson2-databind-java{a} libjakarta-activation-java{a} libjansi-java{a} libjaxb-api-java{a} libjaxb-java{a} libjaxen-java{a} libjbig0{a} libjetty9-java{a} libjgrapht-java{a} libjgraphx-java{a} libjheaps-java{a} libjmol-java{a} libjni-inchi-java{a} libjni-inchi-jni{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-jquery-ui-theme-base{a} libjson-simple-java{a} libjsoup-java{a} libjsp-api-java{a} libjsr305-java{a} libjtidy-java{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libksba8{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblightcouch-java{a} libllvm19{a} liblog4j1.2-java{a} liblog4j2-java{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1t64{a} libmaven-antrun-plugin-java{a} libmaven-archiver-java{a} libmaven-artifact-transfer-java{a} libmaven-assembly-plugin-java{a} libmaven-clean-plugin-java{a} libmaven-common-artifact-filters-java{a} libmaven-compiler-plugin-java{a} libmaven-dependency-analyzer-java{a} libmaven-dependency-plugin-java{a} libmaven-dependency-tree-java{a} libmaven-deploy-plugin-java{a} libmaven-enforcer-plugin-java{a} libmaven-file-management-java{a} libmaven-filtering-java{a} libmaven-install-plugin-java{a} libmaven-invoker-java{a} libmaven-jar-plugin-java{a} libmaven-javadoc-plugin-java{a} libmaven-jaxb2-plugin-java{a} libmaven-parent-java{a} libmaven-plugin-tools-java{a} libmaven-reporting-api-java{a} libmaven-reporting-exec-java{a} libmaven-reporting-impl-java{a} libmaven-resolver-java{a} libmaven-resources-plugin-java{a} libmaven-shared-incremental-java{a} libmaven-shared-io-java{a} libmaven-shared-utils-java{a} libmaven-site-plugin-java{a} libmaven3-core-java{a} libmmtf-java{a} libmodule-runtime-perl{a} libmongodb-java{a} libmoo-perl{a} libmsgpack-java{a} libnaga-java{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnpth0t64{a} libnsl2{a} libnspr4{a} libnss3{a} libopentest4j-java{a} libopentest4j-reporting-java{a} liboro-java{a} libpam-systemd{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libparams-classify-perl{a} libpcsclite1{a} libpicocli-java{a} libpipeline1{a} libpixman-1-0{a} libplexus-ant-factory-java{a} libplexus-archiver-java{a} libplexus-bsh-factory-java{a} libplexus-build-api-java{a} libplexus-cipher-java{a} libplexus-classworlds-java{a} libplexus-compiler-java{a} libplexus-component-annotations-java{a} libplexus-container-default-java{a} libplexus-container-default1.5-java{a} libplexus-i18n-java{a} libplexus-interactivity-api-java{a} libplexus-interpolation-java{a} libplexus-io-java{a} libplexus-languages-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libplexus-velocity-java{a} libplexus-xml-java{a} libpng16-16t64{a} libproc2-0{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libqdox2-java{a} libreadline8t64{a} librelaxng-datatype-java{a} librngom-java{a} librole-tiny-perl{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libservlet-api-java{a} libsharpyuv0{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libstax-ex-java{a} libstreambuffer-java{a} libsub-quote-perl{a} libsurefire-java{a} libsystemd-shared{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libtry-tiny-perl{a} libtxw2-java{a} libuchardet0{a} libunivocity-parsers-java{a} liburi-perl{a} libvecmath-java{a} libvelocity-tools-java{a} libvulkan1{a} libwagon-file-java{a} libwagon-http-java{a} libwagon-http-shaded-java{a} libwagon-provider-api-java{a} libwayland-client0{a} libwayland-cursor0{a} libwayland-egl1{a} libwayland-server0{a} libwebp7{a} libwebsocket-api-java{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxbean-reflect-java{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxerces2-java{a} libxext6{a} libxfixes3{a} libxi6{a} libxinerama1{a} libxkbcommon0{a} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxml2-utils{a} libxmlunit-java{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxsom-java{a} libxtst6{a} libxxf86vm1{a} libxz-java{a} libz3-4{a} m4{a} man-db{a} maven{a} maven-debian-helper{a} maven-repo-helper{a} media-types{a} mesa-libgallium{a} netbase{a} openjdk-21-doc{a} openjdk-21-jdk{a} openjdk-21-jdk-headless{a} openjdk-21-jre{a} openjdk-21-jre-headless{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} procps{a} python3{a} python3-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} systemd{a} systemd-sysv{a} tzdata{a} unzip{a} velocity{a} wdiff{a} x11-common{a} xkb-data{a} 
The following packages are RECOMMENDED but will NOT be installed:
  alsa-topology-conf alsa-ucm-conf at-spi2-core chrony curl debian-keyring dput dput-ng dupload equivs fonts-dejavu-extra gnupg-utils gpg-wks-client javascript-common krb5-locales libarchive-cpio-perl libatk-wrapper-java-jni libdata-dump-perl libdistro-info-perl libgdk-pixbuf2.0-bin libgit-wrapper-perl libgitlab-api-v4-perl libglib2.0-data libgtk-3-bin libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjline3-java libjson-perl libkmod2 libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl libnss-systemd librsvg2-common libsasl2-modules libsoap-lite-perl libstring-shellquote-perl libxstring-perl libxt-dev licensecheck lintian linux-sysctl-defaults lynx mesa-vulkan-drivers ntpsec openntpd pristine-tar psmisc python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg strace systemd-cryptsetup systemd-timesyncd wget xdg-user-dirs 
0 packages upgraded, 423 newly installed, 0 to remove and 0 not upgraded.
Need to get 332 MB of archives. After unpacking 1179 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main arm64 libapparmor1 arm64 3.1.7-1+b2 [41.8 kB]
Get: 2 http://deb.debian.org/debian unstable/main arm64 libsystemd-shared arm64 256.7-3 [1841 kB]
Get: 3 http://deb.debian.org/debian unstable/main arm64 systemd arm64 256.7-3 [3259 kB]
Get: 4 http://deb.debian.org/debian unstable/main arm64 systemd-sysv arm64 256.7-3 [58.7 kB]
Get: 5 http://deb.debian.org/debian unstable/main arm64 libdbus-1-3 arm64 1.14.10-6 [196 kB]
Get: 6 http://deb.debian.org/debian unstable/main arm64 dbus-bin arm64 1.14.10-6 [105 kB]
Get: 7 http://deb.debian.org/debian unstable/main arm64 dbus-session-bus-common all 1.14.10-6 [79.2 kB]
Get: 8 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.3-2 [90.1 kB]
Get: 9 http://deb.debian.org/debian unstable/main arm64 dbus-daemon arm64 1.14.10-6 [178 kB]
Get: 10 http://deb.debian.org/debian unstable/main arm64 dbus-system-bus-common all 1.14.10-6 [80.2 kB]
Get: 11 http://deb.debian.org/debian unstable/main arm64 dbus arm64 1.14.10-6 [97.4 kB]
Get: 12 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB]
Get: 13 http://deb.debian.org/debian unstable/main arm64 binfmt-support arm64 2.2.2-7+b1 [68.2 kB]
Get: 14 http://deb.debian.org/debian unstable/main arm64 libpython3.12-minimal arm64 3.12.7-2 [808 kB]
Get: 15 http://deb.debian.org/debian unstable/main arm64 python3.12-minimal arm64 3.12.7-2 [1939 kB]
Get: 16 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.12.6-1 [26.7 kB]
Get: 17 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB]
Get: 18 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB]
Get: 19 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024b-3 [255 kB]
Get: 20 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB]
Get: 21 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1+b1 [23.1 kB]
Get: 22 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB]
Get: 23 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B]
Get: 24 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB]
Get: 25 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB]
Get: 26 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get: 27 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB]
Get: 28 http://deb.debian.org/debian unstable/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB]
Get: 29 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-5 [69.3 kB]
Get: 30 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-5 [159 kB]
Get: 31 http://deb.debian.org/debian unstable/main arm64 libpython3.12-stdlib arm64 3.12.7-2 [1902 kB]
Get: 32 http://deb.debian.org/debian unstable/main arm64 python3.12 arm64 3.12.7-2 [671 kB]
Get: 33 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.12.6-1 [9692 B]
Get: 34 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.12.6-1 [27.8 kB]
Get: 35 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB]
Get: 36 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-6 [62.3 kB]
Get: 37 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-6 [872 kB]
Get: 38 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB]
Get: 39 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.3.2-2 [1347 kB]
Get: 40 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20240203 [158 kB]
Get: 41 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB]
Get: 42 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB]
Get: 43 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB]
Get: 44 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB]
Get: 45 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB]
Get: 46 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB]
Get: 47 http://deb.debian.org/debian unstable/main arm64 libpam-systemd arm64 256.7-3 [260 kB]
Get: 48 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-10 [96.5 kB]
Get: 49 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB]
Get: 50 http://deb.debian.org/debian unstable/main arm64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [311 kB]
Get: 51 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.82.2-2 [1409 kB]
Get: 52 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB]
Get: 53 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.1 [630 kB]
Get: 54 http://deb.debian.org/debian unstable/main arm64 shared-mime-info arm64 2.4-5+b1 [755 kB]
Get: 55 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB]
Get: 56 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.44-2 [273 kB]
Get: 57 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB]
Get: 58 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB]
Get: 59 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB]
Get: 60 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.4.0-0.1+b1 [112 kB]
Get: 61 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.4.0-0.1+b1 [268 kB]
Get: 62 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB]
Get: 63 http://deb.debian.org/debian unstable/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.12+dfsg-1+b1 [131 kB]
Get: 64 http://deb.debian.org/debian unstable/main arm64 gtk-update-icon-cache arm64 4.16.3+ds-2 [49.7 kB]
Get: 65 http://deb.debian.org/debian unstable/main arm64 hicolor-icon-theme all 0.18-1 [12.0 kB]
Get: 66 http://deb.debian.org/debian unstable/main arm64 adwaita-icon-theme all 47.0-2 [463 kB]
Get: 67 http://deb.debian.org/debian unstable/main arm64 ca-certificates-java all 20240118 [11.6 kB]
Get: 68 http://deb.debian.org/debian unstable/main arm64 java-common all 0.76 [6776 B]
Get: 69 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.16-2 [151 kB]
Get: 70 http://deb.debian.org/debian unstable/main arm64 libnspr4 arm64 2:4.35-1.1+b1 [101 kB]
Get: 71 http://deb.debian.org/debian unstable/main arm64 libnss3 arm64 2:3.105-2 [1292 kB]
Get: 72 http://deb.debian.org/debian unstable/main arm64 libpcsclite1 arm64 2.3.0-3 [55.1 kB]
Get: 73 http://deb.debian.org/debian unstable/main arm64 openjdk-21-jre-headless arm64 21.0.5+11-1 [40.6 MB]
Get: 74 http://deb.debian.org/debian unstable/main arm64 default-jre-headless arm64 2:1.21-76 [3192 B]
Get: 75 http://deb.debian.org/debian unstable/main arm64 ant all 1.10.15-1 [2163 kB]
Get: 76 http://deb.debian.org/debian unstable/main arm64 ant-optional all 1.10.15-1 [456 kB]
Get: 77 http://deb.debian.org/debian unstable/main arm64 at-spi2-common all 2.54.0-1 [170 kB]
Get: 78 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB]
Get: 79 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB]
Get: 80 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get: 81 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get: 82 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB]
Get: 83 http://deb.debian.org/debian unstable/main arm64 dbus-user-session arm64 1.14.10-6 [79.0 kB]
Get: 84 http://deb.debian.org/debian unstable/main arm64 libdconf1 arm64 0.40.0-4+b3 [40.4 kB]
Get: 85 http://deb.debian.org/debian unstable/main arm64 dconf-service arm64 0.40.0-4+b3 [31.1 kB]
Get: 86 http://deb.debian.org/debian unstable/main arm64 dconf-gsettings-backend arm64 0.40.0-4+b3 [27.4 kB]
Get: 87 http://deb.debian.org/debian unstable/main arm64 dctrl-tools arm64 2.24-3+b1 [125 kB]
Get: 88 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB]
Get: 89 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB]
Get: 90 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 91 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 92 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 93 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 94 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get: 95 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get: 96 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB]
Get: 97 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 98 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 99 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB]
Get: 100 http://deb.debian.org/debian unstable/main arm64 libatk1.0-0t64 arm64 2.54.0-1 [49.7 kB]
Get: 101 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB]
Get: 102 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.2-3+b2 [24.4 kB]
Get: 103 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB]
Get: 104 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.10-1 [337 kB]
Get: 105 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.10-1 [788 kB]
Get: 106 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB]
Get: 107 http://deb.debian.org/debian unstable/main arm64 libxi6 arm64 2:1.8.2-1 [77.8 kB]
Get: 108 http://deb.debian.org/debian unstable/main arm64 libatspi2.0-0t64 arm64 2.54.0-1 [72.9 kB]
Get: 109 http://deb.debian.org/debian unstable/main arm64 libatk-bridge2.0-0t64 arm64 2.54.0-1 [64.4 kB]
Get: 110 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b5 [296 kB]
Get: 111 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB]
Get: 112 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get: 113 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB]
Get: 114 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-1.1+b1 [318 kB]
Get: 115 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-1.1+b1 [387 kB]
Get: 116 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB]
Get: 117 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB]
Get: 118 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB]
Get: 119 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b2 [27.2 kB]
Get: 120 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.2-2 [483 kB]
Get: 121 http://deb.debian.org/debian unstable/main arm64 libcairo-gobject2 arm64 1.18.2-2 [130 kB]
Get: 122 http://deb.debian.org/debian unstable/main arm64 libcloudproviders0 arm64 0.3.6-1+b1 [27.7 kB]
Get: 123 http://deb.debian.org/debian unstable/main arm64 libcolord2 arm64 1.4.7-1+b2 [130 kB]
Get: 124 http://deb.debian.org/debian unstable/main arm64 libavahi-common-data arm64 0.8-13+b3 [112 kB]
Get: 125 http://deb.debian.org/debian unstable/main arm64 libavahi-common3 arm64 0.8-13+b3 [42.3 kB]
Get: 126 http://deb.debian.org/debian unstable/main arm64 libavahi-client3 arm64 0.8-13+b3 [46.0 kB]
Get: 127 http://deb.debian.org/debian unstable/main arm64 libcups2t64 arm64 2.4.10-2 [235 kB]
Get: 128 http://deb.debian.org/debian unstable/main arm64 libepoxy0 arm64 1.5.10-2 [200 kB]
Get: 129 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.15-1 [71.8 kB]
Get: 130 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB]
Get: 131 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.0.1-1 [441 kB]
Get: 132 http://deb.debian.org/debian unstable/main arm64 fontconfig arm64 2.15.0-1.1+b1 [463 kB]
Get: 133 http://deb.debian.org/debian unstable/main arm64 libthai-data all 0.1.29-2 [168 kB]
Get: 134 http://deb.debian.org/debian unstable/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB]
Get: 135 http://deb.debian.org/debian unstable/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB]
Get: 136 http://deb.debian.org/debian unstable/main arm64 libpango-1.0-0 arm64 1.54.0+ds-3 [210 kB]
Get: 137 http://deb.debian.org/debian unstable/main arm64 libpangoft2-1.0-0 arm64 1.54.0+ds-3 [51.8 kB]
Get: 138 http://deb.debian.org/debian unstable/main arm64 libpangocairo-1.0-0 arm64 1.54.0+ds-3 [33.5 kB]
Get: 139 http://deb.debian.org/debian unstable/main arm64 libwayland-client0 arm64 1.23.0-1+b1 [26.0 kB]
Get: 140 http://deb.debian.org/debian unstable/main arm64 libwayland-cursor0 arm64 1.23.0-1+b1 [11.5 kB]
Get: 141 http://deb.debian.org/debian unstable/main arm64 libwayland-egl1 arm64 1.23.0-1+b1 [5768 B]
Get: 142 http://deb.debian.org/debian unstable/main arm64 libxcomposite1 arm64 1:0.4.6-1 [16.4 kB]
Get: 143 http://deb.debian.org/debian unstable/main arm64 libxfixes3 arm64 1:6.0.0-2+b2 [20.5 kB]
Get: 144 http://deb.debian.org/debian unstable/main arm64 libxcursor1 arm64 1:1.2.2-1+b1 [37.1 kB]
Get: 145 http://deb.debian.org/debian unstable/main arm64 libxdamage1 arm64 1:1.1.6-1+b2 [15.6 kB]
Get: 146 http://deb.debian.org/debian unstable/main arm64 libxinerama1 arm64 2:1.1.4-3+b2 [16.1 kB]
Get: 147 http://deb.debian.org/debian unstable/main arm64 xkb-data all 2.42-1 [790 kB]
Get: 148 http://deb.debian.org/debian unstable/main arm64 libxkbcommon0 arm64 1.6.0-1+b2 [105 kB]
Get: 149 http://deb.debian.org/debian unstable/main arm64 libxrandr2 arm64 2:1.5.4-1+b1 [36.0 kB]
Get: 150 http://deb.debian.org/debian unstable/main arm64 libgtk-3-common all 3.24.43-4 [4657 kB]
Get: 151 http://deb.debian.org/debian unstable/main arm64 libgtk-3-0t64 arm64 3.24.43-4 [2546 kB]
Get: 152 http://deb.debian.org/debian unstable/main arm64 libglvnd0 arm64 1.7.0-1+b2 [41.6 kB]
Get: 153 http://deb.debian.org/debian unstable/main arm64 libdrm-common all 2.4.123-1 [8084 B]
Get: 154 http://deb.debian.org/debian unstable/main arm64 libdrm2 arm64 2.4.123-1 [38.0 kB]
Get: 155 http://deb.debian.org/debian unstable/main arm64 libglapi-mesa arm64 24.2.6-1 [47.8 kB]
Get: 156 http://deb.debian.org/debian unstable/main arm64 libx11-xcb1 arm64 2:1.8.10-1 [241 kB]
Get: 157 http://deb.debian.org/debian unstable/main arm64 libxcb-dri2-0 arm64 1.17.0-2+b1 [107 kB]
Get: 158 http://deb.debian.org/debian unstable/main arm64 libxcb-dri3-0 arm64 1.17.0-2+b1 [107 kB]
Get: 159 http://deb.debian.org/debian unstable/main arm64 libxcb-glx0 arm64 1.17.0-2+b1 [123 kB]
Get: 160 http://deb.debian.org/debian unstable/main arm64 libxcb-present0 arm64 1.17.0-2+b1 [106 kB]
Get: 161 http://deb.debian.org/debian unstable/main arm64 libxcb-randr0 arm64 1.17.0-2+b1 [117 kB]
Get: 162 http://deb.debian.org/debian unstable/main arm64 libxcb-sync1 arm64 1.17.0-2+b1 [109 kB]
Get: 163 http://deb.debian.org/debian unstable/main arm64 libxcb-xfixes0 arm64 1.17.0-2+b1 [110 kB]
Get: 164 http://deb.debian.org/debian unstable/main arm64 libxshmfence1 arm64 1.3-1+b2 [9076 B]
Get: 165 http://deb.debian.org/debian unstable/main arm64 libxxf86vm1 arm64 1:1.1.4-1+b3 [19.2 kB]
Get: 166 http://deb.debian.org/debian unstable/main arm64 libdrm-amdgpu1 arm64 2.4.123-1 [21.6 kB]
Get: 167 http://deb.debian.org/debian unstable/main arm64 libdrm-radeon1 arm64 2.4.123-1 [21.3 kB]
Get: 168 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20240808-1 [89.2 kB]
Get: 169 http://deb.debian.org/debian unstable/main arm64 libz3-4 arm64 4.13.3-1 [7507 kB]
Get: 170 http://deb.debian.org/debian unstable/main arm64 libllvm19 arm64 1:19.1.3-1 [23.3 MB]
Get: 171 http://deb.debian.org/debian unstable/main arm64 libsensors-config all 1:3.6.0-10 [14.6 kB]
Get: 172 http://deb.debian.org/debian unstable/main arm64 libsensors5 arm64 1:3.6.0-10+b1 [34.3 kB]
Get: 173 http://deb.debian.org/debian unstable/main arm64 mesa-libgallium arm64 24.2.6-1 [7688 kB]
Get: 174 http://deb.debian.org/debian unstable/main arm64 libvulkan1 arm64 1.3.296.0-1 [123 kB]
Get: 175 http://deb.debian.org/debian unstable/main arm64 libwayland-server0 arm64 1.23.0-1+b1 [33.4 kB]
Get: 176 http://deb.debian.org/debian unstable/main arm64 libgbm1 arm64 24.2.6-1 [42.0 kB]
Get: 177 http://deb.debian.org/debian unstable/main arm64 libgl1-mesa-dri arm64 24.2.6-1 [43.6 kB]
Get: 178 http://deb.debian.org/debian unstable/main arm64 libglx-mesa0 arm64 24.2.6-1 [152 kB]
Get: 179 http://deb.debian.org/debian unstable/main arm64 libglx0 arm64 1.7.0-1+b2 [31.1 kB]
Get: 180 http://deb.debian.org/debian unstable/main arm64 libgl1 arm64 1.7.0-1+b2 [90.9 kB]
Get: 181 http://deb.debian.org/debian unstable/main arm64 libasound2-data all 1.2.12-1 [21.0 kB]
Get: 182 http://deb.debian.org/debian unstable/main arm64 libasound2t64 arm64 1.2.12-1+b1 [336 kB]
Get: 183 http://deb.debian.org/debian unstable/main arm64 libgif7 arm64 5.2.2-1+b1 [44.2 kB]
Get: 184 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+23.1 [216 kB]
Get: 185 http://deb.debian.org/debian unstable/main arm64 libxtst6 arm64 2:1.2.3-1.1+b2 [26.0 kB]
Get: 186 http://deb.debian.org/debian unstable/main arm64 openjdk-21-jre arm64 21.0.5+11-1 [193 kB]
Get: 187 http://deb.debian.org/debian unstable/main arm64 default-jre arm64 2:1.21-76 [1068 B]
Get: 188 http://deb.debian.org/debian unstable/main arm64 openjdk-21-jdk-headless arm64 21.0.5+11-1 [81.9 MB]
Get: 189 http://deb.debian.org/debian unstable/main arm64 default-jdk-headless arm64 2:1.21-76 [1124 B]
Get: 190 http://deb.debian.org/debian unstable/main arm64 openjdk-21-jdk arm64 21.0.5+11-1 [3422 kB]
Get: 191 http://deb.debian.org/debian unstable/main arm64 default-jdk arm64 2:1.21-76 [1076 B]
Get: 192 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 193 http://deb.debian.org/debian unstable/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get: 194 http://deb.debian.org/debian unstable/main arm64 libjs-jquery-ui-theme-base all 1.12.1+dfsg-1.1 [44.3 kB]
Get: 195 http://deb.debian.org/debian unstable/main arm64 openjdk-21-doc all 21.0.5+11-1 [13.2 MB]
Get: 196 http://deb.debian.org/debian unstable/main arm64 default-jdk-doc arm64 2:1.21-76 [3264 B]
Get: 197 http://deb.debian.org/debian unstable/main arm64 libassuan9 arm64 3.0.1-2 [58.1 kB]
Get: 198 http://deb.debian.org/debian unstable/main arm64 gpgconf arm64 2.2.45-2 [114 kB]
Get: 199 http://deb.debian.org/debian unstable/main arm64 libksba8 arm64 1.6.7-2+b1 [125 kB]
Get: 200 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB]
Get: 201 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB]
Get: 202 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3+b1 [175 kB]
Get: 203 http://deb.debian.org/debian unstable/main arm64 libnpth0t64 arm64 1.6-3.1+b1 [18.1 kB]
Get: 204 http://deb.debian.org/debian unstable/main arm64 dirmngr arm64 2.2.45-2 [343 kB]
Get: 205 http://deb.debian.org/debian unstable/main arm64 gnupg-l10n all 2.2.45-2 [705 kB]
Get: 206 http://deb.debian.org/debian unstable/main arm64 gpg arm64 2.2.45-2 [481 kB]
Get: 207 http://deb.debian.org/debian unstable/main arm64 pinentry-curses arm64 1.2.1-4+b1 [76.7 kB]
Get: 208 http://deb.debian.org/debian unstable/main arm64 gpg-agent arm64 2.2.45-2 [230 kB]
Get: 209 http://deb.debian.org/debian unstable/main arm64 gpgsm arm64 2.2.45-2 [232 kB]
Get: 210 http://deb.debian.org/debian unstable/main arm64 gnupg all 2.2.45-2 [376 kB]
Get: 211 http://deb.debian.org/debian unstable/main arm64 libfile-dirlist-perl all 0.05-3 [7600 B]
Get: 212 http://deb.debian.org/debian unstable/main arm64 libfile-which-perl all 1.27-2 [15.1 kB]
Get: 213 http://deb.debian.org/debian unstable/main arm64 libfile-homedir-perl all 1.006-2 [42.4 kB]
Get: 214 http://deb.debian.org/debian unstable/main arm64 libfile-touch-perl all 0.12-2 [8816 B]
Get: 215 http://deb.debian.org/debian unstable/main arm64 libio-pty-perl arm64 1:1.20-1+b2 [34.0 kB]
Get: 216 http://deb.debian.org/debian unstable/main arm64 libipc-run-perl all 20231003.0-2 [101 kB]
Get: 217 http://deb.debian.org/debian unstable/main arm64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB]
Get: 218 http://deb.debian.org/debian unstable/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b4 [34.9 kB]
Get: 219 http://deb.debian.org/debian unstable/main arm64 libb-hooks-op-check-perl arm64 0.22-3+b2 [10.6 kB]
Get: 220 http://deb.debian.org/debian unstable/main arm64 libdynaloader-functions-perl all 0.004-1 [12.1 kB]
Get: 221 http://deb.debian.org/debian unstable/main arm64 libdevel-callchecker-perl arm64 0.009-1+b1 [16.3 kB]
Get: 222 http://deb.debian.org/debian unstable/main arm64 libparams-classify-perl arm64 0.015-2+b4 [22.3 kB]
Get: 223 http://deb.debian.org/debian unstable/main arm64 libmodule-runtime-perl all 0.016-2 [19.6 kB]
Get: 224 http://deb.debian.org/debian unstable/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB]
Get: 225 http://deb.debian.org/debian unstable/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB]
Get: 226 http://deb.debian.org/debian unstable/main arm64 libsub-quote-perl all 2.006008-1 [21.8 kB]
Get: 227 http://deb.debian.org/debian unstable/main arm64 libmoo-perl all 2.005005-1 [58.0 kB]
Get: 228 http://deb.debian.org/debian unstable/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB]
Get: 229 http://deb.debian.org/debian unstable/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB]
Get: 230 http://deb.debian.org/debian unstable/main arm64 libhttp-date-perl all 6.06-1 [10.7 kB]
Get: 231 http://deb.debian.org/debian unstable/main arm64 libfile-listing-perl all 6.16-1 [12.4 kB]
Get: 232 http://deb.debian.org/debian unstable/main arm64 libhtml-tagset-perl all 3.24-1 [14.7 kB]
Get: 233 http://deb.debian.org/debian unstable/main arm64 liburi-perl all 5.30-1 [105 kB]
Get: 234 http://deb.debian.org/debian unstable/main arm64 libhtml-parser-perl arm64 3.83-1+b1 [97.5 kB]
Get: 235 http://deb.debian.org/debian unstable/main arm64 libhtml-tree-perl all 5.07-3 [211 kB]
Get: 236 http://deb.debian.org/debian unstable/main arm64 libclone-perl arm64 0.47-1+b1 [13.7 kB]
Get: 237 http://deb.debian.org/debian unstable/main arm64 libio-html-perl all 1.004-3 [16.2 kB]
Get: 238 http://deb.debian.org/debian unstable/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB]
Get: 239 http://deb.debian.org/debian unstable/main arm64 libhttp-message-perl all 7.00-2 [79.8 kB]
Get: 240 http://deb.debian.org/debian unstable/main arm64 libhttp-cookies-perl all 6.11-1 [19.1 kB]
Get: 241 http://deb.debian.org/debian unstable/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB]
Get: 242 http://deb.debian.org/debian unstable/main arm64 perl-openssl-defaults arm64 7+b2 [6712 B]
Get: 243 http://deb.debian.org/debian unstable/main arm64 libnet-ssleay-perl arm64 1.94-2 [323 kB]
Get: 244 http://deb.debian.org/debian unstable/main arm64 libio-socket-ssl-perl all 2.089-1 [223 kB]
Get: 245 http://deb.debian.org/debian unstable/main arm64 libnet-http-perl all 6.23-1 [23.9 kB]
Get: 246 http://deb.debian.org/debian unstable/main arm64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB]
Get: 247 http://deb.debian.org/debian unstable/main arm64 libtry-tiny-perl all 0.32-1 [22.9 kB]
Get: 248 http://deb.debian.org/debian unstable/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB]
Get: 249 http://deb.debian.org/debian unstable/main arm64 libwww-perl all 6.77-1 [183 kB]
Get: 250 http://deb.debian.org/debian unstable/main arm64 patchutils arm64 0.4.2-1+b1 [71.3 kB]
Get: 251 http://deb.debian.org/debian unstable/main arm64 wdiff arm64 1.2.2-6+b1 [119 kB]
Get: 252 http://deb.debian.org/debian unstable/main arm64 devscripts all 2.24.2 [1076 kB]
Get: 253 http://deb.debian.org/debian unstable/main arm64 fastjar arm64 2:0.98-7+b1 [74.9 kB]
Get: 254 http://deb.debian.org/debian unstable/main arm64 jarwrapper all 0.80 [9692 B]
Get: 255 http://deb.debian.org/debian unstable/main arm64 javahelper all 0.80 [80.4 kB]
Get: 256 http://deb.debian.org/debian unstable/main arm64 junit all 3.8.2-10 [108 kB]
Get: 257 http://deb.debian.org/debian unstable/main arm64 libhamcrest-java all 2.2-2 [121 kB]
Get: 258 http://deb.debian.org/debian unstable/main arm64 junit4 all 4.13.2-5 [350 kB]
Get: 259 http://deb.debian.org/debian unstable/main arm64 libapiguardian-java all 1.1.2-1 [4656 B]
Get: 260 http://deb.debian.org/debian unstable/main arm64 libopentest4j-java all 1.2.0-4 [9516 B]
Get: 261 http://deb.debian.org/debian unstable/main arm64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB]
Get: 262 http://deb.debian.org/debian unstable/main arm64 libpicocli-java all 4.6.2-2 [390 kB]
Get: 263 http://deb.debian.org/debian unstable/main arm64 libunivocity-parsers-java all 2.9.1-1 [397 kB]
Get: 264 http://deb.debian.org/debian unstable/main arm64 junit5 all 5.10.3-1 [2459 kB]
Get: 265 http://deb.debian.org/debian unstable/main arm64 libactivation-java all 1.2.0-2 [84.7 kB]
Get: 266 http://deb.debian.org/debian unstable/main arm64 libantlr4-runtime-java all 4.9.2-2 [317 kB]
Get: 267 http://deb.debian.org/debian unstable/main arm64 libaopalliance-java all 20070526-7 [8572 B]
Get: 268 http://deb.debian.org/debian unstable/main arm64 libapache-pom-java all 33-2 [5852 B]
Get: 269 http://deb.debian.org/debian unstable/main arm64 libapfloat-java all 1.14.0-1 [725 kB]
Get: 270 http://deb.debian.org/debian unstable/main arm64 libargs4j-java all 2.33-2 [138 kB]
Get: 271 http://deb.debian.org/debian unstable/main arm64 libasm-java all 9.7.1-1 [391 kB]
Get: 272 http://deb.debian.org/debian unstable/main arm64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B]
Get: 273 http://deb.debian.org/debian unstable/main arm64 libbsh-java all 2.0b4-20 [291 kB]
Get: 274 http://deb.debian.org/debian unstable/main arm64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B]
Get: 275 http://deb.debian.org/debian unstable/main arm64 libcdi-api-java all 1.2-4 [55.3 kB]
Get: 276 http://deb.debian.org/debian unstable/main arm64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB]
Get: 277 http://deb.debian.org/debian unstable/main arm64 libgoogle-gson-java all 2.10.1-1 [262 kB]
Get: 278 http://deb.debian.org/debian unstable/main arm64 libciftools-java all 6.0.0-1 [2211 kB]
Get: 279 http://deb.debian.org/debian unstable/main arm64 libjaxen-java all 1.1.6-5 [214 kB]
Get: 280 http://deb.debian.org/debian unstable/main arm64 libdom4j-java all 2.1.4-1 [312 kB]
Get: 281 http://deb.debian.org/debian unstable/main arm64 libcommons-parent-java all 56-1 [10.8 kB]
Get: 282 http://deb.debian.org/debian unstable/main arm64 libcommons-io-java all 2.17.0-1 [488 kB]
Get: 283 http://deb.debian.org/debian unstable/main arm64 libslf4j-java all 1.7.32-1 [144 kB]
Get: 284 http://deb.debian.org/debian unstable/main arm64 libmaven-shared-utils-java all 3.4.2-1 [137 kB]
Get: 285 http://deb.debian.org/debian unstable/main arm64 libcommons-cli-java all 1.6.0-1 [60.4 kB]
Get: 286 http://deb.debian.org/debian unstable/main arm64 libcommons-lang3-java all 3.17.0-1 [641 kB]
Get: 287 http://deb.debian.org/debian unstable/main arm64 liberror-prone-java all 2.18.0-1 [22.5 kB]
Get: 288 http://deb.debian.org/debian unstable/main arm64 libjsr305-java all 0.1~+svn49-11 [26.9 kB]
Get: 289 http://deb.debian.org/debian unstable/main arm64 libguava-java all 32.0.1-1 [2708 kB]
Get: 290 http://deb.debian.org/debian unstable/main arm64 libguice-java all 4.2.3-2 [1435 kB]
Get: 291 http://deb.debian.org/debian unstable/main arm64 libmaven-parent-java all 43-2 [6252 B]
Get: 292 http://deb.debian.org/debian unstable/main arm64 libplexus-utils2-java all 3.4.2-1 [258 kB]
Get: 293 http://deb.debian.org/debian unstable/main arm64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB]
Get: 294 http://deb.debian.org/debian unstable/main arm64 libmaven-resolver-java all 1.6.3-1 [548 kB]
Get: 295 http://deb.debian.org/debian unstable/main arm64 libplexus-cipher-java all 2.0-1 [14.9 kB]
Get: 296 http://deb.debian.org/debian unstable/main arm64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB]
Get: 297 http://deb.debian.org/debian unstable/main arm64 libplexus-component-annotations-java all 2.1.1-1 [7660 B]
Get: 298 http://deb.debian.org/debian unstable/main arm64 libplexus-interpolation-java all 1.27-1 [76.8 kB]
Get: 299 http://deb.debian.org/debian unstable/main arm64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB]
Get: 300 http://deb.debian.org/debian unstable/main arm64 libsisu-inject-java all 0.3.4-2 [347 kB]
Get: 301 http://deb.debian.org/debian unstable/main arm64 libsisu-plexus-java all 0.3.4-3 [181 kB]
Get: 302 http://deb.debian.org/debian unstable/main arm64 libmaven3-core-java all 3.8.8-1 [1579 kB]
Get: 303 http://deb.debian.org/debian unstable/main arm64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB]
Get: 304 http://deb.debian.org/debian unstable/main arm64 libmaven-file-management-java all 3.0.0-1 [35.1 kB]
Get: 305 http://deb.debian.org/debian unstable/main arm64 libcommons-codec-java all 1.17.1-1 [303 kB]
Get: 306 http://deb.debian.org/debian unstable/main arm64 libcommons-compress-java all 1.27.1-2 [641 kB]
Get: 307 http://deb.debian.org/debian unstable/main arm64 libplexus-io-java all 3.3.1-2 [65.3 kB]
Get: 308 http://deb.debian.org/debian unstable/main arm64 libsnappy1v5 arm64 1.2.1-1+b1 [28.7 kB]
Get: 309 http://deb.debian.org/debian unstable/main arm64 libsnappy-jni arm64 1.1.10.5-2+b1 [6712 B]
Get: 310 http://deb.debian.org/debian unstable/main arm64 libsnappy-java all 1.1.10.5-2 [87.5 kB]
Get: 311 http://deb.debian.org/debian unstable/main arm64 libxz-java all 1.9-1 [143 kB]
Get: 312 http://deb.debian.org/debian unstable/main arm64 libplexus-archiver-java all 4.6.1-1 [187 kB]
Get: 313 http://deb.debian.org/debian unstable/main arm64 libhttpcore-java all 4.4.16-1 [636 kB]
Get: 314 http://deb.debian.org/debian unstable/main arm64 libcommons-logging-java all 1.3.0-1 [68.6 kB]
Get: 315 http://deb.debian.org/debian unstable/main arm64 libhttpclient-java all 4.5.14-1 [1247 kB]
Get: 316 http://deb.debian.org/debian unstable/main arm64 libjsoup-java all 1.15.3-1 [431 kB]
Get: 317 http://deb.debian.org/debian unstable/main arm64 libwagon-http-java all 3.5.3-1 [49.5 kB]
Get: 318 http://deb.debian.org/debian unstable/main arm64 libistack-commons-java all 3.0.6-5 [145 kB]
Get: 319 http://deb.debian.org/debian unstable/main arm64 libcodemodel-java all 2.6+jaxb2.3.0.1-11 [164 kB]
Get: 320 http://deb.debian.org/debian unstable/main arm64 libcommons-collections3-java all 3.2.2-3 [530 kB]
Get: 321 http://deb.debian.org/debian unstable/main arm64 libcommons-beanutils-java all 1.9.4-2 [233 kB]
Get: 322 http://deb.debian.org/debian unstable/main arm64 libcommons-digester-java all 1.8.1-7 [138 kB]
Get: 323 http://deb.debian.org/debian unstable/main arm64 libcommons-exec-java all 1.3-2 [48.1 kB]
Get: 324 http://deb.debian.org/debian unstable/main arm64 libcommons-lang-java all 2.6-10 [273 kB]
Get: 325 http://deb.debian.org/debian unstable/main arm64 libcommons-math-java all 2.2-9 [933 kB]
Get: 326 http://deb.debian.org/debian unstable/main arm64 libmaven-archiver-java all 3.6.2-1 [26.1 kB]
Get: 327 http://deb.debian.org/debian unstable/main arm64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB]
Get: 328 http://deb.debian.org/debian unstable/main arm64 libcommons-text-java all 1.12.0-1 [222 kB]
Get: 329 http://deb.debian.org/debian unstable/main arm64 libcommons-validator-java all 1:1.7-1 [181 kB]
Get: 330 http://deb.debian.org/debian unstable/main arm64 libdoxia-core-java all 2.0.0-1 [149 kB]
Get: 331 http://deb.debian.org/debian unstable/main arm64 libplexus-xml-java all 3.0.1-2 [93.7 kB]
Get: 332 http://deb.debian.org/debian unstable/main arm64 libdoxia-java all 2.0.0-1 [113 kB]
Get: 333 http://deb.debian.org/debian unstable/main arm64 libmaven-reporting-api-java all 4.0.0-1 [6724 B]
Get: 334 http://deb.debian.org/debian unstable/main arm64 libxbean-reflect-java all 4.5-9 [132 kB]
Get: 335 http://deb.debian.org/debian unstable/main arm64 libplexus-container-default-java all 2.1.1-1 [193 kB]
Get: 336 http://deb.debian.org/debian unstable/main arm64 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB]
Get: 337 http://deb.debian.org/debian unstable/main arm64 velocity all 1.7-7 [431 kB]
Get: 338 http://deb.debian.org/debian unstable/main arm64 libplexus-velocity-java all 1.2-4 [9676 B]
Get: 339 http://deb.debian.org/debian unstable/main arm64 liboro-java all 2.0.8a-14 [70.5 kB]
Get: 340 http://deb.debian.org/debian unstable/main arm64 libvelocity-tools-java all 2.0-9 [311 kB]
Get: 341 http://deb.debian.org/debian unstable/main arm64 libdoxia-sitetools-java all 2.0.0-1 [176 kB]
Get: 342 http://deb.debian.org/debian unstable/main arm64 libdtd-parser-java all 1.2-1 [64.9 kB]
Get: 343 http://deb.debian.org/debian unstable/main arm64 libel-api-java all 3.0.0-3 [64.9 kB]
Get: 344 http://deb.debian.org/debian unstable/main arm64 libexec-maven-plugin-java all 3.1.0-2 [66.7 kB]
Get: 345 http://deb.debian.org/debian unstable/main arm64 libjaxb-api-java all 2.3.1-1 [119 kB]
Get: 346 http://deb.debian.org/debian unstable/main arm64 libstax-ex-java all 1.7.8-3 [40.9 kB]
Get: 347 http://deb.debian.org/debian unstable/main arm64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB]
Get: 348 http://deb.debian.org/debian unstable/main arm64 librelaxng-datatype-java all 1.0+ds1-3.1 [11.7 kB]
Get: 349 http://deb.debian.org/debian unstable/main arm64 libxsom-java all 2.3.0.1-11 [401 kB]
Get: 350 http://deb.debian.org/debian unstable/main arm64 libfastinfoset-java all 1.2.12-3 [343 kB]
Get: 351 http://deb.debian.org/debian unstable/main arm64 libfastutil-java all 8.5.15+dfsg-1 [20.0 MB]
Get: 352 http://deb.debian.org/debian unstable/main arm64 libinchi1.07 arm64 1.07.1+dfsg-4 [499 kB]
Get: 353 http://deb.debian.org/debian unstable/main arm64 libitext5-java all 5.5.13.3-4 [2667 kB]
Get: 354 http://deb.debian.org/debian unstable/main arm64 libjackson2-annotations-java all 2.14.0-1 [68.8 kB]
Get: 355 http://deb.debian.org/debian unstable/main arm64 libjackson2-core-java all 2.14.1-1 [447 kB]
Get: 356 http://deb.debian.org/debian unstable/main arm64 libjackson2-databind-java all 2.14.0-1 [1584 kB]
Get: 357 http://deb.debian.org/debian unstable/main arm64 libjakarta-activation-java all 2.0.0-1 [59.8 kB]
Get: 358 http://deb.debian.org/debian unstable/main arm64 libjansi-java all 2.4.1-2 [100 kB]
Get: 359 http://deb.debian.org/debian unstable/main arm64 librngom-java all 2.3.0.1-11 [292 kB]
Get: 360 http://deb.debian.org/debian unstable/main arm64 libtxw2-java all 2.3.0.1-11 [134 kB]
Get: 361 http://deb.debian.org/debian unstable/main arm64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB]
Get: 362 http://deb.debian.org/debian unstable/main arm64 libjaxb-java all 2.3.0.1-11 [1980 kB]
Get: 363 http://deb.debian.org/debian unstable/main arm64 libjsp-api-java all 2.3.4-3 [53.7 kB]
Get: 364 http://deb.debian.org/debian unstable/main arm64 libservlet-api-java all 4.0.1-2 [81.0 kB]
Get: 365 http://deb.debian.org/debian unstable/main arm64 libwebsocket-api-java all 1.1-2 [40.1 kB]
Get: 366 http://deb.debian.org/debian unstable/main arm64 libjetty9-java all 9.4.56-1 [2964 kB]
Get: 367 http://deb.debian.org/debian unstable/main arm64 libjheaps-java all 0.14-2 [144 kB]
Get: 368 http://deb.debian.org/debian unstable/main arm64 libxml-commons-external-java all 1.4.01-6 [240 kB]
Get: 369 http://deb.debian.org/debian unstable/main arm64 libxerces2-java all 2.12.2-1 [1440 kB]
Get: 370 http://deb.debian.org/debian unstable/main arm64 libjgraphx-java all 2.1.0.7-4 [807 kB]
Get: 371 http://deb.debian.org/debian unstable/main arm64 libjgrapht-java all 1.5.2-1 [1610 kB]
Get: 372 http://deb.debian.org/debian unstable/main arm64 libjni-inchi-jni arm64 0.8+dfsg-8 [9480 B]
Get: 373 http://deb.debian.org/debian unstable/main arm64 libmaven-shared-incremental-java all 1.1-6 [9916 B]
Get: 374 http://deb.debian.org/debian unstable/main arm64 libplexus-compiler-java all 2.13.0-1 [99.5 kB]
Get: 375 http://deb.debian.org/debian unstable/main arm64 libqdox2-java all 2.0.3-1 [296 kB]
Get: 376 http://deb.debian.org/debian unstable/main arm64 libplexus-languages-java all 1.1.1-2 [47.3 kB]
Get: 377 http://deb.debian.org/debian unstable/main arm64 libmaven-compiler-plugin-java all 3.13.0-1 [78.8 kB]
Get: 378 http://deb.debian.org/debian unstable/main arm64 liblog4j1.2-java all 1.2.17-11 [444 kB]
Get: 379 http://deb.debian.org/debian unstable/main arm64 libjni-inchi-java all 0.8+dfsg-8 [33.6 kB]
Get: 380 http://deb.debian.org/debian unstable/main arm64 libnaga-java all 3.0+svn80-5 [43.5 kB]
Get: 381 http://deb.debian.org/debian unstable/main arm64 libjmol-java all 16.2.33+dfsg-1 [10.4 MB]
Get: 382 http://deb.debian.org/debian unstable/main arm64 libjson-simple-java all 2.3.0-1 [63.8 kB]
Get: 383 http://deb.debian.org/debian unstable/main arm64 libjtidy-java all 7+svn20110807-5 [250 kB]
Get: 384 http://deb.debian.org/debian unstable/main arm64 liblightcouch-java all 0.2.0-1 [75.0 kB]
Get: 385 http://deb.debian.org/debian unstable/main arm64 libmongodb-java all 3.6.3-2 [1901 kB]
Get: 386 http://deb.debian.org/debian unstable/main arm64 liblog4j2-java all 2.19.0-2 [2310 kB]
Get: 387 http://deb.debian.org/debian unstable/main arm64 libmaven-antrun-plugin-java all 3.1.0-1 [36.9 kB]
Get: 388 http://deb.debian.org/debian unstable/main arm64 libmaven-common-artifact-filters-java all 3.4.0-1 [47.7 kB]
Get: 389 http://deb.debian.org/debian unstable/main arm64 libmaven-artifact-transfer-java all 0.13.1-2 [158 kB]
Get: 390 http://deb.debian.org/debian unstable/main arm64 libplexus-build-api-java all 0.0.7-4 [10.3 kB]
Get: 391 http://deb.debian.org/debian unstable/main arm64 libmaven-filtering-java all 3.4.0-1 [51.4 kB]
Get: 392 http://deb.debian.org/debian unstable/main arm64 libmaven-assembly-plugin-java all 3.4.2-2 [242 kB]
Get: 393 http://deb.debian.org/debian unstable/main arm64 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB]
Get: 394 http://deb.debian.org/debian unstable/main arm64 libmaven-dependency-analyzer-java all 1.15.1-1 [38.5 kB]
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Get: 397 http://deb.debian.org/debian unstable/main arm64 libmaven-dependency-plugin-java all 3.8.1-1 [191 kB]
Get: 398 http://deb.debian.org/debian unstable/main arm64 libmaven-deploy-plugin-java all 3.1.3-1 [37.1 kB]
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Get: 400 http://deb.debian.org/debian unstable/main arm64 libmaven-install-plugin-java all 3.1.1-1 [28.7 kB]
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Get: 402 http://deb.debian.org/debian unstable/main arm64 libplexus-interactivity-api-java all 1.3-1 [11.6 kB]
Get: 403 http://deb.debian.org/debian unstable/main arm64 libmaven-javadoc-plugin-java all 3.10.1-2 [451 kB]
Get: 404 http://deb.debian.org/debian unstable/main arm64 libplexus-container-default1.5-java all 2.1.1-1 [4476 B]
Get: 405 http://deb.debian.org/debian unstable/main arm64 libplexus-ant-factory-java all 1.0~alpha2.1-4 [11.4 kB]
Get: 406 http://deb.debian.org/debian unstable/main arm64 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B]
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Get: 408 http://deb.debian.org/debian unstable/main arm64 libmaven-jaxb2-plugin-java all 0.15.1-1 [118 kB]
Get: 409 http://deb.debian.org/debian unstable/main arm64 libmaven-reporting-exec-java all 2.0.0-1 [23.9 kB]
Get: 410 http://deb.debian.org/debian unstable/main arm64 libmaven-resources-plugin-java all 3.3.1-1 [27.5 kB]
Get: 411 http://deb.debian.org/debian unstable/main arm64 libmaven-site-plugin-java all 3.21.0-1 [106 kB]
Get: 412 http://deb.debian.org/debian unstable/main arm64 libmsgpack-java all 0.9.6-1 [161 kB]
Get: 413 http://deb.debian.org/debian unstable/main arm64 libmmtf-java all 1.0.11-1 [187 kB]
Get: 414 http://deb.debian.org/debian unstable/main arm64 libsurefire-java all 2.22.3-3 [1284 kB]
Get: 415 http://deb.debian.org/debian unstable/main arm64 libvecmath-java all 1.5.2-7 [97.0 kB]
Get: 416 http://deb.debian.org/debian unstable/main arm64 libwagon-file-java all 3.5.3-1 [8388 B]
Get: 417 http://deb.debian.org/debian unstable/main arm64 libwagon-http-shaded-java all 3.5.3-1 [1341 kB]
Get: 418 http://deb.debian.org/debian unstable/main arm64 libxml2-utils arm64 2.12.7+dfsg+really2.9.14-0.1 [97.4 kB]
Get: 419 http://deb.debian.org/debian unstable/main arm64 libxmlunit-java all 1.6-2 [100 kB]
Get: 420 http://deb.debian.org/debian unstable/main arm64 maven all 3.8.8-1 [19.3 kB]
Get: 421 http://deb.debian.org/debian unstable/main arm64 maven-repo-helper all 1.11 [142 kB]
Get: 422 http://deb.debian.org/debian unstable/main arm64 unzip arm64 6.0-28+b1 [158 kB]
Get: 423 http://deb.debian.org/debian unstable/main arm64 maven-debian-helper all 2.6.5 [108 kB]
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Created symlink '/etc/systemd/system/sysinit.target.wants/systemd-pstore.service' -> '/usr/lib/systemd/system/systemd-pstore.service'.

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Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
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Setting up systemd-sysv (256.7-3) ...
Setting up libxau6:arm64 (1:1.0.11-1) ...
Setting up libxdmcp6:arm64 (1:1.1.2-3+b2) ...
Setting up libplexus-utils2-java (3.4.2-1) ...
Setting up libnpth0t64:arm64 (1.6-3.1+b1) ...
Setting up libkeyutils1:arm64 (1.6.3-4) ...
Setting up libplexus-classworlds-java (2.7.0-1) ...
Setting up libxcb1:arm64 (1.17.0-2+b1) ...
Setting up libopentest4j-reporting-java (0.1.0-M1-2) ...
Setting up libicu72:arm64 (72.1-5+b1) ...
Setting up libplexus-build-api-java (0.0.7-4) ...
Setting up libxcb-xfixes0:arm64 (1.17.0-2+b1) ...
Setting up liblerc4:arm64 (4.0.0+ds-5) ...
Setting up libjsr305-java (0.1~+svn49-11) ...
Setting up bsdextrautils (2.40.2-10) ...
Setting up hicolor-icon-theme (0.18-1) ...
Setting up java-common (0.76) ...
Setting up libdynaloader-functions-perl (0.004-1) ...
Setting up libdatrie1:arm64 (0.2.13-3+b1) ...
Setting up libclass-method-modifiers-perl (2.15-1) ...
Setting up libqdox2-java (2.0.3-1) ...
Setting up libaopalliance-java (20070526-7) ...
Setting up libcommons-cli-java (1.6.0-1) ...
Setting up libjheaps-java (0.14-2) ...
Setting up libio-pty-perl (1:1.20-1+b2) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libcommons-exec-java (1.3-2) ...
Setting up libvecmath-java (1.5.2-7) ...
Setting up libxcb-render0:arm64 (1.17.0-2+b1) ...
Setting up libclone-perl:arm64 (0.47-1+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglvnd0:arm64 (1.7.0-1+b2) ...
Setting up libgoogle-gson-java (2.10.1-1) ...
Setting up libtirpc-common (1.3.4+ds-1.3) ...
Setting up libhtml-tagset-perl (3.24-1) ...
Setting up libxcb-glx0:arm64 (1.17.0-2+b1) ...
Setting up unzip (6.0-28+b1) ...
Setting up libdebhelper-perl (13.20) ...
Setting up libbrotli1:arm64 (1.1.0-2+b5) ...
Setting up libedit2:arm64 (3.1-20240808-1) ...
Setting up liblwp-mediatypes-perl (6.04-2) ...
Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ...
Setting up libmagic1t64:arm64 (1:5.45-3+b1) ...
Setting up libpicocli-java (4.6.2-2) ...
Setting up libasm-java (9.7.1-1) ...
Setting up libjs-jquery-ui-theme-base (1.12.1+dfsg-1.1) ...
Setting up x11-common (1:7.7+23.1) ...
Running in chroot, ignoring request.

Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix.
Setting up libtry-tiny-perl (0.32-1) ...
Setting up libsensors-config (1:3.6.0-10) ...
Setting up libdeflate0:arm64 (1.22-1) ...
Setting up perl-openssl-defaults:arm64 (7+b2) ...
Setting up liblog4j1.2-java (1.2.17-11) ...
Setting up gettext-base (0.22.5-2) ...
Setting up m4 (1.4.19-4) ...
Setting up libel-api-java (3.0.0-3) ...
Setting up xkb-data (2.42-1) ...
Setting up libencode-locale-perl (1.05-3) ...
Setting up libplexus-component-annotations-java (2.1.1-1) ...
Setting up libantlr4-runtime-java (4.9.2-2) ...
Setting up libxcb-shm0:arm64 (1.17.0-2+b1) ...
Setting up libcom-err2:arm64 (1.47.1-1+b1) ...
Setting up file (1:5.45-3+b1) ...
Setting up libjson-simple-java (2.3.0-1) ...
Setting up libunivocity-parsers-java (2.9.1-1) ...
Setting up libjbig0:arm64 (2.1-6.1+b2) ...
Setting up libelf1t64:arm64 (0.192-4) ...
Setting up liboro-java (2.0.8a-14) ...
Setting up libjakarta-activation-java (2.0.0-1) ...
Setting up libsnappy1v5:arm64 (1.2.1-1+b1) ...
Setting up libkrb5support0:arm64 (1.21.3-3) ...
Setting up libexec-maven-plugin-java (3.1.0-2) ...
Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-8) ...
Setting up tzdata (2024b-3) ...

Current default time zone: 'Etc/UTC'
Local time is now:      Tue Nov  5 17:37:52 UTC 2024.
Universal Time is now:  Tue Nov  5 17:37:52 UTC 2024.
Run 'dpkg-reconfigure tzdata' if you wish to change it.

Setting up libxcb-present0:arm64 (1.17.0-2+b1) ...
Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ...
Setting up libgeronimo-interceptor-3.0-spec-java (1.0.1-4) ...
Setting up libcommons-collections3-java (3.2.2-3) ...
Setting up libasound2-data (1.2.12-1) ...
Setting up autotools-dev (20220109.1) ...
Setting up libz3-4:arm64 (4.13.3-1) ...
Setting up libglib2.0-0t64:arm64 (2.82.2-2) ...
Setting up libasound2t64:arm64 (1.2.12-1+b1) ...
Setting up libjpeg62-turbo:arm64 (1:2.1.5-3+b1) ...
Setting up junit (3.8.2-10) ...
Setting up libjaxen-java (1.1.6-5) ...
Setting up libapiguardian-java (1.1.2-1) ...
Setting up libx11-data (2:1.8.10-1) ...
Setting up libepoxy0:arm64 (1.5.10-2) ...
Setting up libnspr4:arm64 (2:4.35-1.1+b1) ...
Setting up gnupg-l10n (2.2.45-2) ...
Setting up libxcb-sync1:arm64 (1.17.0-2+b1) ...
Setting up libjtidy-java (7+svn20110807-5) ...
Setting up libjansi-java (2.4.1-2) ...
Setting up libapache-pom-java (33-2) ...
Setting up libavahi-common-data:arm64 (0.8-13+b3) ...
Setting up libatinject-jsr330-api-java (1.0+ds1-5) ...
Setting up libdbus-1-3:arm64 (1.14.10-6) ...
Setting up libwebsocket-api-java (1.1-2) ...
Setting up libfribidi0:arm64 (1.0.15-1) ...
Setting up libproc2-0:arm64 (2:4.0.4-6) ...
Setting up libplexus-interpolation-java (1.27-1) ...
Setting up fonts-dejavu-mono (2.37-8) ...
Setting up libitext5-java (5.5.13.3-4) ...
Setting up libpng16-16t64:arm64 (1.6.44-2) ...
Setting up libxml-commons-resolver1.1-java (1.2-11) ...
Setting up libxz-java (1.9-1) ...
Setting up libio-html-perl (1.004-3) ...
Setting up autopoint (0.22.5-2) ...
Setting up binfmt-support (2.2.2-7+b1) ...
Running in chroot, ignoring request.

invoke-rc.d: policy-rc.d denied execution of start.
Created symlink '/etc/systemd/system/multi-user.target.wants/binfmt-support.service' -> '/usr/lib/systemd/system/binfmt-support.service'.

Setting up libb-hooks-op-check-perl:arm64 (0.22-3+b2) ...
Setting up fonts-dejavu-core (2.37-8) ...
Setting up libipc-run-perl (20231003.0-2) ...
Setting up libpcsclite1:arm64 (2.3.0-3) ...
Setting up libsensors5:arm64 (1:3.6.0-10+b1) ...
Setting up libmongodb-java (3.6.3-2) ...
Setting up libk5crypto3:arm64 (1.21.3-3) ...
Setting up libactivation-java (1.2.0-2) ...
Setting up libhamcrest-java (2.2-2) ...
Setting up libglapi-mesa:arm64 (24.2.6-1) ...
Setting up libbsh-java (2.0b4-20) ...
Setting up libjsp-api-java (2.3.4-3) ...
Setting up libsasl2-2:arm64 (2.1.28+dfsg1-8) ...
Setting up libvulkan1:arm64 (1.3.296.0-1) ...
Setting up autoconf (2.72-3) ...
Setting up libapfloat-java (1.14.0-1) ...
Setting up libwebp7:arm64 (1.4.0-0.1+b1) ...
Setting up libtimedate-perl (2.3300-2) ...
Setting up libxcb-dri2-0:arm64 (1.17.0-2+b1) ...
Setting up libgif7:arm64 (5.2.2-1+b1) ...
Setting up dwz (0.15-1+b1) ...
Setting up libplexus-interactivity-api-java (1.3-1) ...
Setting up sensible-utils (0.0.24) ...
Setting up libxshmfence1:arm64 (1.3-1+b2) ...
Setting up libjsoup-java (1.15.3-1) ...
Setting up at-spi2-common (2.54.0-1) ...
Setting up libcommons-math-java (2.2-9) ...
Setting up libtiff6:arm64 (4.5.1+git230720-5) ...
Setting up libxcb-randr0:arm64 (1.17.0-2+b1) ...
Setting up dbus-session-bus-common (1.14.10-6) ...
Setting up libuchardet0:arm64 (0.0.8-1+b2) ...
Setting up libassuan9:arm64 (3.0.1-2) ...
Setting up libxml-commons-external-java (1.4.01-6) ...
Setting up procps (2:4.0.4-6) ...
Setting up libxbean-reflect-java (4.5-9) ...
Setting up libservlet-api-java (4.0.1-2) ...
Setting up libplexus-xml-java (3.0.1-2) ...
Setting up librole-tiny-perl (2.002004-1) ...
Setting up libopentest4j-java (1.2.0-4) ...
Setting up libjackson2-core-java (2.14.1-1) ...
Setting up libx11-6:arm64 (2:1.8.10-1) ...
Setting up libthai-data (0.1.29-2) ...
Setting up netbase (6.4) ...
Setting up sgml-base (1.31) ...
Setting up libsub-quote-perl (2.006008-1) ...
Setting up libclass-xsaccessor-perl (1.19-4+b4) ...
Setting up libkrb5-3:arm64 (1.21.3-3) ...
Setting up libwagon-http-shaded-java (3.5.3-1) ...
Setting up libwayland-egl1:arm64 (1.23.0-1+b1) ...
Setting up libhttpcore-java (4.4.16-1) ...
Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Setting up libxerces2-java (2.12.2-1) ...
Setting up libfile-dirlist-perl (0.05-3) ...
Setting up dbus-system-bus-common (1.14.10-6) ...
useradd: Warning: missing or non-executable shell '/usr/sbin/nologin'
Setting up libfile-homedir-perl (1.006-2) ...
Setting up librelaxng-datatype-java (1.0+ds1-3.1) ...
Setting up openssl (3.3.2-2) ...
Setting up libinchi1.07 (1.07.1+dfsg-4) ...
Setting up libdrm-common (2.4.123-1) ...
Setting up libcdi-api-java (1.2-4) ...
Setting up libsnappy-jni (1.1.10.5-2+b1) ...
Setting up libxcomposite1:arm64 (1:0.4.6-1) ...
Setting up readline-common (8.2-5) ...
Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.1) ...
Setting up liburi-perl (5.30-1) ...
Setting up dbus-bin (1.14.10-6) ...
Setting up libargs4j-java (2.33-2) ...
Setting up libfile-touch-perl (0.12-2) ...
Setting up dctrl-tools (2.24-3+b1) ...
Setting up libxkbcommon0:arm64 (1.6.0-1+b2) ...
Setting up libnaga-java (3.0+svn80-5) ...
Setting up libwayland-client0:arm64 (1.23.0-1+b1) ...
Setting up libnet-ssleay-perl:arm64 (1.94-2) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up pinentry-curses (1.2.1-4+b1) ...
Setting up libdom4j-java (2.1.4-1) ...
Setting up libjaxb-api-java (2.3.1-1) ...
Setting up libfile-stripnondeterminism-perl (1.14.0-1) ...
Setting up libxcb-dri3-0:arm64 (1.17.0-2+b1) ...
Setting up libwagon-provider-api-java (3.5.3-1) ...
Setting up libllvm19:arm64 (1:19.1.3-1) ...
Setting up libx11-xcb1:arm64 (2:1.8.10-1) ...
Setting up libhttp-date-perl (6.06-1) ...
Setting up gettext (0.22.5-2) ...
Setting up libjetty9-java (9.4.56-1) ...
Setting up libxdamage1:arm64 (1:1.1.6-1+b2) ...
Setting up libatk1.0-0t64:arm64 (2.54.0-1) ...
Setting up libfile-listing-perl (6.16-1) ...
Setting up libplexus-languages-java (1.1.1-2) ...
Setting up libxrender1:arm64 (1:0.9.10-1.1+b2) ...
Setting up jarwrapper (0.80) ...
Setting up libtool (2.4.7-8) ...
Setting up fontconfig-config (2.15.0-1.1+b1) ...
Setting up libstax-ex-java (1.7.8-3) ...
Setting up libmaven-parent-java (43-2) ...
Setting up libcommons-parent-java (56-1) ...
Setting up libavahi-common3:arm64 (0.8-13+b3) ...
Setting up libcloudproviders0:arm64 (0.3.6-1+b1) ...
Setting up libcommons-logging-java (1.3.0-1) ...
Setting up libxext6:arm64 (2:1.3.4-1+b2) ...
Setting up libnet-http-perl (6.23-1) ...
Setting up libsisu-inject-java (0.3.4-2) ...
Setting up libnss3:arm64 (2:3.105-2) ...
Setting up libciftools-java (6.0.0-1) ...
Setting up dbus-daemon (1.14.10-6) ...
Setting up libdevel-callchecker-perl:arm64 (0.009-1+b1) ...
Setting up libcommons-lang-java (2.6-10) ...
Setting up libldap-2.5-0:arm64 (2.5.18+dfsg-3+b1) ...
Setting up libcolord2:arm64 (1.4.7-1+b2) ...
Setting up libmaven-dependency-analyzer-java (1.15.1-1) ...
Setting up libjackson2-databind-java (2.14.0-1) ...
Setting up libplexus-cipher-java (2.0-1) ...
Setting up libxxf86vm1:arm64 (1:1.1.4-1+b3) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libxmlunit-java (1.6-2) ...
Setting up libdconf1:arm64 (0.40.0-4+b3) ...
Setting up dh-autoreconf (20) ...
Setting up patchutils (0.4.2-1+b1) ...
Setting up libthai0:arm64 (0.1.29-2+b1) ...
Setting up ca-certificates (20240203) ...
Updating certificates in /etc/ssl/certs...
146 added, 0 removed; done.
Setting up libsisu-plexus-java (0.3.4-3) ...
Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ...
Setting up libxfixes3:arm64 (1:6.0.0-2+b2) ...
Setting up dbus (1.14.10-6) ...
Running in chroot, ignoring request.

invoke-rc.d: policy-rc.d denied execution of start.
Setting up shared-mime-info (2.4-5+b1) ...
Setting up libxinerama1:arm64 (2:1.1.4-3+b2) ...
Setting up libstreambuffer-java (1.5.4-1.1) ...
Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ...
Setting up libxrandr2:arm64 (2:1.5.4-1+b1) ...
Setting up libcommons-lang3-java (3.17.0-1) ...
Setting up libreadline8t64:arm64 (8.2-5) ...
Setting up dh-strip-nondeterminism (1.14.0-1) ...
Setting up libwww-robotrules-perl (6.02-1) ...
Setting up librngom-java (2.3.0.1-11) ...
Setting up libdrm2:arm64 (2.4.123-1) ...
Setting up libjni-inchi-jni (0.8+dfsg-8) ...
Setting up libjgraphx-java (2.1.0.7-4) ...
Setting up groff-base (1.23.0-5) ...
Setting up libwayland-cursor0:arm64 (1.23.0-1+b1) ...
Setting up libhtml-parser-perl:arm64 (3.83-1+b1) ...
Setting up gpgconf (2.2.45-2) ...
Setting up libpam-systemd:arm64 (256.7-3) ...
Setting up libcommons-beanutils-java (1.9.4-2) ...
Setting up libplexus-sec-dispatcher-java (2.0-3) ...
Setting up libharfbuzz0b:arm64 (10.0.1-1) ...
Setting up libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-1+b1) ...
Setting up libsnappy-java (1.1.10.5-2) ...
Setting up libfontconfig1:arm64 (2.15.0-1.1+b1) ...
Setting up libxsom-java (2.3.0.1-11) ...
Setting up ca-certificates-java (20240118) ...
No JRE found. Skipping Java certificates setup.
Setting up libwagon-file-java (3.5.3-1) ...
Setting up libxml2-utils (2.12.7+dfsg+really2.9.14-0.1) ...
Setting up libcommons-codec-java (1.17.1-1) ...
Setting up libavahi-client3:arm64 (0.8-13+b3) ...
Setting up libio-socket-ssl-perl (2.089-1) ...
Setting up gpg (2.2.45-2) ...
Setting up libhttp-message-perl (7.00-2) ...
Setting up libdrm-amdgpu1:arm64 (2.4.123-1) ...
Setting up gtk-update-icon-cache (4.16.3+ds-2) ...
Setting up libhttp-negotiate-perl (6.01-2) ...
Setting up velocity (1.7-7) ...
Setting up fontconfig (2.15.0-1.1+b1) ...
Regenerating fonts cache... done.
Setting up gpg-agent (2.2.45-2) ...
Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent-browser.socket' -> '/usr/lib/systemd/user/gpg-agent-browser.socket'.

Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent-extra.socket' -> '/usr/lib/systemd/user/gpg-agent-extra.socket'.

Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent-ssh.socket' -> '/usr/lib/systemd/user/gpg-agent-ssh.socket'.

Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent.socket' -> '/usr/lib/systemd/user/gpg-agent.socket'.

Setting up openjdk-21-jre-headless:arm64 (21.0.5+11-1) ...
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
Setting up libxi6:arm64 (2:1.8.2-1) ...
Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ...
Setting up libhttp-cookies-perl (6.11-1) ...
Setting up libcommons-io-java (2.17.0-1) ...
Setting up libdrm-radeon1:arm64 (2.4.123-1) ...
Setting up libcommons-digester-java (1.8.1-7) ...
Setting up libxtst6:arm64 (2:1.2.3-1.1+b2) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libhtml-tree-perl (5.07-3) ...
Setting up libxcursor1:arm64 (1:1.2.2-1+b1) ...
Setting up libparams-classify-perl:arm64 (0.015-2+b4) ...
Setting up gpgsm (2.2.45-2) ...
Setting up libpango-1.0-0:arm64 (1.54.0+ds-3) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Created symlink '/etc/systemd/system/timers.target.wants/man-db.timer' -> '/usr/lib/systemd/system/man-db.timer'.

Setting up libcairo2:arm64 (1.18.2-2) ...
Setting up dirmngr (2.2.45-2) ...
Created symlink '/etc/systemd/user/sockets.target.wants/dirmngr.socket' -> '/usr/lib/systemd/user/dirmngr.socket'.

Setting up libmaven-filtering-java (3.4.0-1) ...
Setting up openjdk-21-doc (21.0.5+11-1) ...
Setting up dbus-user-session (1.14.10-6) ...
Setting up libmaven-resolver-java (1.6.3-1) ...
Setting up adwaita-icon-theme (47.0-2) ...
update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode
Setting up libmodule-runtime-perl (0.016-2) ...
Setting up libatspi2.0-0t64:arm64 (2.54.0-1) ...
Setting up libhttpclient-java (4.5.14-1) ...
Setting up libmaven-common-artifact-filters-java (3.4.0-1) ...
Setting up libmaven-dependency-tree-java (3.3.0-1) ...
Setting up libnsl2:arm64 (1.3.0-3+b3) ...
Setting up gnupg (2.2.45-2) ...
Setting up liblightcouch-java (0.2.0-1) ...
Setting up libwagon-http-java (3.5.3-1) ...
Setting up libcairo-gobject2:arm64 (1.18.2-2) ...
Setting up libmaven-shared-utils-java (3.4.2-1) ...
Setting up libfastinfoset-java (1.2.12-3) ...
Setting up libpangoft2-1.0-0:arm64 (1.54.0+ds-3) ...
Setting up libmaven-resources-plugin-java (3.3.1-1) ...
Setting up libcups2t64:arm64 (2.4.10-2) ...
Setting up libpangocairo-1.0-0:arm64 (1.54.0+ds-3) ...
Setting up libatk-bridge2.0-0t64:arm64 (2.54.0-1) ...
Setting up mesa-libgallium:arm64 (24.2.6-1) ...
Setting up libplexus-io-java (3.3.1-2) ...
Setting up libpython3.12-stdlib:arm64 (3.12.7-2) ...
Setting up libmaven-install-plugin-java (3.1.1-1) ...
Setting up libcommons-compress-java (1.27.1-2) ...
Setting up libcommons-validator-java (1:1.7-1) ...
Setting up libgbm1:arm64 (24.2.6-1) ...
Setting up libimport-into-perl (1.002005-2) ...
Setting up libmoo-perl (2.005005-1) ...
Setting up liblog4j2-java (2.19.0-2) ...
Setting up python3.12 (3.12.7-2) ...
Setting up libgl1-mesa-dri:arm64 (24.2.6-1) ...
Setting up libmaven-invoker-java (3.3.0-1) ...
Setting up debhelper (13.20) ...
Setting up dconf-service (0.40.0-4+b3) ...
Setting up default-jdk-doc (2:1.21-76) ...
Setting up libmaven-deploy-plugin-java (3.1.3-1) ...
Setting up libmaven-clean-plugin-java (3.2.0-2) ...
Setting up libplexus-archiver-java (4.6.1-1) ...
Setting up libpython3-stdlib:arm64 (3.12.6-1) ...
Setting up libglx-mesa0:arm64 (24.2.6-1) ...
Setting up libglx0:arm64 (1.7.0-1+b2) ...
Setting up dconf-gsettings-backend:arm64 (0.40.0-4+b3) ...
Setting up libmaven-archiver-java (3.6.2-1) ...
Setting up python3 (3.12.6-1) ...
Setting up libgl1:arm64 (1.7.0-1+b2) ...
Setting up libgtk-3-common (3.24.43-4) ...
Setting up libgtk-3-0t64:arm64 (3.24.43-4) ...
Setting up liberror-prone-java (2.18.0-1) ...
Setting up libwww-perl (6.77-1) ...
Setting up devscripts (2.24.2) ...
Setting up libguava-java (32.0.1-1) ...
Setting up javahelper (0.80) ...
Setting up libplexus-container-default-java (2.1.1-1) ...
Setting up liblwp-protocol-https-perl (6.14-1) ...
Setting up libguice-java (4.2.3-2) ...
Setting up libplexus-i18n-java (1.0-beta-10-6) ...
Setting up libplexus-container-default1.5-java (2.1.1-1) ...
Setting up libplexus-velocity-java (1.2-4) ...
Setting up libmaven3-core-java (3.8.8-1) ...
Setting up libmaven-shared-incremental-java (1.1-6) ...
Setting up libmaven-shared-io-java (3.0.0-4) ...
Setting up libplexus-bsh-factory-java (1.0~alpha7-5) ...
Setting up libplexus-compiler-java (2.13.0-1) ...
Setting up libmaven-compiler-plugin-java (3.13.0-1) ...
Setting up libjni-inchi-java (0.8+dfsg-8) ...
Setting up libmaven-artifact-transfer-java (0.13.1-2) ...
Setting up libmaven-file-management-java (3.0.0-1) ...
Setting up libjmol-java (16.2.33+dfsg-1) ...
Setting up libmaven-enforcer-plugin-java (3.5.0-1) ...
Setting up libmaven-jar-plugin-java (3.3.0-2) ...
Setting up libmaven-assembly-plugin-java (3.4.2-2) ...
Setting up libcommons-text-java (1.12.0-1) ...
Setting up libmsgpack-java (0.9.6-1) ...
Setting up libmmtf-java (1.0.11-1) ...
Setting up libjgrapht-java (1.5.2-1) ...
Setting up libdoxia-core-java (2.0.0-1) ...
Setting up libdoxia-java (2.0.0-1) ...
Setting up libmaven-reporting-api-java (4.0.0-1) ...
Setting up libmaven-reporting-exec-java (2.0.0-1) ...
Processing triggers for libc-bin (2.40-3) ...
Processing triggers for systemd (256.7-3) ...
Processing triggers for ca-certificates-java (20240118) ...
Adding debian:ACCVRAIZ1.pem
Adding debian:AC_RAIZ_FNMT-RCM.pem
Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
Adding debian:ANF_Secure_Server_Root_CA.pem
Adding debian:Actalis_Authentication_Root_CA.pem
Adding debian:AffirmTrust_Commercial.pem
Adding debian:AffirmTrust_Networking.pem
Adding debian:AffirmTrust_Premium.pem
Adding debian:AffirmTrust_Premium_ECC.pem
Adding debian:Amazon_Root_CA_1.pem
Adding debian:Amazon_Root_CA_2.pem
Adding debian:Amazon_Root_CA_3.pem
Adding debian:Amazon_Root_CA_4.pem
Adding debian:Atos_TrustedRoot_2011.pem
Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem
Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
Adding debian:BJCA_Global_Root_CA1.pem
Adding debian:BJCA_Global_Root_CA2.pem
Adding debian:Baltimore_CyberTrust_Root.pem
Adding debian:Buypass_Class_2_Root_CA.pem
Adding debian:Buypass_Class_3_Root_CA.pem
Adding debian:CA_Disig_Root_R2.pem
Adding debian:CFCA_EV_ROOT.pem
Adding debian:COMODO_Certification_Authority.pem
Adding debian:COMODO_ECC_Certification_Authority.pem
Adding debian:COMODO_RSA_Certification_Authority.pem
Adding debian:Certainly_Root_E1.pem
Adding debian:Certainly_Root_R1.pem
Adding debian:Certigna.pem
Adding debian:Certigna_Root_CA.pem
Adding debian:Certum_EC-384_CA.pem
Adding debian:Certum_Trusted_Network_CA.pem
Adding debian:Certum_Trusted_Network_CA_2.pem
Adding debian:Certum_Trusted_Root_CA.pem
Adding debian:CommScope_Public_Trust_ECC_Root-01.pem
Adding debian:CommScope_Public_Trust_ECC_Root-02.pem
Adding debian:CommScope_Public_Trust_RSA_Root-01.pem
Adding debian:CommScope_Public_Trust_RSA_Root-02.pem
Adding debian:Comodo_AAA_Services_root.pem
Adding debian:D-TRUST_BR_Root_CA_1_2020.pem
Adding debian:D-TRUST_EV_Root_CA_1_2020.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
Adding debian:DigiCert_Assured_ID_Root_CA.pem
Adding debian:DigiCert_Assured_ID_Root_G2.pem
Adding debian:DigiCert_Assured_ID_Root_G3.pem
Adding debian:DigiCert_Global_Root_CA.pem
Adding debian:DigiCert_Global_Root_G2.pem
Adding debian:DigiCert_Global_Root_G3.pem
Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem
Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem
Adding debian:DigiCert_Trusted_Root_G4.pem
Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
Adding debian:Entrust_Root_Certification_Authority.pem
Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
Adding debian:Entrust_Root_Certification_Authority_-_G4.pem
Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
Adding debian:GLOBALTRUST_2020.pem
Adding debian:GTS_Root_R1.pem
Adding debian:GTS_Root_R2.pem
Adding debian:GTS_Root_R3.pem
Adding debian:GTS_Root_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
Adding debian:GlobalSign_Root_CA.pem
Adding debian:GlobalSign_Root_CA_-_R3.pem
Adding debian:GlobalSign_Root_CA_-_R6.pem
Adding debian:GlobalSign_Root_E46.pem
Adding debian:GlobalSign_Root_R46.pem
Adding debian:Go_Daddy_Class_2_CA.pem
Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem
Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
Adding debian:HiPKI_Root_CA_-_G1.pem
Adding debian:Hongkong_Post_Root_CA_3.pem
Adding debian:ISRG_Root_X1.pem
Adding debian:ISRG_Root_X2.pem
Adding debian:IdenTrust_Commercial_Root_CA_1.pem
Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
Adding debian:Izenpe.com.pem
Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
Adding debian:NAVER_Global_Root_Certification_Authority.pem
Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
Adding debian:QuoVadis_Root_CA_1_G3.pem
Adding debian:QuoVadis_Root_CA_2.pem
Adding debian:QuoVadis_Root_CA_2_G3.pem
Adding debian:QuoVadis_Root_CA_3.pem
Adding debian:QuoVadis_Root_CA_3_G3.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem
Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem
Adding debian:SZAFIR_ROOT_CA2.pem
Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem
Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem
Adding debian:SecureSign_RootCA11.pem
Adding debian:SecureTrust_CA.pem
Adding debian:Secure_Global_CA.pem
Adding debian:Security_Communication_ECC_RootCA1.pem
Adding debian:Security_Communication_RootCA2.pem
Adding debian:Security_Communication_RootCA3.pem
Adding debian:Security_Communication_Root_CA.pem
Adding debian:Starfield_Class_2_CA.pem
Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
Adding debian:SwissSign_Gold_CA_-_G2.pem
Adding debian:SwissSign_Silver_CA_-_G2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
Adding debian:TWCA_Global_Root_CA.pem
Adding debian:TWCA_Root_Certification_Authority.pem
Adding debian:TeliaSonera_Root_CA_v1.pem
Adding debian:Telia_Root_CA_v2.pem
Adding debian:TrustAsia_Global_Root_CA_G3.pem
Adding debian:TrustAsia_Global_Root_CA_G4.pem
Adding debian:Trustwave_Global_Certification_Authority.pem
Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
Adding debian:TunTrust_Root_CA.pem
Adding debian:UCA_Extended_Validation_Root.pem
Adding debian:UCA_Global_G2_Root.pem
Adding debian:USERTrust_ECC_Certification_Authority.pem
Adding debian:USERTrust_RSA_Certification_Authority.pem
Adding debian:XRamp_Global_CA_Root.pem
Adding debian:certSIGN_ROOT_CA.pem
Adding debian:certSIGN_Root_CA_G2.pem
Adding debian:e-Szigno_Root_CA_2017.pem
Adding debian:ePKI_Root_Certification_Authority.pem
Adding debian:emSign_ECC_Root_CA_-_C3.pem
Adding debian:emSign_ECC_Root_CA_-_G3.pem
Adding debian:emSign_Root_CA_-_C1.pem
Adding debian:emSign_Root_CA_-_G1.pem
Adding debian:vTrus_ECC_Root_CA.pem
Adding debian:vTrus_Root_CA.pem
done.
Setting up maven (3.8.8-1) ...
update-alternatives: using /usr/share/maven/bin/mvn to provide /usr/bin/mvn (mvn) in auto mode
Setting up openjdk-21-jre:arm64 (21.0.5+11-1) ...
Setting up ant (1.10.15-1) ...
Setting up junit4 (4.13.2-5) ...
Setting up openjdk-21-jdk-headless:arm64 (21.0.5+11-1) ...
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jar to provide /usr/bin/jar (jar) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javac to provide /usr/bin/javac (javac) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javap to provide /usr/bin/javap (javap) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jps to provide /usr/bin/jps (jps) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jwebserver to provide /usr/bin/jwebserver (jwebserver) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode
Setting up default-jre-headless (2:1.21-76) ...
Setting up maven-repo-helper (1.11) ...
Setting up default-jre (2:1.21-76) ...
Setting up libmaven-antrun-plugin-java (3.1.0-1) ...
Setting up libplexus-ant-factory-java (1.0~alpha2.1-4) ...
Setting up ant-optional (1.10.15-1) ...
Setting up openjdk-21-jdk:arm64 (21.0.5+11-1) ...
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode
Setting up default-jdk-headless (2:1.21-76) ...
Setting up junit5 (5.10.3-1) ...
Setting up libmaven-plugin-tools-java (3.10.2-1) ...
Setting up libistack-commons-java (3.0.6-5) ...
Setting up default-jdk (2:1.21-76) ...
Setting up libsurefire-java (2.22.3-3) ...
Setting up libcodemodel-java (2.6+jaxb2.3.0.1-11) ...
Setting up libtxw2-java (2.3.0.1-11) ...
Setting up libjaxb-java (2.3.0.1-11) ...
Setting up libmaven-jaxb2-plugin-java (0.15.1-1) ...
Processing triggers for sgml-base (1.31) ...
Setting up libvelocity-tools-java (2.0-9) ...
Setting up libdoxia-sitetools-java (2.0.0-1) ...
Setting up libmaven-site-plugin-java (3.21.0-1) ...
Setting up maven-debian-helper (2.6.5) ...
Setting up libmaven-javadoc-plugin-java (3.10.1-2) ...
Setting up libmaven-reporting-impl-java (4.0.0-1) ...
Setting up libmaven-dependency-plugin-java (3.8.1-1) ...
Processing triggers for ca-certificates (20240203) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Processing triggers for ca-certificates-java (20240118) ...
done.
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
 -> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/2957838/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for unstable
I: user script /srv/workspace/pbuilder/2957838/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/biojava6-live-6.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S  > ../biojava6-live_6.1.0+dfsg-5_source.changes
dpkg-buildpackage: info: source package biojava6-live
dpkg-buildpackage: info: source version 6.1.0+dfsg-5
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Pierre Gruet <pgt@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
 debian/rules clean
dpkg: warning: --compare-versions used with obsolete relation operator '>'
dh clean  --with javahelper
   dh_auto_clean
	bash -c "for dir in \$(find . -name target -type d); do if [ -f \$(echo \$dir | sed -e s/target\$/pom.xml/) ]; then rm -Rf \$dir; fi done"
	mh_unpatchpoms -plibbiojava6-java
   jh_clean
Duplicate specification "unlink|u" for option "u"
   debian/rules override_dh_clean
make[1]: Entering directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg'
dpkg: warning: --compare-versions used with obsolete relation operator '>'
dh_clean
rm -rf target
rm -rf biojava-*/target
find . -type f -name \*.java.json-simple \
  -exec sh -c 'file={} && mv $file ${file%.json-simple}' \; -print
rm -rf biojava-forester
rm -rf biojava-jcolorbrewer
make[1]: Leaving directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg'
 debian/rules binary
dpkg: warning: --compare-versions used with obsolete relation operator '>'
dh binary  --with javahelper
   dh_update_autotools_config
   dh_autoreconf
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg'
dpkg: warning: --compare-versions used with obsolete relation operator '>'
# Creating the directories for forester and jcolorbrewer, with symlinks.
mkdir -p biojava-forester/src/main/java/
cp -a forester/org biojava-forester/src/main/java/
mkdir -p biojava-jcolorbrewer/src/main/java/
cp -a jcolorbrewer/org biojava-jcolorbrewer/src/main/java/
# Putting the pom.xml files of forester and jcolorbrewer into their dirs.
sed 's/\(VERSION_PACKAGE\)/\16.1.0+dfsg/; s/VERSION_PACKAGE\(.*\)+dfsg[0-9]*/\1/' debian/poms/pomForester.xml > biojava-forester/pom.xml
sed 's/\(VERSION_PACKAGE\)/\16.1.0+dfsg/; s/VERSION_PACKAGE\(.*\)+dfsg[0-9]*/\1/' debian/poms/pomJcolorbrewer.xml > biojava-jcolorbrewer/pom.xml
dh_auto_configure
	mh_patchpoms -plibbiojava6-java --debian-build --keep-pom-version --maven-repo=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven-repo
make[1]: Leaving directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg'
   jh_linkjars
   debian/rules override_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg'
dpkg: warning: --compare-versions used with obsolete relation operator '>'
# Insert the correct JSON_SIMPLE_PACKAGE in the code.
find . -type f -name \*.java -exec grep -q 'import @JSON_SIMPLE_PACKAGE@' {} \; \
  -exec sed -i.json-simple \
	    -e 's,@JSON_SIMPLE_PACKAGE@,org.json.simple,' \
	    {} \; -print
./biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
dh_auto_build
	/usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/biojava6-live-6.1.0\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf -Dproperties.file.manual=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven.properties org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven-repo --batch-mode package javadoc:jar javadoc:aggregate -DskipTests -Dnotimestamp=true -Dlocale=en_US
OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release.
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.biojava:biojava-structure-gui:jar:6.1.0
[WARNING] 'dependencies.dependency.systemPath' for net.sourceforge.jmol:jmol:jar should use a variable instead of a hard-coded path /usr/share/java/Jmol.jar @ line 48, column 16
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] biojava                                                            [pom]
[INFO] biojava-core                                                       [jar]
[INFO] biojava-forester                                                   [jar]
[INFO] biojava-alignment                                                  [jar]
[INFO] biojava-structure                                                  [jar]
[INFO] biojava-jcolorbrewer                                               [jar]
[INFO] biojava-structure-gui                                              [jar]
[INFO] biojava-genome                                                     [jar]
[INFO] biojava-modfinder                                                  [jar]
[INFO] biojava-ws                                                         [jar]
[INFO] biojava-protein-disorder                                           [jar]
[INFO] biojava-aa-prop                                                    [jar]
[INFO] biojava-survival                                                   [jar]
[INFO] biojava-ontology                                                   [jar]
[INFO] biojava-protein-comparison-tool                                    [jar]
[WARNING] The artifact org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 has been relocated to org.apache.maven.plugins:maven-antrun-plugin:jar:3.1.0
[WARNING] The artifact org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 has been relocated to org.apache.maven.plugins:maven-assembly-plugin:jar:3.4.2
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before.
[WARNING] The POM for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before.
[WARNING] The POM for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before.
[INFO] 
[INFO] ------------------------< org.biojava:biojava >-------------------------
[INFO] Building biojava 6.1.0                                            [1/15]
[INFO]   from pom.xml
[INFO] --------------------------------[ pom ]---------------------------------
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before.
[WARNING] The POM for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before.
[INFO] 
[INFO] --- maven-javadoc-plugin:3.10.1:jar (default-cli) @ biojava ---
[INFO] Not executing Javadoc as the project is not a Java classpath-capable package
[INFO] 
[INFO] ----------------------< org.biojava:biojava-core >----------------------
[INFO] Building biojava-core 6.1.0                                       [2/15]
[INFO]   from biojava-core/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before.
[WARNING] The POM for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-core ---
[INFO] Copying 24 resources from src/main/resources to target/classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-core ---
[INFO] Recompiling the module because of changed source code.
[INFO] Compiling 188 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java:[202,39] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java:[139,53] Double(java.lang.String) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java:[155,75] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java:[154,80] Double(java.lang.String) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java:[153,73] Double(java.lang.String) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java:[152,71] Double(java.lang.String) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java:[151,70] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java:[150,72] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java:[149,72] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java:[148,74] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java:[147,69] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java:[146,73] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java:[123,57] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java:[120,61] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java:[142,60] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java:[138,60] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java:[153,65] Double(java.lang.String) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java:[172,81] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java:[171,77] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java:[170,81] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java:[169,81] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java:[168,81] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java:[167,83] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java:[166,78] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java:[165,80] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java:[164,80] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java:[163,82] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java:[161,78] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java:[160,81] Double(java.lang.String) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java:[159,76] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java: Recompile with -Xlint:deprecation for details.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java: Some input files use unchecked or unsafe operations.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java: Recompile with -Xlint:unchecked for details.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biojava-core ---
[INFO] Copying 48 resources from src/test/resources to target/test-classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biojava-core ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 60 source files with javac [debug target 1.8] to target/test-classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java: Recompile with -Xlint:deprecation for details.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/test/java/org/biojava/nbio/core/search/io/HspTest.java: Some input files use unchecked or unsafe operations.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/test/java/org/biojava/nbio/core/search/io/HspTest.java: Recompile with -Xlint:unchecked for details.
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-core ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-core ---
[INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/biojava-core-6.1.0.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.10.1:jar (default-cli) @ biojava-core ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java:74: warning: reference not found: #getAllSubLocations()
[WARNING] * {@link #getAllSubLocations()}.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:41: warning: reference not found: Aligner
[WARNING] * Defines an alignment step in order to pass alignment information from an {@link Aligner} to a constructor.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:68: warning: invalid input: '<'
[WARNING] * @throws IndexOutOfBoundsException if sequenceIndex < 1 or sequenceIndex >
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:133: warning: invalid input: '<'
[WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:157: warning: invalid input: '<'
[WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:41: warning: reference not found: Aligner
[WARNING] * Defines an alignment step in order to pass alignment information from an {@link Aligner} to a constructor.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java:67: warning: invalid input: '&'
[WARNING] * Class is immutable & so this is unsupported
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java:75: warning: invalid input: '&'
[WARNING] * Class is immutable & so this is unsupported
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java:67: warning: invalid input: '&'
[WARNING] * Class is immutable & so this is unsupported
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java:75: warning: invalid input: '&'
[WARNING] * Class is immutable & so this is unsupported
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.java:524: warning: invalid input: '<'
[WARNING] * @exception  IllegalArgumentException  If readAheadLimit is < 0
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java:35: warning: invalid usage of tag {@link http://www.sequenceontology.org/gff3.shtml
[WARNING] * to a gff3 file. {@link http://www.sequenceontology.org/gff3.shtml}
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java:93: warning: invalid usage of tag {@link http://www.sequenceontology.org/gff3.shtml
[WARNING] * {@link http://www.sequenceontology.org/gff3.shtml}
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java:94: warning: invalid usage of tag {@link http://biowiki.org/~yam/bioe131/GFF.ppt
[WARNING] * {@link http://biowiki.org/~yam/bioe131/GFF.ppt}
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java:127: warning: Tag @author cannot be used in method documentation.  It can only be used in the following types of documentation: overview, module, package, class/interface.
[WARNING] * @author Amr ALHOSSARY
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriterHelper.java:99: warning: @param argument "dnaSequences" is not a parameter name.
[WARNING] * @param dnaSequences
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureInterface.java:72: warning: @return tag cannot be used in method with void return type.
[WARNING] public void setDescription(String description);
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java:291: warning: invalid input: '&'
[WARNING] * Recursively delete a folder & contents
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java:266: warning: invalid input: '&'
[WARNING] * Recursively delete a folder & contents
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java:171: warning: Tag @author cannot be used in method documentation.  It can only be used in the following types of documentation: overview, module, package, class/interface.
[WARNING] * @author Peter Rose
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java:220: warning: Tag @author cannot be used in method documentation.  It can only be used in the following types of documentation: overview, module, package, class/interface.
[WARNING] * @author BalusC,
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java:256: warning: Tag @author cannot be used in method documentation.  It can only be used in the following types of documentation: overview, module, package, class/interface.
[WARNING] * @author Jacek Grzebyta
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java:266: warning: invalid input: '&'
[WARNING] * Recursively delete a folder & contents
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java:291: warning: invalid input: '&'
[WARNING] * Recursively delete a folder & contents
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.java:59: warning: @param argument "fastaFile" is not a parameter name.
[WARNING] * @param fastaFile
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.java:58: warning: @param argument "fastaFile" is not a parameter name.
[WARNING] * @param fastaFile
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.java:59: warning: @param argument "fastaFile" is not a parameter name.
[WARNING] * @param fastaFile
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/FlatFileCache.java:126: warning: invalid input: '{@'
[WARNING] * If the cache is {@}, returns -1
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.java:36: warning: Tag @param cannot be used in field documentation.  It can only be used in the following types of documentation: class/interface, constructor, method.
[WARNING] * @param sequence
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.java:37: warning: Tag @return cannot be used in field documentation.  It can only be used in the following types of documentation: method.
[WARNING] * @return
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java:45: warning: invalid input: '<'
[WARNING] * @author Karl Nicholas <github:karlnicholas>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java:46: warning: invalid input: '<'
[WARNING] * @author Jacek Grzebyta <github:jgrzebyta>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java:142: warning: Tag @author cannot be used in method documentation.  It can only be used in the following types of documentation: overview, module, package, class/interface.
[WARNING] * @author Amr ALHOSSARY
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriter.java:85: warning: @param argument "lineSeparator" is not a parameter name.
[WARNING] * @param lineSeparator
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:185: warning: @inheritDoc used but setAccession(String) does not override or implement any method.
[WARNING] public void setAccession(String accession) throws ParserException {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:219: warning: @inheritDoc used but setComment(String) does not override or implement any method.
[WARNING] public void setComment(String comment) throws ParserException {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:193: warning: @inheritDoc used but setDescription(String) does not override or implement any method.
[WARNING] public void setDescription(String description) throws ParserException {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:201: warning: @inheritDoc used but setIdentifier(String) does not override or implement any method.
[WARNING] public void setIdentifier(String identifier) throws ParserException {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:210: warning: @inheritDoc used but setName(String) does not override or implement any method.
[WARNING] public void setName(String name) throws ParserException {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:168: warning: @inheritDoc used but setVersion(int) does not override or implement any method.
[WARNING] public void setVersion(int version) throws ParserException {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:168: warning: @inheritDoc used but setVersion(int) does not override or implement any method.
[WARNING] public void setVersion(int version) throws ParserException {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:185: warning: @inheritDoc used but setAccession(String) does not override or implement any method.
[WARNING] public void setAccession(String accession) throws ParserException {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:193: warning: @inheritDoc used but setDescription(String) does not override or implement any method.
[WARNING] public void setDescription(String description) throws ParserException {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:201: warning: @inheritDoc used but setIdentifier(String) does not override or implement any method.
[WARNING] public void setIdentifier(String identifier) throws ParserException {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:210: warning: @inheritDoc used but setName(String) does not override or implement any method.
[WARNING] public void setName(String name) throws ParserException {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:219: warning: @inheritDoc used but setComment(String) does not override or implement any method.
[WARNING] public void setComment(String comment) throws ParserException {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java:181: warning: reference not found: IOUtils#processReader(String)
[WARNING] * {@link IOUtils#processReader(String)}. Each time a line is encountered
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java:160: warning: cannot find exception type by name
[WARNING] * @throws IOExceptio n
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java:181: warning: reference not found: IOUtils#processReader(String)
[WARNING] * {@link IOUtils#processReader(String)}. Each time a line is encountered
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java:264: warning: @param argument "nucleotides" is not a parameter name.
[WARNING] * @param nucleotides The nucleotide set to use when building BioJava
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java:69: warning: invalid input: '<'
[WARNING] * Allows creation of the store from List<Sequence<C>>. CompoundSet
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java:220: warning: invalid input: '&'
[WARNING] * attempting to skip onto the next sequence as & when it is asked to
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java:69: warning: invalid input: '<'
[WARNING] * Allows creation of the store from List<Sequence<C>>. CompoundSet
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java:220: warning: invalid input: '&'
[WARNING] * attempting to skip onto the next sequence as & when it is asked to
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/LightweightProfile.java:55: warning: invalid input: '<'
[WARNING] * @throws IndexOutOfBoundsException if listIndex < 1 or listIndex > number of sequences
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/LightweightProfile.java:71: warning: invalid input: '<'
[WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java:74: warning: reference not found: #getAllSubLocations()
[WARNING] * {@link #getAllSubLocations()}.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java:169: warning: @param argument "location" is not a parameter name.
[WARNING] * @param location The location which currently expresses the outer
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java:310: warning: invalid input: '&'
[WARNING] * Assumes that the first element is the start & clones it
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java:116: warning: @param argument "location" is not a parameter name.
[WARNING] * @param location The location which currently expresses the outer
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java:310: warning: invalid input: '&'
[WARNING] * Assumes that the first element is the start & clones it
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:61: warning: invalid input: '<'
[WARNING] * @throws IndexOutOfBoundsException if listIndex < 1 or listIndex > number of sequences
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:104: warning: invalid input: '<'
[WARNING] * @throws IndexOutOfBoundsException if listIndex < 1, listIndex > number of sequences, alignmentIndex < 1, or
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:104: warning: invalid input: '<'
[WARNING] * @throws IndexOutOfBoundsException if listIndex < 1, listIndex > number of sequences, alignmentIndex < 1, or
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:116: warning: invalid input: '<'
[WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:125: warning: invalid input: '<'
[WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:135: warning: invalid input: '<'
[WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:144: warning: invalid input: '<'
[WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:160: warning: invalid input: '<'
[WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:170: warning: invalid input: '<'
[WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:180: warning: invalid input: '<'
[WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:239: warning: invalid input: '<'
[WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:247: warning: reference not found: SequenceBackingStore
[WARNING] * elements in a new instance of {@link SequenceBackingStore} which behaves
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:165: warning: reference not found: Compound#toString()
[WARNING] * filled with the results of {@link Compound#toString()}. Does not
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:153: warning: @param argument "writer" is not a parameter name.
[WARNING] * @param writer The writer to send data to
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:165: warning: reference not found: Compound#toString()
[WARNING] * filled with the results of {@link Compound#toString()}. Does not
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:247: warning: reference not found: SequenceBackingStore
[WARNING] * elements in a new instance of {@link SequenceBackingStore} which behaves
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:288: warning: invalid input: '&'
[WARNING] * ATG, TGT & GTA
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:346: warning: invalid input: '&'
[WARNING] * length & compound sets used. The code will also bail out the moment
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:362: warning: invalid input: '&'
[WARNING] * length & compound sets used. The code will also bail out the moment
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:44: warning: invalid input: '<'
[WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:53: warning: invalid input: '<'
[WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:62: warning: invalid input: '<'
[WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:71: warning: invalid input: '<'
[WARNING] * @throws IndexOutOfBoundsException if targetIndex < 1 or targetIndex > {@link #getTarget()}.getLength()
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:80: warning: invalid input: '<'
[WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:89: warning: invalid input: '<'
[WARNING] * @throws IndexOutOfBoundsException if queryIndex < 1 or queryIndex > {@link #getQuery()}.getLength()
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.java:35: warning: @param argument "dataInput" is not a parameter name.
[WARNING] * @param dataInput
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java:162: warning: cannot find exception type by name
[WARNING] * @throws IllegalArgument if aligned sequences differ in length or
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java:171: warning: reference not found: SequenceMixin#countCompounds(org.biojava.nbio.core.sequence.template.Sequence, C[])
[WARNING] * Delegates to {@link SequenceMixin#countCompounds(org.biojava.nbio.core.sequence.template.Sequence, C[]) }
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java:171: warning: reference not found: SequenceMixin#countCompounds(org.biojava.nbio.core.sequence.template.Sequence, C[])
[WARNING] * Delegates to {@link SequenceMixin#countCompounds(org.biojava.nbio.core.sequence.template.Sequence, C[]) }
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/StringManipulationHelper.java:81: warning: Tag @author cannot be used in method documentation.  It can only be used in the following types of documentation: overview, module, package, class/interface.
[WARNING] * @author andreas
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/StringManipulationHelper.java:207: warning: invalid input: '<'
[WARNING] * @throws IllegalArgumentException if n <= 0
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/StringManipulationHelper.java:219: warning: invalid input: '<'
[WARNING] * @throws IllegalArgumentException if n <= 0
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SubstitutionMatrix.java:106: warning: invalid input: '<'
[WARNING] * @throws IllegalArgumentException if scale < 1
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:81: warning: invalid input: '&'
[WARNING] * Returns Blosum 100 matrix by Henikoff & Henikoff
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:89: warning: invalid input: '&'
[WARNING] * Returns Blosum 30 matrix by Henikoff & Henikoff
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:97: warning: invalid input: '&'
[WARNING] * Returns Blosum 35 matrix by Henikoff & Henikoff
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:105: warning: invalid input: '&'
[WARNING] * Returns Blosum 40 matrix by Henikoff & Henikoff
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:113: warning: invalid input: '&'
[WARNING] * Returns Blosum 45 matrix by Henikoff & Henikoff
[WARNING] ^
[WARNING] 100 warnings
[INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/biojava-core-6.1.0-javadoc.jar
[INFO] 
[INFO] --------------------< org.biojava:biojava-forester >--------------------
[INFO] Building biojava-forester 6.1.0                                   [3/15]
[INFO]   from biojava-forester/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before.
[WARNING] The POM for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-forester ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-forester ---
[INFO] Recompiling the module because of changed source code.
[INFO] Compiling 359 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/TreePanel.java:[84,19] javax.swing.JApplet in javax.swing has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/MainFrame.java:[42,19] javax.swing.JApplet in javax.swing has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/AptxUtil.java:[60,19] javax.swing.JApplet in javax.swing has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/MainFrameApplet.java:[42,19] javax.swing.JApplet in javax.swing has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/ArchaeopteryxA.java:[35,19] javax.swing.JApplet in javax.swing has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/MainPanelApplets.java:[34,19] javax.swing.JApplet in javax.swing has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/ArchaeopteryxE.java:[19,19] javax.swing.JApplet in javax.swing has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/tools/Blast.java:[36,19] javax.swing.JApplet in javax.swing has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/io/parsers/phyloxml/XmlElement.java:[130,19] Boolean(java.lang.String) in java.lang.Boolean has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/phylogeny/data/DomainArchitecture.java:[69,28] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/phylogeny/data/DomainArchitecture.java:[75,22] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/phylogeny/data/DomainArchitecture.java:[76,34] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/phylogeny/data/DomainArchitecture.java:[77,40] Double(java.lang.String) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/util/BasicDescriptiveStatistics.java:[57,20] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/evoinference/matrix/distance/BasicSymmetricalDistanceMatrix.java:[106,31] Double(java.lang.String) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/ControlPanel.java:[494,34] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/TreePanel.java:[694,17] javax.swing.JApplet in javax.swing has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/TreePanel.java:[5295,11] javax.swing.JApplet in javax.swing has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/AptxUtil.java:[233,54] javax.swing.JApplet in javax.swing has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/AptxUtil.java:[810,85] javax.swing.JApplet in javax.swing has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/MainFrame.java:[328,9] javax.swing.JApplet in javax.swing has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/TextFrame.java:[80,15] java.lang.SecurityManager in java.lang has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/TextFrame.java:[80,42] getSecurityManager() in java.lang.System has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/util/CommandLineArguments.java:[122,17] Double(java.lang.String) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/util/CommandLineArguments.java:[133,17] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/util/CommandLineArguments.java:[144,17] Long(java.lang.String) in java.lang.Long has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/MainFrameApplet.java:[341,5] javax.swing.JApplet in javax.swing has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/ArchaeopteryxA.java:[41,37] javax.swing.JApplet in javax.swing has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/MainPanelApplets.java:[39,19] javax.swing.JApplet in javax.swing has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/MainPanelApplets.java:[83,5] javax.swing.JApplet in javax.swing has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/ArchaeopteryxE.java:[61,37] javax.swing.JApplet in javax.swing has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/application/goac.java:[73,45] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.java:[176,16] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/application/support_transfer.java:[84,36] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/tools/Blast.java:[50,54] javax.swing.JApplet in javax.swing has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/tools/SupportCount.java:[132,51] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/tools/SupportCount.java:[249,52] Long(long) in java.lang.Long has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/surfacing/SurfacingUtil.java:[1707,30] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/surfacing/SurfacingUtil.java:[1708,30] Double(java.lang.String) in java.lang.Double has been deprecated and marked for removal
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/pccx/BasicExternalNodeBasedCoverageExtender.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/pccx/BasicExternalNodeBasedCoverageExtender.java: Recompile with -Xlint:deprecation for details.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biojava-forester ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biojava-forester ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-forester ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-forester ---
[INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/biojava-forester-6.1.0.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.10.1:jar (default-cli) @ biojava-forester ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+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] * @author Herve Menager
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+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] * @author Herve Menager
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/pccx/ScoringMethodForExternalNode.java:47: warning: invalid input: '<'
[WARNING] *            SortedMap<PhylogenyNode, Double> in which the external node
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/surfacing/DomainSimilarity.java:255: warning: invalid input: '<'
[WARNING] * @return SortedMap<String, SpeciesSpecificDomainSimilariyData>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/phylogeny/iterators/ExternalForwardIterator.java:42: warning: @param argument "tree" is not a parameter name.
[WARNING] * @param tree
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+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] * @param ignored_engulfed_domains
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+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] * @param ignored_engulfed_domains
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/phylogeny/Phylogeny.java:90: warning: @param argument "n" is not a parameter name.
[WARNING] * @param n
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/phylogeny/data/PhylogenyData.java:54: warning: @param argument "PhylogenyData" is not a parameter name.
[WARNING] * @param PhylogenyData
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/phylogeny/PhylogenyNode.java:99: warning: @param argument "n" is not a parameter name.
[WARNING] * @param n
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/phylogeny/PhylogenyNode.java:292: warning: @param argument "n" is not a parameter name.
[WARNING] * @param n
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/phylogeny/PhylogenyNode.java:778: warning: @param argument "n" is not a parameter name.
[WARNING] * @param n
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/io/parsers/util/PhylogenyParserException.java:48: warning: @param argument "arg0" is not a parameter name.
[WARNING] * @param arg0
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/phylogeny/iterators/PostorderTreeIterator.java:45: warning: @param argument "t" is not a parameter name.
[WARNING] * @param t
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/pccx/ScoringMethodForExternalNode.java:55: warning: @param argument "annotate_phylogeny" is not a parameter name.
[WARNING] * @param annotate_phylogeny
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/pccx/ScoringMethodForExternalNode.java:47: warning: invalid input: '<'
[WARNING] *            SortedMap<PhylogenyNode, Double> in which the external node
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/sdi/SDI.java:85: warning: reference not found: #infer(boolean)
[WARNING] * @see #infer(boolean)
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/sdi/SDIR.java:80: warning: reference not found: #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
[WARNING] * @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/sdi/SDIR.java:101: warning: reference not found: #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
[WARNING] * @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/sdi/SDIR.java:117: warning: reference not found: #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
[WARNING] * @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/sdi/SDIR.java:130: warning: reference not found: #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
[WARNING] * @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/sdi/SDIR.java:146: warning: reference not found: #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
[WARNING] * @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/application/support_transfer.java:55: warning: Parameter "args" is documented more than once.
[WARNING] * @param args[1]
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/application/support_transfer.java:60: warning: Parameter "args" is documented more than once.
[WARNING] * @param args[2]
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/application/support_transfer.java:62: warning: Parameter "args" is documented more than once.
[WARNING] * @param args[3]
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+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] * @param protein_length_stats_by_dc
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+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] * @param consider_directedness_and_adjacency_for_bin_combinations
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+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] * @param all_binary_domains_combination_gained if null ignored, otherwise this is to list all binary domain combinations
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/tools/TreeSplitMatrix.java:73: warning: @param argument "target" is not a parameter name.
[WARNING] * @param target
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/ws/wabi/TxSearch.java:41: warning: invalid input: '&mode'
[WARNING] * See: http://xml.nig.ac.jp/wabi/Method?serviceName=TxSearch&mode=methodList
[WARNING] ^
[WARNING] 31 warnings
[INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/biojava-forester-6.1.0-javadoc.jar
[INFO] 
[INFO] -------------------< org.biojava:biojava-alignment >--------------------
[INFO] Building biojava-alignment 6.1.0                                  [4/15]
[INFO]   from biojava-alignment/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before.
[WARNING] The POM for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-alignment ---
[INFO] Copying 2 resources from src/main/resources to target/classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-alignment ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 53 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java:[259,108] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java:[261,106] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/demo/DemoAlignProteins.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/demo/DemoAlignProteins.java: Recompile with -Xlint:deprecation for details.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biojava-alignment ---
[INFO] Copying 11 resources from src/test/resources to target/test-classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biojava-alignment ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 24 source files with javac [debug target 1.8] to target/test-classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookMSA.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookMSA.java: Recompile with -Xlint:deprecation for details.
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-alignment ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-alignment ---
[INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/biojava-alignment-6.1.0.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.10.1:jar (default-cli) @ biojava-alignment ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java:49: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.java:40: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java:46: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/Aligner.java:35: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:125: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:206: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:312: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:542: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:615: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:45: warning: invalid input: '<'
[WARNING] * counterpoint to this reduction in space complexity is a modest (a multiple < 2) increase in time.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:70: warning: @param argument "cutsPerSection" is not a parameter name.
[WARNING] * @param cutsPerSection the number of cuts added to each section during each pass
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:83: warning: @param argument "cutsPerSection" is not a parameter name.
[WARNING] * @param cutsPerSection the number of cuts added to each section during each pass
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallablePairwiseSequenceAligner.java:37: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java:36: warning: reference not found: Profile
[WARNING] * @param <S> each {@link Sequence} of the {@link Profile} pair is of type S
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java:37: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java:41: warning: @param argument "s1" is not a parameter name.
[WARNING] * @param s1
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java:43: warning: @param argument "s2" is not a parameter name.
[WARNING] * @param s2
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/phylo/DistanceMatrixCalculator.java:119: warning: invalid usage of tag {@link #pamDistance(MultipleSequenceAlignment
[WARNING] * method {@link #pamDistance(MultipleSequenceAlignment}). The gapped
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityScorer.java:37: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityScorer.java:37: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/GuanUberbacher.java:37: warning: invalid input: '<'
[WARNING] * space complexity is a modest (a multiple < 2) increase in time.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/MatrixAligner.java:33: warning: reference not found: Profile
[WARNING] * @param <S> each element of the alignment {@link Profile} is of type S
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/MatrixAligner.java:34: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PairInProfileScorer.java:35: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PairwiseSequenceAligner.java:35: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:34: warning: reference not found: Profile
[WARNING] * @param <S> each element of the alignment {@link Profile} is of type S
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:35: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:34: warning: reference not found: Profile
[WARNING] * @param <S> each {@link Sequence} in the pair of alignment {@link Profile}s is of type S
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:35: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: reference not found: Profile
[WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileScorer.java:35: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:36: warning: reference not found: Profile
[WARNING] * @param <S> each element of the alignment {@link Profile} is of type S
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:37: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java:44: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileAnnotation.java:163: warning: @param argument "dbReference" is not a parameter name.
[WARNING] * @param dbReference the string without the initial annotation identifier ( #=GS DR )
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: reference not found: Profile
[WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: reference not found: Profile
[WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: reference not found: Profile
[WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: reference not found: Profile
[WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: reference not found: Profile
[WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: reference not found: Profile
[WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: reference not found: Profile
[WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: reference not found: Profile
[WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and
[WARNING] ^
[WARNING] 58 warnings
[INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/biojava-alignment-6.1.0-javadoc.jar
[INFO] 
[INFO] -------------------< org.biojava:biojava-structure >--------------------
[INFO] Building biojava-structure 6.1.0                                  [5/15]
[INFO]   from biojava-structure/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before.
[WARNING] The POM for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before.
[WARNING] The artifact java3d:vecmath:jar:debian has been relocated to javax.vecmath:vecmath:jar:debian
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-structure ---
[INFO] Copying 3 resources from src/main/resources to target/classes
[INFO] Copying 61 resources from src/main/resources to target/classes
[INFO] The encoding used to copy filtered properties files has not been set. This means that the same encoding will be used to copy filtered properties files as when copying other filtered resources. This might not be what you want! Run your build with --debug to see which files might be affected. Read more at https://maven.apache.org/plugins/maven-resources-plugin/examples/filtering-properties-files.html
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-structure ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 431 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java:[235,29] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java:[236,29] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java:[450,24] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java:[451,24] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[128,48] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[128,71] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[129,33] Float(float) in java.lang.Float has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[130,33] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[131,33] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[131,64] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[131,96] Float(float) in java.lang.Float has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[132,33] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[133,33] Float(float) in java.lang.Float has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[133,56] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[134,33] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[134,70] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[134,97] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[135,33] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[135,60] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[135,90] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[136,33] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[136,62] Float(float) in java.lang.Float has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[136,88] Float(float) in java.lang.Float has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[136,110] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[137,33] Float(float) in java.lang.Float has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[137,53] Float(float) in java.lang.Float has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[137,78] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[137,108] Float(float) in java.lang.Float has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/ClusterDomains.java:[80,53] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/ClusterDomains.java:[81,53] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/ClusterDomains.java:[93,60] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/ClusterDomains.java:[94,74] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java:[205,73] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java:[228,52] Double(java.lang.String) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java:[244,48] Double(java.lang.String) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java:[267,44] Long(java.lang.String) in java.lang.Long has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java:[272,53] Long(java.lang.String) in java.lang.Long has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/SynchronizedOutFile.java:[73,17] attempt to synchronize on an instance of a value-based class
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/SynchronizedOutFile.java:[86,17] attempt to synchronize on an instance of a value-based class
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java:[2034,29] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java:[2091,47] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/CliTools.java:[156,67] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/CliTools.java:[162,67] Double(java.lang.String) in java.lang.Double has been deprecated and marked for removal
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java: Recompile with -Xlint:deprecation for details.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biojava-structure ---
[INFO] Copying 55 resources from src/test/resources to target/test-classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biojava-structure ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 100 source files with javac [debug target 1.8] to target/test-classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityHeuristics.java:[252,40] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfStructureWriter.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfStructureWriter.java: Recompile with -Xlint:deprecation for details.
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-structure ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-structure ---
[INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/biojava-structure-6.1.0.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.10.1:jar (default-cli) @ biojava-structure ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java:1311: warning: reference not found: org.biojava.nbio.structure.gui.JMatrixPanel
[WARNING] * A {@link org.biojava.nbio.structure.gui.JMatrixPanel}, which is used in
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java:56: warning: invalid input: '<'
[WARNING] // AFP(k-1) < AFP(k)(refer AFP.h definition),
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java:57: warning: invalid input: '<'
[WARNING] // ie i(k-1) < i(k) and j(k-1) < j(k)
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java:57: warning: invalid input: '<'
[WARNING] // ie i(k-1) < i(k) and j(k-1) < j(k)
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLParser.java:59: warning: Parameter "name1" is documented more than once.
[WARNING] * @param name1
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:506: warning: invalid input: '<'
[WARNING] * A Map<K,V> can be viewed as a function from K to V. This class represents
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:306: warning: invalid input: '<'
[WARNING] * If none are found at <i>n</i><=maxSymmetry, the alignment is reported as
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:317: warning: invalid input: '<'
[WARNING] * @return The order of symmetry of alignment, or 1 if no order <=
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:474: warning: invalid input: '<'
[WARNING] * List<List<List<Integer>>> aln = getOptAlnAsList(AFPChain afpChain);
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:474: warning: invalid input: '<'
[WARNING] * List<List<List<Integer>>> aln = getOptAlnAsList(AFPChain afpChain);
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:506: warning: invalid input: '<'
[WARNING] * A Map<K,V> can be viewed as a function from K to V. This class represents
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java:48: warning: @param argument "error" is not a parameter name.
[WARNING] * @param error
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java:64: warning: @param argument "error" is not a parameter name.
[WARNING] * @param error
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java:85: warning: @param argument "error" is not a parameter name.
[WARNING] * @param error
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java:621: warning: invalid usage of tag {@link Element().N
[WARNING] * unknown type (element) the vdw radius of {@link Element().N} is returned
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java:263: warning: @return tag cannot be used in method with void return type.
[WARNING] public void setCharge(short charge);
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:227: warning: invalid input: '<'
[WARNING] * @throws StructureException if biassemblyId < 0 or other problems while loading structure
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:251: warning: invalid input: '<'
[WARNING] * @throws StructureException if biassemblyId < 0 or other problems while loading structure
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:471: warning: reference not found: #setStrictSCOP(boolean)
[WARNING] * see {@link #setStrictSCOP(boolean)}</li>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:677: warning: reference not found: #isAutoFetch()
[WARNING] * if {@link #isAutoFetch()} is false. Note that an obsolete entry may still be
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:680: warning: @param argument "fetchFileEvenIfObsolete" is not a parameter name.
[WARNING] * @param fetchFileEvenIfObsolete Whether to fetch obsolete records
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:681: warning: reference not found: #setFetchCurrent(boolean)
[WARNING] * @see #setFetchCurrent(boolean)
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:691: warning: reference not found: #isAutoFetch()
[WARNING] * such as when {@link #isAutoFetch()} is false.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:795: warning: @param argument "pdbId" is not a parameter name.
[WARNING] * @param pdbId
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java:61: warning: @param argument "pdbCode" is not a parameter name.
[WARNING] * @param pdbCode
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java:51: warning: reference not found: #toString()
[WARNING] * It is recommended that the {@link #toString()} method also return the
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java:95: warning: reference not found: StructureTools#getReducedStructure(Structure, String)
[WARNING] * @see StructureTools#getReducedStructure(Structure, String)
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java:265: warning: @param argument "structure" is not a parameter name.
[WARNING] * @param structure
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java:75: warning: reference not found: #setAlignRes()
[WARNING] * @see #setAlignRes()
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java:111: warning: reference not found: #updateCoreLength()
[WARNING] * @see #updateCoreLength()
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java:55: warning: Tag @return cannot be used in constructor documentation.  It can only be used in the following types of documentation: method.
[WARNING] * @return BlockImpl a BlockImpl instance linked to its parent BlockSet.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java:72: warning: Tag @return cannot be used in constructor documentation.  It can only be used in the following types of documentation: method.
[WARNING] * @return BlockImpl an identical copy of the input BlockImpl object.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java:75: warning: reference not found: #setAlignRes()
[WARNING] * @see #setAlignRes()
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java:111: warning: reference not found: #updateCoreLength()
[WARNING] * @see #updateCoreLength()
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSet.java:114: warning: @param argument "matrices" is not a parameter name.
[WARNING] * @param matrices
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java:58: warning: Tag @return cannot be used in constructor documentation.  It can only be used in the following types of documentation: method.
[WARNING] * @return BlockSet an instance linked to the parent alignment.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java:79: warning: Tag @return cannot be used in constructor documentation.  It can only be used in the following types of documentation: method.
[WARNING] * @return BlockSet an identical copy of the input object.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/Bond.java:29: warning: invalid input: '<'
[WARNING] * @author Jules Jacobsen <jacobsen@ebi.ac.uk>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java:30: warning: invalid input: '<'
[WARNING] * @author Jules Jacobsen <jacobsen@ebi.ac.uk>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java:47: warning: reference not found: #Bond(Atom, Atom, int, boolean)
[WARNING] * {@link #Bond(Atom, Atom, int, boolean)} with the
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/BondType.java:26: warning: invalid input: '<'
[WARNING] * @author Jules Jacobsen <jacobsen@ebi.ac.uk>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/BridgeType.java:25: warning: invalid input: '<'
[WARNING] * (i-1,i,i+1) and (j-1,j,j+1), where i<j.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java:330: warning: invalid input: '<'
[WARNING] * Test if two amino acids are connected, i.e. if the distance from C to N <
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java:51: warning: reference not found: #toString()
[WARNING] * It is recommended that the {@link #toString()} method also return the
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java:95: warning: reference not found: StructureTools#getReducedStructure(Structure, String)
[WARNING] * @see StructureTools#getReducedStructure(Structure, String)
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java:64: warning: invalid input: '&'
[WARNING] *  1.4 - Added DuplicationHint parameter & default to duplicating the shorter chain
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java:64: warning: invalid input: '&'
[WARNING] *  1.4 - Added DuplicationHint parameter & default to duplicating the shorter chain
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+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] * @param maxNrIterationsForOptimization
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java:365: warning: @param argument "param" is not a parameter name.
[WARNING] * @param param
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/demo/DemoChangeChemCompProvider.java:39: warning: reference not found: FileParsingParameters#setLoadChemCompInfo(boolean)
[WARNING] *  {@link FileParsingParameters#setLoadChemCompInfo(boolean)} method.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java:51: warning: reference not found: #toString()
[WARNING] * It is recommended that the {@link #toString()} method also return the
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java:95: warning: reference not found: StructureTools#getReducedStructure(Structure, String)
[WARNING] * @see StructureTools#getReducedStructure(Structure, String)
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java:100: warning: @param argument "requestedVersion" is not a parameter name.
[WARNING] * @param requestedVersion ECOD requestedVersion to fetch
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java:298: warning: @param argument "urlFormat" is not a parameter name.
[WARNING] * @param urlFormat the urlFormat to set
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java:54: warning: reference not found: FastaSequence
[WARNING] * A collection of static utilities to convert between {@link AFPChain AFPChains} and {@link FastaSequence FastaSequences}.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java:76: warning: reference not found: cpSite
[WARNING] * {@link cpSite} residues to the right.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java:100: warning: reference not found: cpSite
[WARNING] * {@link cpSite} residues to the right.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java:76: warning: reference not found: cpSite
[WARNING] * {@link cpSite} residues to the right.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java:100: warning: reference not found: cpSite
[WARNING] * {@link cpSite} residues to the right.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GridCell.java:106: warning: @param argument "iAtoms" is not a parameter name.
[WARNING] * @param iAtoms the first set of atom coordinates to which the iIndices correspond
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GridCell.java:107: warning: @param argument "jAtoms" is not a parameter name.
[WARNING] * @param jAtoms the second set of atom coordinates to which the jIndices correspond, if null distances are within the iAtoms only
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GridCell.java:108: warning: @param argument "cutoff" is not a parameter name.
[WARNING] * @param cutoff
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Helix.java:104: warning: @param argument "transformation" is not a parameter name.
[WARNING] * @param transformation helix transformation
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Helix.java:113: warning: @param argument "transformation" is not a parameter name.
[WARNING] * @param transformation helix transformation
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Icosahedron.java:70: warning: @param argument "inscribedRadius" is not a parameter name.
[WARNING] * @param inscribedRadius the inscribedRadius to set
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Icosahedron.java:91: warning: @param argument "midRadius" is not a parameter name.
[WARNING] * @param midRadius the midRadius to set
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java:267: warning: reference not found: #isAutoFetch()
[WARNING] * if {@link #isAutoFetch()} is false. Note that an obsolete entry may still be
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java:270: warning: @param argument "fetchFileEvenIfObsolete" is not a parameter name.
[WARNING] * @param fetchFileEvenIfObsolete Whether to fetch obsolete records
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java:271: warning: reference not found: #setFetchCurrent(boolean)
[WARNING] * @see #setFetchCurrent(boolean)
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java:281: warning: reference not found: #isAutoFetch()
[WARNING] * such as when {@link #isAutoFetch()} is false.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java:302: warning: reference not found: #setAutoFetch(boolean)
[WARNING] * This replaces the {@link #setAutoFetch(boolean)} method with a more
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/LUDecomposition.java:28: warning: invalid input: '<'
[WARNING] If m < n, then L is m-by-m and U is m-by-n.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java:150: warning: reference not found: #updateDistanceMatrix()
[WARNING] * @see #updateDistanceMatrix()
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java:158: warning: reference not found: #setMultipleAlignments()
[WARNING] * @see #setMultipleAlignments()
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java:168: warning: reference not found: #setMultipleAlignments()
[WARNING] * @see #setMultipleAlignments()
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+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] * @return MultipleAlignmentEnsemble an empty ensemble instance.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+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] * @return MultipleAlignmentEnsemble an ensemble with the structures.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+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] * @return MultipleAlignmentEnsemble identical copy of the input ensemble.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+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] * @return MultipleAlignmentEnsemble an ensemble
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java:150: warning: reference not found: #updateDistanceMatrix()
[WARNING] * @see #updateDistanceMatrix()
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java:158: warning: reference not found: #setMultipleAlignments()
[WARNING] * @see #setMultipleAlignments()
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java:168: warning: reference not found: #setMultipleAlignments()
[WARNING] * @see #setMultipleAlignments()
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java:56: warning: Tag @return cannot be used in constructor documentation.  It can only be used in the following types of documentation: method.
[WARNING] * @return MultipleAlignment an empty MultipleAlignment instance.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java:68: warning: Tag @return cannot be used in constructor documentation.  It can only be used in the following types of documentation: method.
[WARNING] * @return MultipleAlignment an alignment instance part of an ensemble.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java:90: warning: Tag @return cannot be used in constructor documentation.  It can only be used in the following types of documentation: method.
[WARNING] * @return MultipleAlignmentImpl identical copy of the alignment.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+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] * @param reference
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+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] * @param alignment
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+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] * @param alignment
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+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] * @param multAln
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+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] * @param alignment
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java:197: warning: @param argument "afpChain" is not a parameter name.
[WARNING] * @param afpChain
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java:292: warning: invalid input: '&'
[WARNING] * Column 1 -30: Atom & Residue records of query sequence.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+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] * @param pairwise the pairwise structure alignment used to generate the
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Octahedron.java:65: warning: @param argument "inscribedRadius" is not a parameter name.
[WARNING] * @param inscribedRadius the inscribedRadius to set
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Octahedron.java:86: warning: @param argument "midRadius" is not a parameter name.
[WARNING] * @param midRadius the midRadius to set
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Octahedron.java:95: warning: @param argument "n" is not a parameter name.
[WARNING] * @param n
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Octahedron.java:96: warning: @param argument "radius" is not a parameter name.
[WARNING] * @param radius
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Octahedron.java:97: warning: @param argument "center" is not a parameter name.
[WARNING] * @param center
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/OptimalCECPMain.java:461: warning: reference not found: #alignHeuristic(Atom[], Atom[], Object)
[WARNING] * quite slow. Use {@link #alignHeuristic(Atom[], Atom[], Object)} for a
[WARNING] ^
[WARNING] 100 warnings
[INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/biojava-structure-6.1.0-javadoc.jar
[INFO] 
[INFO] ------------------< org.biojava:biojava-jcolorbrewer >------------------
[INFO] Building biojava-jcolorbrewer 6.1.0                               [6/15]
[INFO]   from biojava-jcolorbrewer/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before.
[WARNING] The POM for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-jcolorbrewer ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-jcolorbrewer ---
[INFO] Recompiling the module because of changed source code.
[INFO] Compiling 7 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java uses or overrides a deprecated API.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java: Recompile with -Xlint:deprecation for details.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biojava-jcolorbrewer ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biojava-jcolorbrewer ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-jcolorbrewer ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-jcolorbrewer ---
[INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/biojava-jcolorbrewer-6.1.0.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.10.1:jar (default-cli) @ biojava-jcolorbrewer ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java:82: warning: reference not found: ColorChooserDialog
[WARNING] *  @see	ColorChooserDialog
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java:436: warning: @param argument "color" is not a parameter name.
[WARNING] * @param	color		the new color
[WARNING] ^
[WARNING] 3 warnings
[INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/biojava-jcolorbrewer-6.1.0-javadoc.jar
[INFO] 
[INFO] -----------------< org.biojava:biojava-structure-gui >------------------
[INFO] Building biojava-structure-gui 6.1.0                              [7/15]
[INFO]   from biojava-structure-gui/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before.
[WARNING] The POM for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-structure-gui ---
[INFO] Copying 49 resources from src/main/resources to target/classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-structure-gui ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 131 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java:[260,32] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java:[261,32] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java:[262,32] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java:[263,32] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java:[264,32] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java:[265,32] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.java:[129,38] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.java:[130,38] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.java:[131,38] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.java:[132,38] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.java:[133,38] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.java:[134,38] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/SequenceDisplay.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/SequenceDisplay.java: Recompile with -Xlint:deprecation for details.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/BiojavaJmol.java: Some input files use unchecked or unsafe operations.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/BiojavaJmol.java: Recompile with -Xlint:unchecked for details.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biojava-structure-gui ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biojava-structure-gui ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 6 source files with javac [debug target 1.8] to target/test-classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-structure-gui ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-structure-gui ---
[INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/biojava-structure-gui-6.1.0.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.10.1:jar (default-cli) @ biojava-structure-gui ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java:199: warning: @param argument "label" is not a parameter name.
[WARNING] * @param label
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ContinuousColorMapperTransform.java:63: warning: @param argument "the" is not a parameter name.
[WARNING] * @param the input value
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DotPlotPanel.java:59: warning: @param argument "background" is not a parameter name.
[WARNING] * @param background [Optional]A matrix of 'background colors' over which to draw the alignment.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/HSVColorSpace.java:83: warning: @param argument "type" is not a parameter name.
[WARNING] * @param type
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/HSVColorSpace.java:84: warning: @param argument "numcomponents" is not a parameter name.
[WARNING] * @param numcomponents
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGenerator.java:41: warning: @param argument "rotationGroup" is not a parameter name.
[WARNING] * @param rotationGroup
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/LinearColorInterpolator.java:145: warning: @param argument "interpDirection" is not a parameter name.
[WARNING] * @param interpDirection An array of size colorSpace.getNumComponents()
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java:54: warning: invalid input: '&'
[WARNING] * Tracks Memory allocated & used, displayed in graph form.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java:157: warning: @param argument "multAln" is not a parameter name.
[WARNING] * @param multAln
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java:158: warning: @param argument "colors" is not a parameter name.
[WARNING] * @param colors
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java:46: warning: invalid input: '&'
[WARNING] /** A Panel that allows user to specify PDB & chain ID, as well as sub-ranges
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java:107: warning: @param argument "msa" is not a parameter name.
[WARNING] * @param msa
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java:54: warning: invalid input: '&'
[WARNING] * Tracks Memory allocated & used, displayed in graph form.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java:46: warning: invalid input: '&'
[WARNING] /** A Panel that allows user to specify PDB & chain ID, as well as sub-ranges
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java:46: warning: invalid input: '&'
[WARNING] /** A Panel that allows user to specify PDB & chain ID, as well as sub-ranges
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java:54: warning: invalid input: '&'
[WARNING] * Tracks Memory allocated & used, displayed in graph form.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java:46: warning: invalid input: '&'
[WARNING] /** A Panel that allows user to specify PDB & chain ID, as well as sub-ranges
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java:54: warning: invalid input: '&'
[WARNING] * Tracks Memory allocated & used, displayed in graph form.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java:46: warning: invalid input: '&'
[WARNING] /** A Panel that allows user to specify PDB & chain ID, as well as sub-ranges
[WARNING] ^
[WARNING] 20 warnings
[INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/biojava-structure-gui-6.1.0-javadoc.jar
[INFO] 
[INFO] ---------------------< org.biojava:biojava-genome >---------------------
[INFO] Building biojava-genome 6.1.0                                     [8/15]
[INFO]   from biojava-genome/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before.
[WARNING] The POM for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-genome ---
[INFO] Copying 1 resource from src/main/resources to target/classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-genome ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 51 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.java: Recompile with -Xlint:deprecation for details.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biojava-genome ---
[INFO] Copying 83 resources from src/test/resources to target/test-classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biojava-genome ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 20 source files with javac [debug target 1.8] to target/test-classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/AbstractFastqReaderTest.java: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/AbstractFastqReaderTest.java uses or overrides a deprecated API.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/AbstractFastqReaderTest.java: Recompile with -Xlint:deprecation for details.
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-genome ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-genome ---
[INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/biojava-genome-6.1.0.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.10.1:jar (default-cli) @ biojava-genome ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java:807: warning: Tag @author cannot be used in method documentation.  It can only be used in the following types of documentation: overview, module, package, class/interface.
[WARNING] * @author Yana Valasatava
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java:854: warning: Tag @author cannot be used in method documentation.  It can only be used in the following types of documentation: overview, module, package, class/interface.
[WARNING] * @author Yana Valasatava
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java:41: warning: @param argument "fileName" is not a parameter name.
[WARNING] * @param fileName
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java:42: warning: @param argument "chromosomeSequence" is not a parameter name.
[WARNING] * @param chromosomeSequence
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java:414: warning: invalid input: '<'
[WARNING] * For position < 0, return Location( start, end + position ).
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java:456: warning: invalid input: '<'
[WARNING] * For position < 0, return Location( end - position, end ).
[WARNING] ^
[WARNING] 7 warnings
[INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/biojava-genome-6.1.0-javadoc.jar
[INFO] 
[INFO] -------------------< org.biojava:biojava-modfinder >--------------------
[INFO] Building biojava-modfinder 6.1.0                                  [9/15]
[INFO]   from biojava-modfinder/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before.
[WARNING] The POM for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-modfinder ---
[INFO] Copying 2 resources from src/main/resources to target/classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-modfinder ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 23 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Dataset.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Dataset.java: Recompile with -Xlint:deprecation for details.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biojava-modfinder ---
[INFO] Copying 2 resources from src/test/resources to target/test-classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biojava-modfinder ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 5 source files with javac [debug target 1.8] to target/test-classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/phosphosite/TestAcetylation.java: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/phosphosite/TestAcetylation.java uses or overrides a deprecated API.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/phosphosite/TestAcetylation.java: Recompile with -Xlint:deprecation for details.
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-modfinder ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-modfinder ---
[INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/biojava-modfinder-6.1.0.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.10.1:jar (default-cli) @ biojava-modfinder ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java:33: warning: reference not found: register
[WARNING] * you have to use one of the {@link register} and {@link of} methods.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java:112: warning: @param argument "pdbccIds" is not a parameter name.
[WARNING] * @param pdbccIds possible Protein Data Bank ID.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationLinkage.java:57: warning: @param argument "labelOfAtomOnComponent1" is not a parameter name.
[WARNING] * @param labelOfAtomOnComponent1 label of the atom on the first
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationLinkage.java:60: warning: @param argument "labelOfAtomOnComponent2" is not a parameter name.
[WARNING] * @param labelOfAtomOnComponent2 label of the atom on the second
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationLinkage.java:80: warning: @param argument "labelOfAtomOnComponent1" is not a parameter name.
[WARNING] * @param labelOfAtomOnComponent1 label of the atom on the first
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationLinkage.java:83: warning: @param argument "labelOfAtomOnComponent2" is not a parameter name.
[WARNING] * @param labelOfAtomOnComponent2 label of the atom on the second
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java:50: warning: reference not found: ProteinModificationBean
[WARNING] * @return {@link ProteinModificationBean} occurred on the residue.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java:76: warning: reference not found: #getLinkedGroupPairs
[WARNING] * @see #getLinkedGroupPairs
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java:85: warning: @return tag cannot be used in method with void return type.
[WARNING] public void setAtomLinkages(Set<StructureAtomLinkage> linkages);
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java:88: warning: reference not found: addGroup
[WARNING] * Add a linkage. Add new the involved groups first using {@link addGroup}.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompoundImpl.java:68: warning: Tag @return cannot be used in constructor documentation.  It can only be used in the following types of documentation: method.
[WARNING] * @return a {@link ModifiedCompound}.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java:50: warning: reference not found: ProteinModificationBean
[WARNING] * @return {@link ProteinModificationBean} occurred on the residue.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java:76: warning: reference not found: #getLinkedGroupPairs
[WARNING] * @see #getLinkedGroupPairs
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java:88: warning: reference not found: addGroup
[WARNING] * Add a linkage. Add new the involved groups first using {@link addGroup}.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java:209: warning: @param argument "mod" is not a parameter name.
[WARNING] * @param mod
[WARNING] ^
[WARNING] 16 warnings
[INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/biojava-modfinder-6.1.0-javadoc.jar
[INFO] 
[INFO] -----------------------< org.biojava:biojava-ws >-----------------------
[INFO] Building biojava-ws 6.1.0                                        [10/15]
[INFO]   from biojava-ws/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before.
[WARNING] The POM for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-ws ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/main/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-ws ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 21 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java: Recompile with -Xlint:deprecation for details.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biojava-ws ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biojava-ws ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 1 source file with javac [debug target 1.8] to target/test-classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-ws ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-ws ---
[INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/biojava-ws-6.1.0.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.10.1:jar (default-cli) @ biojava-ws ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/MapToStringTransformer.java:46: warning: invalid input: '&'
[WARNING] * separatorSequence = "&";
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/MapToStringTransformer.java:79: warning: invalid input: '&'
[WARNING] * {@code mappingSequence} is "=" and separator sequence is "&";
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java:140: warning: reference not found: NCBIQBlastService#printRemoteBlastInfo()
[WARNING] * A list of available databases can be acquired by calling {@link NCBIQBlastService#printRemoteBlastInfo()}
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java:144: warning: @param argument "db" is not a parameter name.
[WARNING] * @param db : a valid name to a NCBI blastable database
[WARNING] ^
[WARNING] 5 warnings
[INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/biojava-ws-6.1.0-javadoc.jar
[INFO] 
[INFO] ----------------< org.biojava:biojava-protein-disorder >----------------
[INFO] Building biojava-protein-disorder 6.1.0                          [11/15]
[INFO]   from biojava-protein-disorder/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before.
[WARNING] The POM for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-protein-disorder ---
[INFO] Copying 11 resources from src/main/resources to target/classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-protein-disorder ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 13 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biojava-protein-disorder ---
[INFO] Copying 2 resources from src/test/resources to target/test-classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biojava-protein-disorder ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 3 source files with javac [debug target 1.8] to target/test-classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-protein-disorder ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-protein-disorder ---
[INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/biojava-protein-disorder-6.1.0.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.10.1:jar (default-cli) @ biojava-protein-disorder ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
[WARNING] 1 warning
[INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/biojava-protein-disorder-6.1.0-javadoc.jar
[INFO] 
[INFO] --------------------< org.biojava:biojava-aa-prop >---------------------
[INFO] Building biojava-aa-prop 6.1.0                                   [12/15]
[INFO]   from biojava-aa-prop/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before.
[WARNING] The POM for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-aa-prop ---
[INFO] Copying 11 resources from src/main/resources to target/classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-aa-prop ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 33 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biojava-aa-prop ---
[INFO] Copying 7 resources from src/test/resources to target/test-classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biojava-aa-prop ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 8 source files with javac [debug target 1.8] to target/test-classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java:[348,51] Double(double) in java.lang.Double has been deprecated and marked for removal
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-aa-prop ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-aa-prop ---
[INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/biojava-aa-prop-6.1.0.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.10.1:jar (default-cli) @ biojava-aa-prop ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java:40: warning: Tag @author cannot be used in field documentation.  It can only be used in the following types of documentation: overview, module, package, class/interface.
[WARNING] * @author kohchuanhock
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java:41: warning: Tag @version cannot be used in field documentation.  It can only be used in the following types of documentation: overview, module, package, class/interface.
[WARNING] * @version 2011.06.09
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java:261: warning: invalid input: '<'
[WARNING] * <a href="http://www.innovagen.se/custom-peptide-synthesis/peptide-property-calculator/peptide-property-calculator-notes.asp#NetCharge>here</a>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java:261: warning: invalid input: '<'
[WARNING] * <a href="http://www.innovagen.se/custom-peptide-synthesis/peptide-property-calculator/peptide-property-calculator-notes.asp#NetCharge>here</a>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&'
[WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
[WARNING] ^
[WARNING] 61 warnings
[INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/biojava-aa-prop-6.1.0-javadoc.jar
[INFO] 
[INFO] --------------------< org.biojava:biojava-survival >--------------------
[INFO] Building biojava-survival 6.1.0                                  [13/15]
[INFO]   from biojava-survival/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before.
[WARNING] The POM for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-survival ---
[INFO] Copying 1 resource from src/main/resources to target/classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-survival ---
[INFO] Recompiling the module because of changed source code.
[INFO] Compiling 46 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biojava-survival ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biojava-survival ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-survival ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-survival ---
[INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/biojava-survival-6.1.0.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.10.1:jar (default-cli) @ biojava-survival ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java:78: warning: invalid input: '<'
[WARNING] *                      the percent change in loglikelihood is <= eps.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java:1467: warning: @param argument "f" is not a parameter name.
[WARNING] * @param f
[WARNING] ^
[WARNING] 3 warnings
[INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/biojava-survival-6.1.0-javadoc.jar
[INFO] 
[INFO] --------------------< org.biojava:biojava-ontology >--------------------
[INFO] Building biojava-ontology 6.1.0                                  [14/15]
[INFO]   from biojava-ontology/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before.
[WARNING] The POM for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-ontology ---
[INFO] Copying 3 resources from src/main/resources to target/classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-ontology ---
[INFO] Recompiling the module because of changed source code.
[INFO] Compiling 36 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[70,33] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[70,53] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[71,33] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[71,53] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[72,33] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[72,53] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[73,33] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[73,53] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[74,33] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[74,53] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[75,33] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[75,53] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[76,33] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[76,54] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[77,33] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[77,54] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[78,33] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[78,53] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[79,33] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[79,53] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[80,33] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[80,53] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[81,33] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[81,53] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[82,33] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[82,53] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[83,33] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[83,53] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[84,33] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[84,53] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[420,54] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:[452,38] Character(char) in java.lang.Character has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/IntegerOntology.java:[193,29] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java: Some input files use unchecked or unsafe operations.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java: Recompile with -Xlint:unchecked for details.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biojava-ontology ---
[INFO] Copying 6 resources from src/test/resources to target/test-classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biojava-ontology ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 3 source files with javac [debug target 1.8] to target/test-classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestParseOBO.java: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestParseOBO.java uses unchecked or unsafe operations.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestParseOBO.java: Recompile with -Xlint:unchecked for details.
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-ontology ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-ontology ---
[INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/biojava-ontology-6.1.0.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.10.1:jar (default-cli) @ biojava-ontology ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotatable.java:78: warning: reference not found: org.biojavax.RichAnnotatable
[WARNING] * @see org.biojavax.RichAnnotatable
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java:56: warning: reference not found: org.biojavax.RichAnnotation
[WARNING] * @see org.biojavax.RichAnnotation
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java:99: warning: cannot find exception type by name
[WARNING] * @throws ChangeVetoException if this annotation object can't be changed, or
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java:111: warning: cannot find exception type by name
[WARNING] * @throws ChangeVetoException if the change is vetoed
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:41: warning: invalid input: '&view'
[WARNING] * http://geneontology.cvs.sourceforge.net/geneontology/go-dev/java/oboedit/sources/org/geneontology/oboedit/dataadapter/OBOParseEngine.java?revision=1.10&view=markup
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java:43: warning: reference not found: org.biojavax.ontology.ComparableOntology
[WARNING] * @see org.biojavax.ontology.ComparableOntology
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java:132: warning: cannot find exception type by name
[WARNING] * @throws ChangeVetoException
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java:151: warning: cannot find exception type by name
[WARNING] * @throws ChangeVetoException
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java:171: warning: cannot find exception type by name
[WARNING] * @throws ChangeVetoException
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java:190: warning: cannot find exception type by name
[WARNING] * @throws ChangeVetoException
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java:211: warning: cannot find exception type by name
[WARNING] * @throws ChangeVetoException
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java:231: warning: cannot find exception type by name
[WARNING] * @throws ChangeVetoException
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java:254: warning: cannot find exception type by name
[WARNING] * @throws ChangeVetoException
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java:35: warning: reference not found: org.biojava.nbio.Annotation
[WARNING] * A term in an ontology.  This has an {@link org.biojava.nbio.Annotation Annotation}
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java:54: warning: reference not found: org.biojavax.ontology.ComparableTerm
[WARNING] * @see org.biojavax.ontology.ComparableTerm
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java:116: warning: reference not found: org.biojavax.ontology.SimpleComparableTerm
[WARNING] * @see org.biojavax.ontology.SimpleComparableTerm
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java:44: warning: reference not found: org.biojavax.ontology.ComparableTriple
[WARNING] * @see org.biojavax.ontology.ComparableTriple
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java:98: warning: invalid input: '&'
[WARNING] * return to.getSubject() == getSubject() &&
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java:98: warning: invalid input: '&'
[WARNING] * return to.getSubject() == getSubject() &&
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java:99: warning: invalid input: '&'
[WARNING] *        to.getObject() == getObject() &&
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java:99: warning: invalid input: '&'
[WARNING] *        to.getObject() == getObject() &&
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java:114: warning: reference not found: org.biojavax.ontology.SimpleComparableTriple
[WARNING] * @see org.biojavax.ontology.SimpleComparableTriple
[WARNING] ^
[WARNING] 23 warnings
[INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/biojava-ontology-6.1.0-javadoc.jar
[INFO] 
[INFO] ------------< org.biojava:biojava-protein-comparison-tool >-------------
[INFO] Building biojava-protein-comparison-tool 6.1.0                   [15/15]
[INFO]   from biojava-protein-comparison-tool/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before.
[WARNING] The POM for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-protein-comparison-tool ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/src/main/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-protein-comparison-tool ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 1 source file with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biojava-protein-comparison-tool ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biojava-protein-comparison-tool ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-protein-comparison-tool ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-protein-comparison-tool ---
[INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/biojava-protein-comparison-tool-6.1.0.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.10.1:jar (default-cli) @ biojava-protein-comparison-tool ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
[WARNING] 1 warning
[INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/biojava-protein-comparison-tool-6.1.0-javadoc.jar
[INFO] 
[INFO] ------------------------< org.biojava:biojava >-------------------------
[INFO] Building biojava 6.1.0                                           [16/15]
[INFO]   from pom.xml
[INFO] --------------------------------[ pom ]---------------------------------
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before.
[WARNING] The POM for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before.
[INFO] 
[INFO] >>> maven-javadoc-plugin:3.10.1:aggregate (default-cli) > compile @ biojava >>>
[INFO] 
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO] Forking biojava-core 6.1.0
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-core ---
[INFO] Copying 24 resources from src/main/resources to target/classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-core ---
[INFO] Nothing to compile - all classes are up to date.
[WARNING] Overwriting artifact's file from /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/biojava-core-6.1.0.jar to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/classes
[INFO] 
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO] Forking biojava-forester 6.1.0
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-forester ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-forester ---
[INFO] Nothing to compile - all classes are up to date.
[WARNING] Overwriting artifact's file from /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/biojava-forester-6.1.0.jar to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/classes
[INFO] 
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO] Forking biojava-alignment 6.1.0
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-alignment ---
[INFO] Copying 2 resources from src/main/resources to target/classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-alignment ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 53 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java:[259,108] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java:[261,106] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/demo/DemoAlignProteins.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/demo/DemoAlignProteins.java: Recompile with -Xlint:deprecation for details.
[WARNING] Overwriting artifact's file from /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/biojava-alignment-6.1.0.jar to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/classes
[INFO] 
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO] Forking biojava-structure 6.1.0
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[WARNING] The artifact java3d:vecmath:jar:debian has been relocated to javax.vecmath:vecmath:jar:debian
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-structure ---
[INFO] Copying 3 resources from src/main/resources to target/classes
[INFO] Copying 61 resources from src/main/resources to target/classes
[INFO] The encoding used to copy filtered properties files has not been set. This means that the same encoding will be used to copy filtered properties files as when copying other filtered resources. This might not be what you want! Run your build with --debug to see which files might be affected. Read more at https://maven.apache.org/plugins/maven-resources-plugin/examples/filtering-properties-files.html
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-structure ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 431 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java:[235,29] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java:[236,29] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java:[450,24] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java:[451,24] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[128,48] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[128,71] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[129,33] Float(float) in java.lang.Float has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[130,33] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[131,33] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[131,64] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[131,96] Float(float) in java.lang.Float has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[132,33] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[133,33] Float(float) in java.lang.Float has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[133,56] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[134,33] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[134,70] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[134,97] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[135,33] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[135,60] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[135,90] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[136,33] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[136,62] Float(float) in java.lang.Float has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[136,88] Float(float) in java.lang.Float has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[136,110] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[137,33] Float(float) in java.lang.Float has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[137,53] Float(float) in java.lang.Float has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[137,78] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java:[137,108] Float(float) in java.lang.Float has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/ClusterDomains.java:[80,53] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/ClusterDomains.java:[81,53] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/ClusterDomains.java:[93,60] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/ClusterDomains.java:[94,74] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java:[205,73] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java:[228,52] Double(java.lang.String) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java:[244,48] Double(java.lang.String) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java:[267,44] Long(java.lang.String) in java.lang.Long has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java:[272,53] Long(java.lang.String) in java.lang.Long has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/SynchronizedOutFile.java:[73,17] attempt to synchronize on an instance of a value-based class
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/SynchronizedOutFile.java:[86,17] attempt to synchronize on an instance of a value-based class
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java:[2034,29] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java:[2091,47] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/CliTools.java:[156,67] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/CliTools.java:[162,67] Double(java.lang.String) in java.lang.Double has been deprecated and marked for removal
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java: Recompile with -Xlint:deprecation for details.
[WARNING] Overwriting artifact's file from /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/biojava-structure-6.1.0.jar to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/classes
[INFO] 
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[INFO] Forking biojava-jcolorbrewer 6.1.0
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-jcolorbrewer ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-jcolorbrewer ---
[INFO] Nothing to compile - all classes are up to date.
[WARNING] Overwriting artifact's file from /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/biojava-jcolorbrewer-6.1.0.jar to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/classes
[INFO] 
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO] Forking biojava-structure-gui 6.1.0
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-structure-gui ---
[INFO] Copying 49 resources from src/main/resources to target/classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-structure-gui ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 131 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java:[260,32] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java:[261,32] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java:[262,32] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java:[263,32] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java:[264,32] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java:[265,32] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.java:[129,38] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.java:[130,38] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.java:[131,38] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.java:[132,38] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.java:[133,38] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.java:[134,38] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/SequenceDisplay.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/SequenceDisplay.java: Recompile with -Xlint:deprecation for details.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/BiojavaJmol.java: Some input files use unchecked or unsafe operations.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/BiojavaJmol.java: Recompile with -Xlint:unchecked for details.
[WARNING] Overwriting artifact's file from /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/biojava-structure-gui-6.1.0.jar to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/classes
[INFO] 
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO] Forking biojava-genome 6.1.0
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-genome ---
[INFO] Copying 1 resource from src/main/resources to target/classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-genome ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 51 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.java: Recompile with -Xlint:deprecation for details.
[WARNING] Overwriting artifact's file from /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/biojava-genome-6.1.0.jar to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/classes
[INFO] 
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO] Forking biojava-modfinder 6.1.0
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-modfinder ---
[INFO] Copying 2 resources from src/main/resources to target/classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-modfinder ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 23 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Dataset.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Dataset.java: Recompile with -Xlint:deprecation for details.
[WARNING] Overwriting artifact's file from /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/biojava-modfinder-6.1.0.jar to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/classes
[INFO] 
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO] Forking biojava-ws 6.1.0
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-ws ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/main/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-ws ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 21 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java: Recompile with -Xlint:deprecation for details.
[WARNING] Overwriting artifact's file from /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/biojava-ws-6.1.0.jar to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/classes
[INFO] 
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO] Forking biojava-protein-disorder 6.1.0
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-protein-disorder ---
[INFO] Copying 11 resources from src/main/resources to target/classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-protein-disorder ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 13 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[WARNING] Overwriting artifact's file from /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/biojava-protein-disorder-6.1.0.jar to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/classes
[INFO] 
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO] Forking biojava-aa-prop 6.1.0
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-aa-prop ---
[INFO] Copying 11 resources from src/main/resources to target/classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-aa-prop ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 33 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[WARNING] Overwriting artifact's file from /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/biojava-aa-prop-6.1.0.jar to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/classes
[INFO] 
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO] Forking biojava-survival 6.1.0
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-survival ---
[INFO] Copying 1 resource from src/main/resources to target/classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-survival ---
[INFO] Nothing to compile - all classes are up to date.
[WARNING] Overwriting artifact's file from /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/biojava-survival-6.1.0.jar to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/classes
[INFO] 
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO] Forking biojava-ontology 6.1.0
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-ontology ---
[INFO] Copying 3 resources from src/main/resources to target/classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-ontology ---
[INFO] Nothing to compile - all classes are up to date.
[WARNING] Overwriting artifact's file from /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/biojava-ontology-6.1.0.jar to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/classes
[INFO] 
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO] Forking biojava-protein-comparison-tool 6.1.0
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-protein-comparison-tool ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/src/main/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-protein-comparison-tool ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 1 source file with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[WARNING] Overwriting artifact's file from /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/biojava-protein-comparison-tool-6.1.0.jar to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/classes
[INFO] 
[INFO] <<< maven-javadoc-plugin:3.10.1:aggregate (default-cli) < compile @ biojava <<<
[INFO] 
[WARNING] The artifact java3d:vecmath:jar:debian has been relocated to javax.vecmath:vecmath:jar:debian
[INFO] 
[INFO] --- maven-javadoc-plugin:3.10.1:aggregate (default-cli) @ biojava ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java:199: warning: @param argument "label" is not a parameter name.
[WARNING] * @param label
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java:74: warning: reference not found: #getAllSubLocations()
[WARNING] * {@link #getAllSubLocations()}.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java:49: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.java:40: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java:46: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java:56: warning: invalid input: '<'
[WARNING] // AFP(k-1) < AFP(k)(refer AFP.h definition),
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java:57: warning: invalid input: '<'
[WARNING] // ie i(k-1) < i(k) and j(k-1) < j(k)
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java:57: warning: invalid input: '<'
[WARNING] // ie i(k-1) < i(k) and j(k-1) < j(k)
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLParser.java:59: warning: Parameter "name1" is documented more than once.
[WARNING] * @param name1
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:41: warning: reference not found: Aligner
[WARNING] * Defines an alignment step in order to pass alignment information from an {@link Aligner} to a constructor.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:68: warning: invalid input: '<'
[WARNING] * @throws IndexOutOfBoundsException if sequenceIndex < 1 or sequenceIndex >
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:133: warning: invalid input: '<'
[WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:157: warning: invalid input: '<'
[WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:41: warning: reference not found: Aligner
[WARNING] * Defines an alignment step in order to pass alignment information from an {@link Aligner} to a constructor.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/Aligner.java:35: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:125: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:206: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:312: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:542: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:615: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:506: warning: invalid input: '<'
[WARNING] * A Map<K,V> can be viewed as a function from K to V. This class represents
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:306: warning: invalid input: '<'
[WARNING] * If none are found at <i>n</i><=maxSymmetry, the alignment is reported as
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:317: warning: invalid input: '<'
[WARNING] * @return The order of symmetry of alignment, or 1 if no order <=
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:474: warning: invalid input: '<'
[WARNING] * List<List<List<Integer>>> aln = getOptAlnAsList(AFPChain afpChain);
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:474: warning: invalid input: '<'
[WARNING] * List<List<List<Integer>>> aln = getOptAlnAsList(AFPChain afpChain);
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:506: warning: invalid input: '<'
[WARNING] * A Map<K,V> can be viewed as a function from K to V. This class represents
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:45: warning: invalid input: '<'
[WARNING] * counterpoint to this reduction in space complexity is a modest (a multiple < 2) increase in time.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:70: warning: @param argument "cutsPerSection" is not a parameter name.
[WARNING] * @param cutsPerSection the number of cuts added to each section during each pass
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:83: warning: @param argument "cutsPerSection" is not a parameter name.
[WARNING] * @param cutsPerSection the number of cuts added to each section during each pass
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java:48: warning: @param argument "error" is not a parameter name.
[WARNING] * @param error
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java:64: warning: @param argument "error" is not a parameter name.
[WARNING] * @param error
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java:85: warning: @param argument "error" is not a parameter name.
[WARNING] * @param error
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotatable.java:78: warning: reference not found: org.biojavax.RichAnnotatable
[WARNING] * @see org.biojavax.RichAnnotatable
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java:56: warning: reference not found: org.biojavax.RichAnnotation
[WARNING] * @see org.biojavax.RichAnnotation
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java:99: warning: cannot find exception type by name
[WARNING] * @throws ChangeVetoException if this annotation object can't be changed, or
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java:111: warning: cannot find exception type by name
[WARNING] * @throws ChangeVetoException if the change is vetoed
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+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] * @author Herve Menager
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+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] * @author Herve Menager
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java:621: warning: invalid usage of tag {@link Element().N
[WARNING] * unknown type (element) the vdw radius of {@link Element().N} is returned
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java:263: warning: @return tag cannot be used in method with void return type.
[WARNING] public void setCharge(short charge);
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:227: warning: invalid input: '<'
[WARNING] * @throws StructureException if biassemblyId < 0 or other problems while loading structure
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:251: warning: invalid input: '<'
[WARNING] * @throws StructureException if biassemblyId < 0 or other problems while loading structure
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:471: warning: reference not found: #setStrictSCOP(boolean)
[WARNING] * see {@link #setStrictSCOP(boolean)}</li>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:677: warning: reference not found: #isAutoFetch()
[WARNING] * if {@link #isAutoFetch()} is false. Note that an obsolete entry may still be
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:680: warning: @param argument "fetchFileEvenIfObsolete" is not a parameter name.
[WARNING] * @param fetchFileEvenIfObsolete Whether to fetch obsolete records
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:681: warning: reference not found: #setFetchCurrent(boolean)
[WARNING] * @see #setFetchCurrent(boolean)
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:691: warning: reference not found: #isAutoFetch()
[WARNING] * such as when {@link #isAutoFetch()} is false.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:795: warning: @param argument "pdbId" is not a parameter name.
[WARNING] * @param pdbId
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java:61: warning: @param argument "pdbCode" is not a parameter name.
[WARNING] * @param pdbCode
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java:51: warning: reference not found: #toString()
[WARNING] * It is recommended that the {@link #toString()} method also return the
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java:95: warning: reference not found: StructureTools#getReducedStructure(Structure, String)
[WARNING] * @see StructureTools#getReducedStructure(Structure, String)
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java:265: warning: @param argument "structure" is not a parameter name.
[WARNING] * @param structure
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java:67: warning: invalid input: '&'
[WARNING] * Class is immutable & so this is unsupported
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java:75: warning: invalid input: '&'
[WARNING] * Class is immutable & so this is unsupported
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java:67: warning: invalid input: '&'
[WARNING] * Class is immutable & so this is unsupported
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java:75: warning: invalid input: '&'
[WARNING] * Class is immutable & so this is unsupported
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java:75: warning: reference not found: #setAlignRes()
[WARNING] * @see #setAlignRes()
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java:111: warning: reference not found: #updateCoreLength()
[WARNING] * @see #updateCoreLength()
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java:55: warning: Tag @return cannot be used in constructor documentation.  It can only be used in the following types of documentation: method.
[WARNING] * @return BlockImpl a BlockImpl instance linked to its parent BlockSet.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java:72: warning: Tag @return cannot be used in constructor documentation.  It can only be used in the following types of documentation: method.
[WARNING] * @return BlockImpl an identical copy of the input BlockImpl object.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java:75: warning: reference not found: #setAlignRes()
[WARNING] * @see #setAlignRes()
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java:111: warning: reference not found: #updateCoreLength()
[WARNING] * @see #updateCoreLength()
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSet.java:114: warning: @param argument "matrices" is not a parameter name.
[WARNING] * @param matrices
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java:58: warning: Tag @return cannot be used in constructor documentation.  It can only be used in the following types of documentation: method.
[WARNING] * @return BlockSet an instance linked to the parent alignment.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java:79: warning: Tag @return cannot be used in constructor documentation.  It can only be used in the following types of documentation: method.
[WARNING] * @return BlockSet an identical copy of the input object.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/Bond.java:29: warning: invalid input: '<'
[WARNING] * @author Jules Jacobsen <jacobsen@ebi.ac.uk>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java:30: warning: invalid input: '<'
[WARNING] * @author Jules Jacobsen <jacobsen@ebi.ac.uk>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java:47: warning: reference not found: #Bond(Atom, Atom, int, boolean)
[WARNING] * {@link #Bond(Atom, Atom, int, boolean)} with the
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/BondType.java:26: warning: invalid input: '<'
[WARNING] * @author Jules Jacobsen <jacobsen@ebi.ac.uk>
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/pccx/ScoringMethodForExternalNode.java:47: warning: invalid input: '<'
[WARNING] *            SortedMap<PhylogenyNode, Double> in which the external node
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/BridgeType.java:25: warning: invalid input: '<'
[WARNING] * (i-1,i,i+1) and (j-1,j,j+1), where i<j.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.java:524: warning: invalid input: '<'
[WARNING] * @exception  IllegalArgumentException  If readAheadLimit is < 0
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java:330: warning: invalid input: '<'
[WARNING] * Test if two amino acids are connected, i.e. if the distance from C to N <
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallablePairwiseSequenceAligner.java:37: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java:36: warning: reference not found: Profile
[WARNING] * @param <S> each {@link Sequence} of the {@link Profile} pair is of type S
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java:37: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java:51: warning: reference not found: #toString()
[WARNING] * It is recommended that the {@link #toString()} method also return the
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java:95: warning: reference not found: StructureTools#getReducedStructure(Structure, String)
[WARNING] * @see StructureTools#getReducedStructure(Structure, String)
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java:35: warning: invalid usage of tag {@link http://www.sequenceontology.org/gff3.shtml
[WARNING] * to a gff3 file. {@link http://www.sequenceontology.org/gff3.shtml}
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java:93: warning: invalid usage of tag {@link http://www.sequenceontology.org/gff3.shtml
[WARNING] * {@link http://www.sequenceontology.org/gff3.shtml}
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java:94: warning: invalid usage of tag {@link http://biowiki.org/~yam/bioe131/GFF.ppt
[WARNING] * {@link http://biowiki.org/~yam/bioe131/GFF.ppt}
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java:64: warning: invalid input: '&'
[WARNING] *  1.4 - Added DuplicationHint parameter & default to duplicating the shorter chain
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java:64: warning: invalid input: '&'
[WARNING] *  1.4 - Added DuplicationHint parameter & default to duplicating the shorter chain
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+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] * @param maxNrIterationsForOptimization
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java:365: warning: @param argument "param" is not a parameter name.
[WARNING] * @param param
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java:807: warning: Tag @author cannot be used in method documentation.  It can only be used in the following types of documentation: overview, module, package, class/interface.
[WARNING] * @author Yana Valasatava
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java:854: warning: Tag @author cannot be used in method documentation.  It can only be used in the following types of documentation: overview, module, package, class/interface.
[WARNING] * @author Yana Valasatava
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java:82: warning: reference not found: ColorChooserDialog
[WARNING] *  @see	ColorChooserDialog
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java:436: warning: @param argument "color" is not a parameter name.
[WARNING] * @param	color		the new color
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java:41: warning: @param argument "s1" is not a parameter name.
[WARNING] * @param s1
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java:43: warning: @param argument "s2" is not a parameter name.
[WARNING] * @param s2
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java:33: warning: reference not found: register
[WARNING] * you have to use one of the {@link register} and {@link of} methods.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java:112: warning: @param argument "pdbccIds" is not a parameter name.
[WARNING] * @param pdbccIds possible Protein Data Bank ID.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ContinuousColorMapperTransform.java:63: warning: @param argument "the" is not a parameter name.
[WARNING] * @param the input value
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java:40: warning: Tag @author cannot be used in field documentation.  It can only be used in the following types of documentation: overview, module, package, class/interface.
[WARNING] * @author kohchuanhock
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java:41: warning: Tag @version cannot be used in field documentation.  It can only be used in the following types of documentation: overview, module, package, class/interface.
[WARNING] * @version 2011.06.09
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java:78: warning: invalid input: '<'
[WARNING] *                      the percent change in loglikelihood is <= eps.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/demo/DemoChangeChemCompProvider.java:39: warning: reference not found: FileParsingParameters#setLoadChemCompInfo(boolean)
[WARNING] *  {@link FileParsingParameters#setLoadChemCompInfo(boolean)} method.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/phylo/DistanceMatrixCalculator.java:119: warning: invalid usage of tag {@link #pamDistance(MultipleSequenceAlignment
[WARNING] * method {@link #pamDistance(MultipleSequenceAlignment}). The gapped
[WARNING] ^
[WARNING] 100 warnings
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for biojava 6.1.0:
[INFO] 
[INFO] biojava ............................................ SUCCESS [ 30.274 s]
[INFO] biojava-core ....................................... SUCCESS [ 13.989 s]
[INFO] biojava-forester ................................... SUCCESS [ 16.417 s]
[INFO] biojava-alignment .................................. SUCCESS [  7.481 s]
[INFO] biojava-structure .................................. SUCCESS [ 22.114 s]
[INFO] biojava-jcolorbrewer ............................... SUCCESS [  2.931 s]
[INFO] biojava-structure-gui .............................. SUCCESS [  7.571 s]
[INFO] biojava-genome ..................................... SUCCESS [  5.227 s]
[INFO] biojava-modfinder .................................. SUCCESS [  6.048 s]
[INFO] biojava-ws ......................................... SUCCESS [  4.895 s]
[INFO] biojava-protein-disorder ........................... SUCCESS [  6.084 s]
[INFO] biojava-aa-prop .................................... SUCCESS [  7.373 s]
[INFO] biojava-survival ................................... SUCCESS [  8.052 s]
[INFO] biojava-ontology ................................... SUCCESS [  6.640 s]
[INFO] biojava-protein-comparison-tool .................... SUCCESS [  3.967 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  02:30 min
[INFO] Finished at: 2024-11-06T07:40:54+14:00
[INFO] ------------------------------------------------------------------------
make[1]: Leaving directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg'
   dh_auto_test
	/usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/biojava6-live-6.1.0\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf -Dproperties.file.manual=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven.properties org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven-repo --batch-mode test
OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release.
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.biojava:biojava-structure-gui:jar:6.1.0
[WARNING] 'dependencies.dependency.systemPath' for net.sourceforge.jmol:jmol:jar should use a variable instead of a hard-coded path /usr/share/java/Jmol.jar @ line 48, column 16
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] biojava                                                            [pom]
[INFO] biojava-core                                                       [jar]
[INFO] biojava-forester                                                   [jar]
[INFO] biojava-alignment                                                  [jar]
[INFO] biojava-structure                                                  [jar]
[INFO] biojava-jcolorbrewer                                               [jar]
[INFO] biojava-structure-gui                                              [jar]
[INFO] biojava-genome                                                     [jar]
[INFO] biojava-modfinder                                                  [jar]
[INFO] biojava-ws                                                         [jar]
[INFO] biojava-protein-disorder                                           [jar]
[INFO] biojava-aa-prop                                                    [jar]
[INFO] biojava-survival                                                   [jar]
[INFO] biojava-ontology                                                   [jar]
[INFO] biojava-protein-comparison-tool                                    [jar]
[INFO] 
[INFO] ------------------------< org.biojava:biojava >-------------------------
[INFO] Building biojava 6.1.0                                            [1/15]
[INFO]   from pom.xml
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] ----------------------< org.biojava:biojava-core >----------------------
[INFO] Building biojava-core 6.1.0                                       [2/15]
[INFO]   from biojava-core/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-core ---
[INFO] Copying 24 resources from src/main/resources to target/classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-core ---
[INFO] Nothing to compile - all classes are up to date.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biojava-core ---
[INFO] Copying 48 resources from src/test/resources to target/test-classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biojava-core ---
[INFO] Nothing to compile - all classes are up to date.
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-core ---
[INFO] 
[INFO] -------------------------------------------------------
[INFO]  T E S T S
[INFO] -------------------------------------------------------
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Running org.biojava.nbio.core.TestAmbiguityCompoundSet
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.136 s - in org.biojava.nbio.core.TestAmbiguityCompoundSet
[INFO] Running org.biojava.nbio.core.alignment.SimpleProfileTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.137 s - in org.biojava.nbio.core.alignment.SimpleProfileTest
[INFO] Running org.biojava.nbio.core.alignment.SimpleSequencePairTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 s - in org.biojava.nbio.core.alignment.SimpleSequencePairTest
[INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.409 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest
[INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.107 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest
[INFO] Running org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.379 s - in org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest
[INFO] Running org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.278 s - in org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest
[INFO] Running org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 35, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.136 s - in org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest
[INFO] Running org.biojava.nbio.core.fasta.TestFASTAReader
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.06 s - in org.biojava.nbio.core.fasta.TestFASTAReader
[INFO] Running org.biojava.nbio.core.search.io.SearchIOTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.179 s - in org.biojava.nbio.core.search.io.SearchIOTest
[INFO] Running org.biojava.nbio.core.search.io.HspTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
getAlignment
hashCode
equals
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.132 s - in org.biojava.nbio.core.search.io.HspTest
[INFO] Running org.biojava.nbio.core.search.io.blast.BlastTabularParserTest
createObjects
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
getFileExtensions
setFile
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.493 s - in org.biojava.nbio.core.search.io.blast.BlastTabularParserTest
[INFO] Running org.biojava.nbio.core.search.io.blast.BlastXMLParserTest
getFileExtensions
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
setFile
[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.077 s - in org.biojava.nbio.core.search.io.blast.BlastXMLParserTest
[INFO] Running org.biojava.nbio.core.sequence.RNASequenceTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.248 s - in org.biojava.nbio.core.sequence.RNASequenceTest
[INFO] Running org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.256 s - in org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest
[INFO] Running org.biojava.nbio.core.sequence.ExonSequenceTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.14 s - in org.biojava.nbio.core.sequence.ExonSequenceTest
[INFO] Running org.biojava.nbio.core.sequence.JoiningSequenceReaderTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 s - in org.biojava.nbio.core.sequence.JoiningSequenceReaderTest
[INFO] Running org.biojava.nbio.core.sequence.GeneSequenceTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.165 s - in org.biojava.nbio.core.sequence.GeneSequenceTest
[INFO] Running org.biojava.nbio.core.sequence.ChromosomeSequenceTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.555 s - in org.biojava.nbio.core.sequence.ChromosomeSequenceTest
[INFO] Running org.biojava.nbio.core.sequence.TestSequenceEquals
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.biojava.nbio.core.sequence.TestSequenceEquals
[INFO] Running org.biojava.nbio.core.sequence.TranslationTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.94 s - in org.biojava.nbio.core.sequence.TranslationTest
[INFO] Running org.biojava.nbio.core.sequence.views.WindowViewTests
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.097 s - in org.biojava.nbio.core.sequence.views.WindowViewTests
[INFO] Running org.biojava.nbio.core.sequence.DNATest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.321 s - in org.biojava.nbio.core.sequence.DNATest
[INFO] Running org.biojava.nbio.core.sequence.ProteinSequenceTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.193 s - in org.biojava.nbio.core.sequence.ProteinSequenceTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Running org.biojava.nbio.core.sequence.location.TargetedLocationParserTest
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.065 s - in org.biojava.nbio.core.sequence.location.TargetedLocationParserTest
[INFO] Running org.biojava.nbio.core.sequence.location.LocationParserTest
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.025 s - in org.biojava.nbio.core.sequence.location.LocationParserTest
[INFO] Running org.biojava.nbio.core.sequence.location.InsdcParserTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.308 s - in org.biojava.nbio.core.sequence.location.InsdcParserTest
[INFO] Running org.biojava.nbio.core.sequence.location.LocationTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 s - in org.biojava.nbio.core.sequence.location.LocationTest
[INFO] Running org.biojava.nbio.core.sequence.TranscriptSequenceTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.216 s - in org.biojava.nbio.core.sequence.TranscriptSequenceTest
[INFO] Running org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 s - in org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest
[INFO] Running org.biojava.nbio.core.sequence.EditSequenceTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 s - in org.biojava.nbio.core.sequence.EditSequenceTest
[INFO] Running org.biojava.nbio.core.sequence.TaxonomyIDTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 s - in org.biojava.nbio.core.sequence.TaxonomyIDTest
[INFO] Running org.biojava.nbio.core.sequence.StrandTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.059 s - in org.biojava.nbio.core.sequence.StrandTest
[INFO] Running org.biojava.nbio.core.sequence.ExonComparatorTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 s - in org.biojava.nbio.core.sequence.ExonComparatorTest
[INFO] Running org.biojava.nbio.core.sequence.SequenceViewTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 s - in org.biojava.nbio.core.sequence.SequenceViewTest
[INFO] Running org.biojava.nbio.core.sequence.io.GenbankCookbookTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.139 s - in org.biojava.nbio.core.sequence.io.GenbankCookbookTest
[INFO] Running org.biojava.nbio.core.sequence.io.GenbankReaderTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.119 s - in org.biojava.nbio.core.sequence.io.GenbankReaderTest
[INFO] Running org.biojava.nbio.core.sequence.io.FastaWriterTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 s - in org.biojava.nbio.core.sequence.io.FastaWriterTest
[INFO] Running org.biojava.nbio.core.sequence.io.GenbankWriterTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.115 s - in org.biojava.nbio.core.sequence.io.GenbankWriterTest
[INFO] Running org.biojava.nbio.core.sequence.io.FastaReaderTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.156 s - in org.biojava.nbio.core.sequence.io.FastaReaderTest
[INFO] Running org.biojava.nbio.core.sequence.io.embl.EmblReaderTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojava.nbio.core.sequence.io.embl.EmblReaderTest
[INFO] Running org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest
[INFO] Running org.biojava.nbio.core.sequence.io.FastaGeneWriterTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 s - in org.biojava.nbio.core.sequence.io.FastaGeneWriterTest
[INFO] Running org.biojava.nbio.core.sequence.io.ABITracerTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.507 s - in org.biojava.nbio.core.sequence.io.ABITracerTest
[INFO] Running org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.111 s - in org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Running org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest
[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest
[INFO] Running org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.279 s - in org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest
[INFO] Running org.biojava.nbio.core.util.HashcoderTest
[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.117 s - in org.biojava.nbio.core.util.HashcoderTest
[INFO] Running org.biojava.nbio.core.util.FlatFileCacheTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 s - in org.biojava.nbio.core.util.FlatFileCacheTest
[INFO] Running org.biojava.nbio.core.util.EqualsTest
[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.078 s - in org.biojava.nbio.core.util.EqualsTest
[INFO] Running org.biojava.nbio.core.util.FileDownloadUtilsTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 18, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.287 s - in org.biojava.nbio.core.util.FileDownloadUtilsTest
[INFO] Running org.biojava.nbio.core.util.SequenceToolsTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 21, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.274 s - in org.biojava.nbio.core.util.SequenceToolsTest
[INFO] Running org.biojava.nbio.core.util.SingleLinkageClustererTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 s - in org.biojava.nbio.core.util.SingleLinkageClustererTest
[INFO] Running org.biojava.nbio.core.util.XMLHelperTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.296 s - in org.biojava.nbio.core.util.XMLHelperTest
[INFO] Running org.biojava.nbio.core.util.CRC64ChecksumTest
[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.123 s - in org.biojava.nbio.core.util.CRC64ChecksumTest
[INFO] Running org.biojava.nbio.core.util.StringManipulationHelperTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.216 s - in org.biojava.nbio.core.util.StringManipulationHelperTest
[INFO] Running org.biojava.nbio.core.util.SoftHashMapTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.067 s - in org.biojava.nbio.core.util.SoftHashMapTest
[INFO] Running org.biojava.nbio.core.util.TestUncompressInputStream
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojava.nbio.core.util.TestUncompressInputStream
[INFO] Running org.biojava.nbio.core.util.PrettyXMLWriterTest
<to>
  <a>22</a>
  <b>43.22</b>
  <text>some text</text>
  <dt tz="UTC">2021-08-15</dt>
</to>

SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.137 s - in org.biojava.nbio.core.util.PrettyXMLWriterTest
[INFO] 
[INFO] Results:
[INFO] 
[WARNING] Tests run: 501, Failures: 0, Errors: 0, Skipped: 15
[INFO] 
[INFO] 
[INFO] --------------------< org.biojava:biojava-forester >--------------------
[INFO] Building biojava-forester 6.1.0                                   [3/15]
[INFO]   from biojava-forester/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-forester ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-forester ---
[INFO] Nothing to compile - all classes are up to date.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biojava-forester ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biojava-forester ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-forester ---
[INFO] No tests to run.
[INFO] 
[INFO] -------------------< org.biojava:biojava-alignment >--------------------
[INFO] Building biojava-alignment 6.1.0                                  [4/15]
[INFO]   from biojava-alignment/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-alignment ---
[INFO] Copying 2 resources from src/main/resources to target/classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-alignment ---
[INFO] Nothing to compile - all classes are up to date.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biojava-alignment ---
[INFO] Copying 11 resources from src/test/resources to target/test-classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biojava-alignment ---
[INFO] Nothing to compile - all classes are up to date.
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-alignment ---
[INFO] 
[INFO] -------------------------------------------------------
[INFO]  T E S T S
[INFO] -------------------------------------------------------
[INFO] Running org.biojava.nbio.phylo.TestForesterWrapper
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.129 s - in org.biojava.nbio.phylo.TestForesterWrapper
[INFO] Running org.biojava.nbio.phylo.TestDistanceTreeEvaluator
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.117 s - in org.biojava.nbio.phylo.TestDistanceTreeEvaluator
[INFO] Running org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.096 s - in org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest
[INFO] Running org.biojava.nbio.alignment.LocalAlignmentTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.23 s - in org.biojava.nbio.alignment.LocalAlignmentTest
[INFO] Running org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.204 s - in org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest
[INFO] Running org.biojava.nbio.alignment.TestSubOptimalMSA
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.348 s - in org.biojava.nbio.alignment.TestSubOptimalMSA
[INFO] Running org.biojava.nbio.alignment.SimpleGapPenaltyTest
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.14 s - in org.biojava.nbio.alignment.SimpleGapPenaltyTest
[INFO] Running org.biojava.nbio.alignment.TestDNAAlignment
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.521 s - in org.biojava.nbio.alignment.TestDNAAlignment
[INFO] Running org.biojava.nbio.alignment.NeedlemanWunschTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.233 s - in org.biojava.nbio.alignment.NeedlemanWunschTest
[INFO] Running org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.44 s - in org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading
[INFO] Running org.biojava.nbio.alignment.SimpleProfilePairTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.256 s - in org.biojava.nbio.alignment.SimpleProfilePairTest
[INFO] Running org.biojava.nbio.alignment.FractionalIdentityScorerTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.139 s - in org.biojava.nbio.alignment.FractionalIdentityScorerTest
[INFO] Running org.biojava.nbio.alignment.SmithWatermanTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.141 s - in org.biojava.nbio.alignment.SmithWatermanTest
[INFO] Running org.biojava.nbio.alignment.GuideTreeTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.178 s - in org.biojava.nbio.alignment.GuideTreeTest
[INFO] Running org.biojava.nbio.alignment.FractionalSimilarityScorerTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.259 s - in org.biojava.nbio.alignment.FractionalSimilarityScorerTest
[INFO] Running org.biojava.nbio.alignment.routines.GuanUberbacherTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.273 s - in org.biojava.nbio.alignment.routines.GuanUberbacherTest
[INFO] Running org.biojava.nbio.alignment.routines.AlignerHelperTest
[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.172 s - in org.biojava.nbio.alignment.routines.AlignerHelperTest
[INFO] Running org.biojava.nbio.alignment.io.TestStockholmParser
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.22 s - in org.biojava.nbio.alignment.io.TestStockholmParser
[INFO] 
[INFO] Results:
[INFO] 
[WARNING] Tests run: 127, Failures: 0, Errors: 0, Skipped: 1
[INFO] 
[INFO] 
[INFO] -------------------< org.biojava:biojava-structure >--------------------
[INFO] Building biojava-structure 6.1.0                                  [5/15]
[INFO]   from biojava-structure/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The artifact java3d:vecmath:jar:debian has been relocated to javax.vecmath:vecmath:jar:debian
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-structure ---
[INFO] Copying 3 resources from src/main/resources to target/classes
[INFO] Copying 61 resources from src/main/resources to target/classes
[INFO] The encoding used to copy filtered properties files has not been set. This means that the same encoding will be used to copy filtered properties files as when copying other filtered resources. This might not be what you want! Run your build with --debug to see which files might be affected. Read more at https://maven.apache.org/plugins/maven-resources-plugin/examples/filtering-properties-files.html
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-structure ---
[INFO] Nothing to compile - all classes are up to date.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biojava-structure ---
[INFO] Copying 55 resources from src/test/resources to target/test-classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biojava-structure ---
[INFO] Nothing to compile - all classes are up to date.
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-structure ---
[INFO] 
[INFO] -------------------------------------------------------
[INFO]  T E S T S
[INFO] -------------------------------------------------------
[INFO] Running org.biojava.nbio.structure.ResidueNumberTest
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 s - in org.biojava.nbio.structure.ResidueNumberTest
[INFO] Running org.biojava.nbio.structure.TestVeryLongFileName
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.biojava.nbio.structure.TestVeryLongFileName
[INFO] Running org.biojava.nbio.structure.TestAtomIterator
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.009 s - in org.biojava.nbio.structure.TestAtomIterator
[INFO] Running org.biojava.nbio.structure.TestBioAssemblyIdentifier
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.01 s - in org.biojava.nbio.structure.TestBioAssemblyIdentifier
[INFO] Running org.biojava.nbio.structure.geometry.TestSuperPosition
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.121 s - in org.biojava.nbio.structure.geometry.TestSuperPosition
[INFO] Running org.biojava.nbio.structure.geometry.TestSuperPositionQCP
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.036 s - in org.biojava.nbio.structure.geometry.TestSuperPositionQCP
[INFO] Running org.biojava.nbio.structure.geometry.TestUnitQuaternions
[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.022 s - in org.biojava.nbio.structure.geometry.TestUnitQuaternions
[INFO] Running org.biojava.nbio.structure.redmine.Test1DARSeqAlign
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.009 s - in org.biojava.nbio.structure.redmine.Test1DARSeqAlign
[INFO] Running org.biojava.nbio.structure.TestCalc
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.12 s - in org.biojava.nbio.structure.TestCalc
[INFO] Running org.biojava.nbio.structure.Test2JA5
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.01 s - in org.biojava.nbio.structure.Test2JA5
[INFO] Running org.biojava.nbio.structure.TestLoadStructureFromURL
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.009 s - in org.biojava.nbio.structure.TestLoadStructureFromURL
[INFO] Running org.biojava.nbio.structure.TestPdbId
[1ABC, PDB_00011ABC, 2ABC, 1ABA, 1100]
[1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC]
[1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC]
[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 s - in org.biojava.nbio.structure.TestPdbId
[INFO] Running org.biojava.nbio.structure.TestStructureSerialization
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.249 s - in org.biojava.nbio.structure.TestStructureSerialization
[INFO] Running org.biojava.nbio.structure.TestURLIdentifier
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.12 s - in org.biojava.nbio.structure.TestURLIdentifier
[INFO] Running org.biojava.nbio.structure.ChemCompTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.275 s - in org.biojava.nbio.structure.ChemCompTest
[INFO] Running org.biojava.nbio.structure.TestChargeAdder
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.009 s - in org.biojava.nbio.structure.TestChargeAdder
[INFO] Running org.biojava.nbio.structure.asa.TestAsaCalc
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.039 s - in org.biojava.nbio.structure.asa.TestAsaCalc
[INFO] Running org.biojava.nbio.structure.TestNucleotides
[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.009 s - in org.biojava.nbio.structure.TestNucleotides
[INFO] Running org.biojava.nbio.structure.PdbFileFormat30Test
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.943 s - in org.biojava.nbio.structure.PdbFileFormat30Test
[INFO] Running org.biojava.nbio.structure.TestAtomCache
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.397 s - in org.biojava.nbio.structure.TestAtomCache
[INFO] Running org.biojava.nbio.structure.TestEntityHeuristics
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.768 s - in org.biojava.nbio.structure.TestEntityHeuristics
[INFO] Running org.biojava.nbio.structure.contact.TestInterfaceFinder
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
Interface <A, B>
<CA R 0 3.0 3.0 3.0, CA R 0 7.0 3.0 3.0> - 4.0
Interface <A, C>
<CA R 0 3.0 3.0 3.0, CA R 0 5.0 8.0 4.0> - 5.477225575051661
Interface <B, C>
<CA R 0 7.0 3.0 3.0, CA R 0 5.0 8.0 4.0> - 5.477225575051661
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.136 s - in org.biojava.nbio.structure.contact.TestInterfaceFinder
[INFO] Running org.biojava.nbio.structure.contact.TestContactCalc
[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.013 s - in org.biojava.nbio.structure.contact.TestContactCalc
[INFO] Running org.biojava.nbio.structure.PDBStatusTest
[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.01 s - in org.biojava.nbio.structure.PDBStatusTest
[INFO] Running org.biojava.nbio.structure.Test4hhb
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.098 s - in org.biojava.nbio.structure.Test4hhb
[INFO] Running org.biojava.nbio.structure.AtomPositionMapTest
[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.01 s - in org.biojava.nbio.structure.AtomPositionMapTest
[INFO] Running org.biojava.nbio.structure.TestParsingCalcium
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.011 s - in org.biojava.nbio.structure.TestParsingCalcium
[INFO] Running org.biojava.nbio.structure.basepairs.TestBasePairParameters
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.01 s - in org.biojava.nbio.structure.basepairs.TestBasePairParameters
[INFO] Running org.biojava.nbio.structure.HetatomImplTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.073 s - in org.biojava.nbio.structure.HetatomImplTest
[INFO] Running org.biojava.nbio.structure.SourceCompoundTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.304 s - in org.biojava.nbio.structure.SourceCompoundTest
[INFO] Running org.biojava.nbio.structure.ElementTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 s - in org.biojava.nbio.structure.ElementTest
[INFO] Running org.biojava.nbio.structure.TestStructureImpl
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.125 s - in org.biojava.nbio.structure.TestStructureImpl
[INFO] Running org.biojava.nbio.structure.TestExperimentalTechniques
[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.036 s - in org.biojava.nbio.structure.TestExperimentalTechniques
[INFO] Running org.biojava.nbio.structure.align.ce.CeCPMainTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.171 s - in org.biojava.nbio.structure.align.ce.CeCPMainTest
[INFO] Running org.biojava.nbio.structure.align.ce.TestSmallAlignment
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.088 s - in org.biojava.nbio.structure.align.ce.TestSmallAlignment
[INFO] Running org.biojava.nbio.structure.align.client.TestStructureName
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.066 s - in org.biojava.nbio.structure.align.client.TestStructureName
[INFO] Running org.biojava.nbio.structure.align.util.AtomCacheTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 10, Failures: 0, Errors: 0, Skipped: 8, Time elapsed: 0.237 s - in org.biojava.nbio.structure.align.util.AtomCacheTest
[INFO] Running org.biojava.nbio.structure.align.util.RotationAxisTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.103 s - in org.biojava.nbio.structure.align.util.RotationAxisTest
[INFO] Running org.biojava.nbio.structure.align.TestAlignmentConsistency
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.024 s - in org.biojava.nbio.structure.align.TestAlignmentConsistency
[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.047 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser
[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.096 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools
[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter
[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.016 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter
[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.093 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer
[INFO] Running org.biojava.nbio.structure.align.multiple.TestAFPChainConversion
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.biojava.nbio.structure.align.multiple.TestAFPChainConversion
[INFO] Running org.biojava.nbio.structure.SiteTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.113 s - in org.biojava.nbio.structure.SiteTest
[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalCell
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 s - in org.biojava.nbio.structure.xtal.TestCrystalCell
[INFO] Running org.biojava.nbio.structure.xtal.TestInterfaceClustering
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 7.81 s - in org.biojava.nbio.structure.xtal.TestInterfaceClustering
[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalInfo
[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.021 s - in org.biojava.nbio.structure.xtal.TestCrystalInfo
[INFO] Running org.biojava.nbio.structure.xtal.TestSpaceGroup
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.291 s - in org.biojava.nbio.structure.xtal.TestSpaceGroup
[INFO] Running org.biojava.nbio.structure.TestDNAAlignment
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.02 s - in org.biojava.nbio.structure.TestDNAAlignment
[INFO] Running org.biojava.nbio.structure.TestEntityResIndexMapping
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 1.114 s - in org.biojava.nbio.structure.TestEntityResIndexMapping
[INFO] Running org.biojava.nbio.structure.chem.TestDownloadChemCompProvider
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.705 s - in org.biojava.nbio.structure.chem.TestDownloadChemCompProvider
[INFO] Running org.biojava.nbio.structure.TestAltLocs
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 11, Time elapsed: 0.437 s - in org.biojava.nbio.structure.TestAltLocs
[INFO] Running org.biojava.nbio.structure.ResidueRangeTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.102 s - in org.biojava.nbio.structure.ResidueRangeTest
[INFO] Running org.biojava.nbio.structure.TestKeywords
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.642 s - in org.biojava.nbio.structure.TestKeywords
[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitCluster
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.203 s - in org.biojava.nbio.structure.cluster.TestSubunitCluster
[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitExtractor
[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.009 s - in org.biojava.nbio.structure.cluster.TestSubunitExtractor
[INFO] Running org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools
[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes
[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 s - in org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner
[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.009 s - in org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector
[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestCeSymm
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.009 s - in org.biojava.nbio.structure.symmetry.internal.TestCeSymm
[INFO] Running org.biojava.nbio.structure.TestStructureCrossReferences
[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.008 s - in org.biojava.nbio.structure.TestStructureCrossReferences
[INFO] Running org.biojava.nbio.structure.TestCloning
[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.01 s - in org.biojava.nbio.structure.TestCloning
[INFO] Running org.biojava.nbio.structure.TestBond
[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 15, Time elapsed: 0.01 s - in org.biojava.nbio.structure.TestBond
[INFO] Running org.biojava.nbio.structure.io.TestDBRefParsing
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 s - in org.biojava.nbio.structure.io.TestDBRefParsing
[INFO] Running org.biojava.nbio.structure.io.TestTitleParsing
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.016 s - in org.biojava.nbio.structure.io.TestTitleParsing
[INFO] Running org.biojava.nbio.structure.io.TestSiftsParsing
[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.028 s - in org.biojava.nbio.structure.io.TestSiftsParsing
[INFO] Running org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.835 s - in org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest
[INFO] Running org.biojava.nbio.structure.io.StructureSequenceMatcherTest
[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.018 s - in org.biojava.nbio.structure.io.StructureSequenceMatcherTest
[INFO] Running org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.024 s - in org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB
[INFO] Running org.biojava.nbio.structure.io.TestParseOnAsymId
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.023 s - in org.biojava.nbio.structure.io.TestParseOnAsymId
[INFO] Running org.biojava.nbio.structure.io.TestShortLines
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.64 s - in org.biojava.nbio.structure.io.TestShortLines
[INFO] Running org.biojava.nbio.structure.io.FastaAFPChainConverterTest
[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.032 s - in org.biojava.nbio.structure.io.FastaAFPChainConverterTest
[INFO] Running org.biojava.nbio.structure.io.TestNonDepositedFiles
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 3.809 s - in org.biojava.nbio.structure.io.TestNonDepositedFiles
[INFO] Running org.biojava.nbio.structure.io.TestMMCIFWriting
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.313 s - in org.biojava.nbio.structure.io.TestMMCIFWriting
[INFO] Running org.biojava.nbio.structure.io.TestHardBioUnits
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.024 s - in org.biojava.nbio.structure.io.TestHardBioUnits
[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFLigands
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.02 s - in org.biojava.nbio.structure.io.TestParseMmCIFLigands
[INFO] Running org.biojava.nbio.structure.io.TestQuaternaryStructureProviders
[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.028 s - in org.biojava.nbio.structure.io.TestQuaternaryStructureProviders
[INFO] Running org.biojava.nbio.structure.io.TestMMcifOrganismParsing
[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.036 s - in org.biojava.nbio.structure.io.TestMMcifOrganismParsing
[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFFeatures
[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.01 s - in org.biojava.nbio.structure.io.TestParseMmCIFFeatures
[INFO] Running org.biojava.nbio.structure.io.TestURLBasedFileParsing
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.009 s - in org.biojava.nbio.structure.io.TestURLBasedFileParsing
[INFO] Running org.biojava.nbio.structure.io.TestDifficultMmCIFFiles
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 1.034 s - in org.biojava.nbio.structure.io.TestDifficultMmCIFFiles
[INFO] Running org.biojava.nbio.structure.io.TestHeaderOnly
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 1.046 s - in org.biojava.nbio.structure.io.TestHeaderOnly
[INFO] Running org.biojava.nbio.structure.io.mmcif.TestChemCompProvider
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
Using PDB_DIR=/tmp as temporary file directory
[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.361 s - in org.biojava.nbio.structure.io.mmcif.TestChemCompProvider
[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.014 s - in org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId
[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.14 s - in org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader
[INFO] Running org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.009 s - in org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType
[INFO] Running org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.984 s - in org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes
[INFO] Running org.biojava.nbio.structure.io.mmtf.TestBondFinding
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.01 s - in org.biojava.nbio.structure.io.mmtf.TestBondFinding
[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.169 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader
[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfUtils
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 16, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.212 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfUtils
[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.016 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip
[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.012 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance
[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.076 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter
[INFO] Running org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 s - in org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest
[INFO] Running org.biojava.nbio.structure.secstruc.TestDSSPParser
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.01 s - in org.biojava.nbio.structure.secstruc.TestDSSPParser
[INFO] Running org.biojava.nbio.structure.secstruc.TestSecStrucCalc
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.032 s - in org.biojava.nbio.structure.secstruc.TestSecStrucCalc
[INFO] 
[INFO] Results:
[INFO] 
[WARNING] Tests run: 374, Failures: 0, Errors: 0, Skipped: 188
[INFO] 
[INFO] 
[INFO] ------------------< org.biojava:biojava-jcolorbrewer >------------------
[INFO] Building biojava-jcolorbrewer 6.1.0                               [6/15]
[INFO]   from biojava-jcolorbrewer/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-jcolorbrewer ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-jcolorbrewer ---
[INFO] Nothing to compile - all classes are up to date.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biojava-jcolorbrewer ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biojava-jcolorbrewer ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-jcolorbrewer ---
[INFO] No tests to run.
[INFO] 
[INFO] -----------------< org.biojava:biojava-structure-gui >------------------
[INFO] Building biojava-structure-gui 6.1.0                              [7/15]
[INFO]   from biojava-structure-gui/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-structure-gui ---
[INFO] Copying 49 resources from src/main/resources to target/classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-structure-gui ---
[INFO] Nothing to compile - all classes are up to date.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biojava-structure-gui ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biojava-structure-gui ---
[INFO] Nothing to compile - all classes are up to date.
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-structure-gui ---
[INFO] 
[INFO] -------------------------------------------------------
[INFO]  T E S T S
[INFO] -------------------------------------------------------
[INFO] Running org.biojava.nbio.structure.gui.ViewerTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.185 s - in org.biojava.nbio.structure.gui.ViewerTest
[INFO] Running org.biojava.nbio.structure.gui.TestAtomInfo
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.131 s - in org.biojava.nbio.structure.gui.TestAtomInfo
[INFO] Running org.biojava.nbio.structure.gui.RenderStyleTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 s - in org.biojava.nbio.structure.gui.RenderStyleTest
[INFO] Running org.biojava.nbio.structure.gui.StructureViewerTest
[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 s - in org.biojava.nbio.structure.gui.StructureViewerTest
[INFO] Running org.biojava.nbio.structure.gui.JmolViewerImplTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.065 s - in org.biojava.nbio.structure.gui.JmolViewerImplTest
[INFO] Running org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.064 s - in org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator
[INFO] 
[INFO] Results:
[INFO] 
[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 1
[INFO] 
[INFO] 
[INFO] ---------------------< org.biojava:biojava-genome >---------------------
[INFO] Building biojava-genome 6.1.0                                     [8/15]
[INFO]   from biojava-genome/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-genome ---
[INFO] Copying 1 resource from src/main/resources to target/classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-genome ---
[INFO] Nothing to compile - all classes are up to date.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biojava-genome ---
[INFO] Copying 83 resources from src/test/resources to target/test-classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biojava-genome ---
[INFO] Nothing to compile - all classes are up to date.
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-genome ---
[INFO] 
[INFO] -------------------------------------------------------
[INFO]  T E S T S
[INFO] -------------------------------------------------------
[INFO] Running org.biojava.nbio.genome.TestIssue355
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 s - in org.biojava.nbio.genome.TestIssue355
[INFO] Running org.biojava.nbio.genome.TestGenomeMapping
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.079 s - in org.biojava.nbio.genome.TestGenomeMapping
[INFO] Running org.biojava.nbio.genome.TestLocation
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.065 s - in org.biojava.nbio.genome.TestLocation
[INFO] Running org.biojava.nbio.genome.TestChromosomeMappingTools
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.073 s - in org.biojava.nbio.genome.TestChromosomeMappingTools
[INFO] Running org.biojava.nbio.genome.GeneFeatureHelperTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.532 s - in org.biojava.nbio.genome.GeneFeatureHelperTest
[INFO] Running org.biojava.nbio.genome.FeatureListTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.064 s - in org.biojava.nbio.genome.FeatureListTest
[INFO] Running org.biojava.nbio.genome.io.fastq.ConvertTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.21 s - in org.biojava.nbio.genome.io.fastq.ConvertTest
[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest
[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.241 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest
[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest
[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.153 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest
[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest
[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.123 s - in org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest
[INFO] Running org.biojava.nbio.genome.io.fastq.FastqVariantTest
[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 s - in org.biojava.nbio.genome.io.fastq.FastqVariantTest
[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest
[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.109 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest
[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest
[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.108 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest
[INFO] Running org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 s - in org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest
[INFO] Running org.biojava.nbio.genome.io.fastq.FastqToolsTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.312 s - in org.biojava.nbio.genome.io.fastq.FastqToolsTest
[INFO] Running org.biojava.nbio.genome.io.fastq.FastqBuilderTest
[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.2 s - in org.biojava.nbio.genome.io.fastq.FastqBuilderTest
[INFO] Running org.biojava.nbio.genome.io.fastq.FastqTest
[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.18 s - in org.biojava.nbio.genome.io.fastq.FastqTest
[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest
[INFO] Tests run: 29, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.413 s - in org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest
[INFO] 
[INFO] Results:
[INFO] 
[WARNING] Tests run: 204, Failures: 0, Errors: 0, Skipped: 2
[INFO] 
[INFO] 
[INFO] -------------------< org.biojava:biojava-modfinder >--------------------
[INFO] Building biojava-modfinder 6.1.0                                  [9/15]
[INFO]   from biojava-modfinder/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-modfinder ---
[INFO] Copying 2 resources from src/main/resources to target/classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-modfinder ---
[INFO] Nothing to compile - all classes are up to date.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biojava-modfinder ---
[INFO] Copying 2 resources from src/test/resources to target/test-classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biojava-modfinder ---
[INFO] Nothing to compile - all classes are up to date.
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-modfinder ---
[INFO] 
[INFO] -------------------------------------------------------
[INFO]  T E S T S
[INFO] -------------------------------------------------------
[INFO] Running org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.235 s - in org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest
[INFO] Running org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.271 s - in org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest
[INFO] Running org.biojava.nbio.protmod.structure.ProteinModificationParserTest
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.132 s - in org.biojava.nbio.protmod.structure.ProteinModificationParserTest
[INFO] Running org.biojava.nbio.protmod.phosphosite.TestAcetylation
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.06 s - in org.biojava.nbio.protmod.phosphosite.TestAcetylation
[INFO] 
[INFO] Results:
[INFO] 
[WARNING] Tests run: 12, Failures: 0, Errors: 0, Skipped: 8
[INFO] 
[INFO] 
[INFO] -----------------------< org.biojava:biojava-ws >-----------------------
[INFO] Building biojava-ws 6.1.0                                        [10/15]
[INFO]   from biojava-ws/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-ws ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/main/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-ws ---
[INFO] Nothing to compile - all classes are up to date.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biojava-ws ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biojava-ws ---
[INFO] Nothing to compile - all classes are up to date.
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-ws ---
[INFO] 
[INFO] -------------------------------------------------------
[INFO]  T E S T S
[INFO] -------------------------------------------------------
[INFO] Running org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.164 s - in org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan
[INFO] 
[INFO] Results:
[INFO] 
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1
[INFO] 
[INFO] 
[INFO] ----------------< org.biojava:biojava-protein-disorder >----------------
[INFO] Building biojava-protein-disorder 6.1.0                          [11/15]
[INFO]   from biojava-protein-disorder/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-protein-disorder ---
[INFO] Copying 11 resources from src/main/resources to target/classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-protein-disorder ---
[INFO] Nothing to compile - all classes are up to date.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biojava-protein-disorder ---
[INFO] Copying 2 resources from src/test/resources to target/test-classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biojava-protein-disorder ---
[INFO] Nothing to compile - all classes are up to date.
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-protein-disorder ---
[INFO] 
[INFO] -------------------------------------------------------
[INFO]  T E S T S
[INFO] -------------------------------------------------------
[INFO] Running org.biojava.nbio.ronn.NonstandardProteinCompoundTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.188 s - in org.biojava.nbio.ronn.NonstandardProteinCompoundTest
[INFO] Running org.biojava.nbio.ronn.JronnTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.72 s - in org.biojava.nbio.ronn.JronnTest
[INFO] 
[INFO] Results:
[INFO] 
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0
[INFO] 
[INFO] 
[INFO] --------------------< org.biojava:biojava-aa-prop >---------------------
[INFO] Building biojava-aa-prop 6.1.0                                   [12/15]
[INFO]   from biojava-aa-prop/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-aa-prop ---
[INFO] Copying 11 resources from src/main/resources to target/classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-aa-prop ---
[INFO] Nothing to compile - all classes are up to date.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biojava-aa-prop ---
[INFO] Copying 7 resources from src/test/resources to target/test-classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biojava-aa-prop ---
[INFO] Nothing to compile - all classes are up to date.
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-aa-prop ---
[INFO] 
[INFO] -------------------------------------------------------
[INFO]  T E S T S
[INFO] -------------------------------------------------------
[INFO] Running org.biojava.nbio.aaproperties.CookBookTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.48 s - in org.biojava.nbio.aaproperties.CookBookTest
[INFO] Running org.biojava.nbio.aaproperties.PeptidePropertiesImplTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.567 s - in org.biojava.nbio.aaproperties.PeptidePropertiesImplTest
[INFO] Running org.biojava.nbio.aaproperties.GenbankCommandPromptTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint
NP_000257                133 aa            linear   PRI 27-MAR-2008,15043.5262,5960.0,6585.0,9.1715
SequenceName,A,N,MolecularWeight
NP_000257                133 aa            linear   PRI 27-MAR-2008,0.0451,0.0075,15043.5262
SequenceName,A,N,MolecularWeight
NP_000257                133 aa            linear   PRI 27-MAR-2008,0.0451,0.0075,15043.5262
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.544 s - in org.biojava.nbio.aaproperties.GenbankCommandPromptTest
[INFO] Running org.biojava.nbio.aaproperties.profeat.CookBookTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.082 s - in org.biojava.nbio.aaproperties.profeat.CookBookTest
[INFO] Running org.biojava.nbio.aaproperties.CommandPromptTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint
SAOV_0114,53660.5723,41370.0,41370.0,4.986
SAOV_0094,45884.0164,57760.0,57760.0,8.5193
SAA6008_00126,95002.026,55240.0,55740.0,5.7263
SequenceName,A,N,MolecularWeight
SAOV_0114,0.101,0.0525,53660.5723
SAOV_0094,0.0537,0.0767,45884.0164
SAA6008_00126,0.0955,0.0414,95002.026
SequenceName,A,N,MolecularWeight
SAOV_0114,0.101,0.0525,53660.5723
SAOV_0094,0.0537,0.0767,45884.0164
SAA6008_00126,0.0955,0.0414,95002.026
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.261 s - in org.biojava.nbio.aaproperties.CommandPromptTest
[INFO] Running org.biojava.nbio.aaproperties.xml.AminoAcidTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.44 s - in org.biojava.nbio.aaproperties.xml.AminoAcidTest
[INFO] Running org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 s - in org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest
[INFO] Running org.biojava.nbio.aaproperties.xml.ElementTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.553 s - in org.biojava.nbio.aaproperties.xml.ElementTest
[INFO] 
[INFO] Results:
[INFO] 
[INFO] Tests run: 52, Failures: 0, Errors: 0, Skipped: 0
[INFO] 
[INFO] 
[INFO] --------------------< org.biojava:biojava-survival >--------------------
[INFO] Building biojava-survival 6.1.0                                  [13/15]
[INFO]   from biojava-survival/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-survival ---
[INFO] Copying 1 resource from src/main/resources to target/classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-survival ---
[INFO] Nothing to compile - all classes are up to date.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biojava-survival ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biojava-survival ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-survival ---
[INFO] No tests to run.
[INFO] 
[INFO] --------------------< org.biojava:biojava-ontology >--------------------
[INFO] Building biojava-ontology 6.1.0                                  [14/15]
[INFO]   from biojava-ontology/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-ontology ---
[INFO] Copying 3 resources from src/main/resources to target/classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-ontology ---
[INFO] Nothing to compile - all classes are up to date.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biojava-ontology ---
[INFO] Copying 6 resources from src/test/resources to target/test-classes
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biojava-ontology ---
[INFO] Nothing to compile - all classes are up to date.
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-ontology ---
[INFO] 
[INFO] -------------------------------------------------------
[INFO]  T E S T S
[INFO] -------------------------------------------------------
[INFO] Running org.biojava.nbio.ontology.TestParseOBO
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.14 s - in org.biojava.nbio.ontology.TestParseOBO
[INFO] Running org.biojava.nbio.ontology.TestOboFileParsing
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.234 s - in org.biojava.nbio.ontology.TestOboFileParsing
[INFO] Running org.biojava.nbio.ontology.TestParseSBO
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.21 s - in org.biojava.nbio.ontology.TestParseSBO
[INFO] 
[INFO] Results:
[INFO] 
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0
[INFO] 
[INFO] 
[INFO] ------------< org.biojava:biojava-protein-comparison-tool >-------------
[INFO] Building biojava-protein-comparison-tool 6.1.0                   [15/15]
[INFO]   from biojava-protein-comparison-tool/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ biojava-protein-comparison-tool ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/src/main/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:compile (default-compile) @ biojava-protein-comparison-tool ---
[INFO] Nothing to compile - all classes are up to date.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ biojava-protein-comparison-tool ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.13.0:testCompile (default-testCompile) @ biojava-protein-comparison-tool ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-protein-comparison-tool ---
[INFO] No tests to run.
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for biojava 6.1.0:
[INFO] 
[INFO] biojava ............................................ SUCCESS [  0.005 s]
[INFO] biojava-core ....................................... SUCCESS [31:07 min]
[INFO] biojava-forester ................................... SUCCESS [  0.095 s]
[INFO] biojava-alignment .................................. SUCCESS [09:21 min]
[INFO] biojava-structure .................................. SUCCESS [52:23 min]
[INFO] biojava-jcolorbrewer ............................... SUCCESS [  0.046 s]
[INFO] biojava-structure-gui .............................. SUCCESS [03:05 min]
[INFO] biojava-genome ..................................... SUCCESS [09:18 min]
[INFO] biojava-modfinder .................................. SUCCESS [02:04 min]
[INFO] biojava-ws ......................................... SUCCESS [ 31.641 s]
[INFO] biojava-protein-disorder ........................... SUCCESS [01:17 min]
[INFO] biojava-aa-prop .................................... SUCCESS [04:11 min]
[INFO] biojava-survival ................................... SUCCESS [  0.034 s]
[INFO] biojava-ontology ................................... SUCCESS [01:32 min]
[INFO] biojava-protein-comparison-tool .................... SUCCESS [  0.082 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  01:54 h
[INFO] Finished at: 2024-11-06T09:35:51+14:00
[INFO] ------------------------------------------------------------------------
   create-stamp debian/debhelper-build-stamp
   dh_prep
   dh_auto_install
	/usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/biojava6-live-6.1.0\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf -Dproperties.file.manual=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven.properties org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven-repo --batch-mode -Ddebian.dir=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian -Ddebian.package=libbiojava6-java -Dmaven.repo.local=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven-repo -Dinstall.to.usj=true org.debian.maven:debian-maven-plugin:2.6:install
OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release.
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.biojava:biojava-structure-gui:jar:6.1.0
[WARNING] 'dependencies.dependency.systemPath' for net.sourceforge.jmol:jmol:jar should use a variable instead of a hard-coded path /usr/share/java/Jmol.jar @ line 48, column 16
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] biojava                                                            [pom]
[INFO] biojava-core                                                       [jar]
[INFO] biojava-forester                                                   [jar]
[INFO] biojava-alignment                                                  [jar]
[INFO] biojava-structure                                                  [jar]
[INFO] biojava-jcolorbrewer                                               [jar]
[INFO] biojava-structure-gui                                              [jar]
[INFO] biojava-genome                                                     [jar]
[INFO] biojava-modfinder                                                  [jar]
[INFO] biojava-ws                                                         [jar]
[INFO] biojava-protein-disorder                                           [jar]
[INFO] biojava-aa-prop                                                    [jar]
[INFO] biojava-survival                                                   [jar]
[INFO] biojava-ontology                                                   [jar]
[INFO] biojava-protein-comparison-tool                                    [jar]
[INFO] 
[INFO] ------------------------< org.biojava:biojava >-------------------------
[INFO] Building biojava 6.1.0                                            [1/15]
[INFO]   from pom.xml
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava ---
[INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/pom.xml.save with options:
[INFO] 	--keep-pom-version --package=libbiojava6-java
[INFO] 	--rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules
[INFO] 	--ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules
[INFO] 	--published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules
[INFO] 	--no-parent
[INFO] 
[INFO] ----------------------< org.biojava:biojava-core >----------------------
[INFO] Building biojava-core 6.1.0                                       [2/15]
[INFO]   from biojava-core/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-core ---
[INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/pom.xml.save with options:
[INFO] 	--keep-pom-version --package=libbiojava6-java
[INFO] 	--rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules
[INFO] 	--ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules
[INFO] 	--published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules
[INFO] Install jar for biojava-core into /usr/share/java
[INFO] 
[INFO] --------------------< org.biojava:biojava-forester >--------------------
[INFO] Building biojava-forester 6.1.0                                   [3/15]
[INFO]   from biojava-forester/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-forester ---
[INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/pom.xml.save with options:
[INFO] 	--keep-pom-version --package=libbiojava6-java
[INFO] 	--rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules
[INFO] 	--ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules
[INFO] 	--published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules
[INFO] Install jar for biojava-forester into /usr/share/java
[INFO] 
[INFO] -------------------< org.biojava:biojava-alignment >--------------------
[INFO] Building biojava-alignment 6.1.0                                  [4/15]
[INFO]   from biojava-alignment/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-alignment ---
[INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/pom.xml.save with options:
[INFO] 	--keep-pom-version --package=libbiojava6-java
[INFO] 	--rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules
[INFO] 	--ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules
[INFO] 	--published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules
[INFO] Install jar for biojava-alignment into /usr/share/java
[INFO] 
[INFO] -------------------< org.biojava:biojava-structure >--------------------
[INFO] Building biojava-structure 6.1.0                                  [5/15]
[INFO]   from biojava-structure/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-structure ---
[INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/pom.xml.save with options:
[INFO] 	--keep-pom-version --package=libbiojava6-java
[INFO] 	--rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules
[INFO] 	--ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules
[INFO] 	--published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules
[INFO] Install jar for biojava-structure into /usr/share/java
[INFO] 
[INFO] ------------------< org.biojava:biojava-jcolorbrewer >------------------
[INFO] Building biojava-jcolorbrewer 6.1.0                               [6/15]
[INFO]   from biojava-jcolorbrewer/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-jcolorbrewer ---
[INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/pom.xml.save with options:
[INFO] 	--keep-pom-version --package=libbiojava6-java
[INFO] 	--rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules
[INFO] 	--ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules
[INFO] 	--published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules
[INFO] Install jar for biojava-jcolorbrewer into /usr/share/java
[INFO] 
[INFO] -----------------< org.biojava:biojava-structure-gui >------------------
[INFO] Building biojava-structure-gui 6.1.0                              [7/15]
[INFO]   from biojava-structure-gui/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-structure-gui ---
[INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/pom.xml.save with options:
[INFO] 	--keep-pom-version --package=libbiojava6-java
[INFO] 	--rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules
[INFO] 	--ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules
[INFO] 	--published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules
[INFO] Install jar for biojava-structure-gui into /usr/share/java
[INFO] 
[INFO] ---------------------< org.biojava:biojava-genome >---------------------
[INFO] Building biojava-genome 6.1.0                                     [8/15]
[INFO]   from biojava-genome/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-genome ---
[INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/pom.xml.save with options:
[INFO] 	--keep-pom-version --package=libbiojava6-java
[INFO] 	--rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules
[INFO] 	--ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules
[INFO] 	--published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules
[INFO] Install jar for biojava-genome into /usr/share/java
[INFO] 
[INFO] -------------------< org.biojava:biojava-modfinder >--------------------
[INFO] Building biojava-modfinder 6.1.0                                  [9/15]
[INFO]   from biojava-modfinder/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-modfinder ---
[INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/pom.xml.save with options:
[INFO] 	--keep-pom-version --package=libbiojava6-java
[INFO] 	--rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules
[INFO] 	--ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules
[INFO] 	--published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules
[INFO] Install jar for biojava-modfinder into /usr/share/java
[INFO] 
[INFO] -----------------------< org.biojava:biojava-ws >-----------------------
[INFO] Building biojava-ws 6.1.0                                        [10/15]
[INFO]   from biojava-ws/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-ws ---
[INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/pom.xml.save with options:
[INFO] 	--keep-pom-version --package=libbiojava6-java
[INFO] 	--rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules
[INFO] 	--ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules
[INFO] 	--published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules
[INFO] Install jar for biojava-ws into /usr/share/java
[INFO] 
[INFO] ----------------< org.biojava:biojava-protein-disorder >----------------
[INFO] Building biojava-protein-disorder 6.1.0                          [11/15]
[INFO]   from biojava-protein-disorder/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-protein-disorder ---
[INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/pom.xml.save with options:
[INFO] 	--keep-pom-version --package=libbiojava6-java
[INFO] 	--rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules
[INFO] 	--ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules
[INFO] 	--published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules
[INFO] Install jar for biojava-protein-disorder into /usr/share/java
[INFO] 
[INFO] --------------------< org.biojava:biojava-aa-prop >---------------------
[INFO] Building biojava-aa-prop 6.1.0                                   [12/15]
[INFO]   from biojava-aa-prop/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-aa-prop ---
[INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/pom.xml.save with options:
[INFO] 	--keep-pom-version --package=libbiojava6-java
[INFO] 	--rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules
[INFO] 	--ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules
[INFO] 	--published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules
[INFO] Install jar for biojava-aa-prop into /usr/share/java
[INFO] 
[INFO] --------------------< org.biojava:biojava-survival >--------------------
[INFO] Building biojava-survival 6.1.0                                  [13/15]
[INFO]   from biojava-survival/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-survival ---
[INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/pom.xml.save with options:
[INFO] 	--keep-pom-version --package=libbiojava6-java
[INFO] 	--rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules
[INFO] 	--ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules
[INFO] 	--published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules
[INFO] Install jar for biojava-survival into /usr/share/java
[INFO] 
[INFO] --------------------< org.biojava:biojava-ontology >--------------------
[INFO] Building biojava-ontology 6.1.0                                  [14/15]
[INFO]   from biojava-ontology/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-ontology ---
[INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/pom.xml.save with options:
[INFO] 	--keep-pom-version --package=libbiojava6-java
[INFO] 	--rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules
[INFO] 	--ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules
[INFO] 	--published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules
[INFO] Install jar for biojava-ontology into /usr/share/java
[INFO] 
[INFO] ------------< org.biojava:biojava-protein-comparison-tool >-------------
[INFO] Building biojava-protein-comparison-tool 6.1.0                   [15/15]
[INFO]   from biojava-protein-comparison-tool/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-protein-comparison-tool ---
[INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/pom.xml.save with options:
[INFO] 	--keep-pom-version --package=libbiojava6-java
[INFO] 	--rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules
[INFO] 	--ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules
[INFO] 	--published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules
[INFO] Install jar for biojava-protein-comparison-tool into /usr/share/java
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for biojava 6.1.0:
[INFO] 
[INFO] biojava ............................................ SUCCESS [  0.468 s]
[INFO] biojava-core ....................................... SUCCESS [  0.077 s]
[INFO] biojava-forester ................................... SUCCESS [  0.034 s]
[INFO] biojava-alignment .................................. SUCCESS [  0.044 s]
[INFO] biojava-structure .................................. SUCCESS [  0.068 s]
[INFO] biojava-jcolorbrewer ............................... SUCCESS [  0.051 s]
[INFO] biojava-structure-gui .............................. SUCCESS [  0.085 s]
[INFO] biojava-genome ..................................... SUCCESS [  0.067 s]
[INFO] biojava-modfinder .................................. SUCCESS [  0.058 s]
[INFO] biojava-ws ......................................... SUCCESS [  0.062 s]
[INFO] biojava-protein-disorder ........................... SUCCESS [  0.051 s]
[INFO] biojava-aa-prop .................................... SUCCESS [  0.059 s]
[INFO] biojava-survival ................................... SUCCESS [  0.033 s]
[INFO] biojava-ontology ................................... SUCCESS [  0.046 s]
[INFO] biojava-protein-comparison-tool .................... SUCCESS [  0.039 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  1.555 s
[INFO] Finished at: 2024-11-06T09:35:54+14:00
[INFO] ------------------------------------------------------------------------
	mh_resolve_dependencies --non-interactive --offline --build -plibbiojava6-java --javadoc --base-directory=/build/reproducible-path/biojava6-live-6.1.0\+dfsg --non-explore
Analysing pom.xml...
Analysing biojava-aa-prop/pom.xml...
Checking the parent dependency in the sub project biojava-aa-prop/pom.xml
Analysing biojava-alignment/pom.xml...
Checking the parent dependency in the sub project biojava-alignment/pom.xml
Analysing biojava-core/pom.xml...
Checking the parent dependency in the sub project biojava-core/pom.xml
Analysing biojava-forester/pom.xml...
Checking the parent dependency in the sub project biojava-forester/pom.xml
Analysing biojava-genome/pom.xml...
Checking the parent dependency in the sub project biojava-genome/pom.xml
Analysing biojava-jcolorbrewer/pom.xml...
Checking the parent dependency in the sub project biojava-jcolorbrewer/pom.xml
Analysing biojava-modfinder/pom.xml...
Checking the parent dependency in the sub project biojava-modfinder/pom.xml
Analysing biojava-ontology/pom.xml...
Checking the parent dependency in the sub project biojava-ontology/pom.xml
Analysing biojava-protein-comparison-tool/pom.xml...
Checking the parent dependency in the sub project biojava-protein-comparison-tool/pom.xml
Analysing biojava-protein-disorder/pom.xml...
Checking the parent dependency in the sub project biojava-protein-disorder/pom.xml
Analysing biojava-structure/pom.xml...
Checking the parent dependency in the sub project biojava-structure/pom.xml
Analysing biojava-structure-gui/pom.xml...
Checking the parent dependency in the sub project biojava-structure-gui/pom.xml
Analysing biojava-survival/pom.xml...
Checking the parent dependency in the sub project biojava-survival/pom.xml
Analysing biojava-ws/pom.xml...
Checking the parent dependency in the sub project biojava-ws/pom.xml
Checking dependencies for documentation packages...
> dpkg --search /usr/share/doc/libciftools-java/api/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libciftools-java/api/index.html
> dpkg --search /usr/share/doc/libciftools-java-doc/api/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libciftools-java-doc/api/index.html
> dpkg --search /usr/share/doc/libciftools-java/apidocs/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libciftools-java/apidocs/index.html
> dpkg --search /usr/share/doc/libciftools-java-doc/apidocs/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libciftools-java-doc/apidocs/index.html
> dpkg --search /usr/share/doc/libcommons-codec-java/api/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libcommons-codec-java/api/index.html
> dpkg --search /usr/share/doc/libcommons-codec-java-doc/api/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libcommons-codec-java-doc/api/index.html
> dpkg --search /usr/share/doc/libcommons-codec-java/apidocs/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libcommons-codec-java/apidocs/index.html
> dpkg --search /usr/share/doc/libcommons-codec-java-doc/apidocs/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libcommons-codec-java-doc/apidocs/index.html
> dpkg --search /usr/share/doc/libcommons-math-java/api/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libcommons-math-java/api/index.html
> dpkg --search /usr/share/doc/libcommons-math-java-doc/api/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libcommons-math-java-doc/api/index.html
> dpkg --search /usr/share/doc/libcommons-math-java/apidocs/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libcommons-math-java/apidocs/index.html
> dpkg --search /usr/share/doc/libcommons-math-java-doc/apidocs/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libcommons-math-java-doc/apidocs/index.html
> dpkg --search /usr/share/doc/libguava-java/api/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libguava-java/api/index.html
> dpkg --search /usr/share/doc/libguava-java-doc/api/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libguava-java-doc/api/index.html
> dpkg --search /usr/share/doc/libguava-java/apidocs/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libguava-java/apidocs/index.html
> dpkg --search /usr/share/doc/libguava-java-doc/apidocs/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libguava-java-doc/apidocs/index.html
> dpkg --search /usr/share/doc/libitext5-java/api/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libitext5-java/api/index.html
> dpkg --search /usr/share/doc/libitext5-java-doc/api/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libitext5-java-doc/api/index.html
> dpkg --search /usr/share/doc/libitext5-java/apidocs/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libitext5-java/apidocs/index.html
> dpkg --search /usr/share/doc/libitext5-java-doc/apidocs/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libitext5-java-doc/apidocs/index.html
> dpkg --search /usr/share/doc/libjackson2-databind-java/api/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libjackson2-databind-java/api/index.html
> dpkg --search /usr/share/doc/libjackson2-databind-java-doc/api/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libjackson2-databind-java-doc/api/index.html
> dpkg --search /usr/share/doc/libjackson2-databind-java/apidocs/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libjackson2-databind-java/apidocs/index.html
> dpkg --search /usr/share/doc/libjackson2-databind-java-doc/apidocs/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libjackson2-databind-java-doc/apidocs/index.html
> dpkg --search /usr/share/doc/libjaxb-api-java/api/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-api-java/api/index.html
> dpkg --search /usr/share/doc/libjaxb-api-java-doc/api/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-api-java-doc/api/index.html
> dpkg --search /usr/share/doc/libjaxb-api-java/apidocs/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-api-java/apidocs/index.html
> dpkg --search /usr/share/doc/libjaxb-api-java-doc/apidocs/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-api-java-doc/apidocs/index.html
> dpkg --search /usr/share/doc/libjaxb-java/api/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-java/api/index.html
> dpkg --search /usr/share/doc/libjaxb-java-doc/api/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-java-doc/api/index.html
> dpkg --search /usr/share/doc/libjaxb-java/apidocs/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-java/apidocs/index.html
> dpkg --search /usr/share/doc/libjaxb-java-doc/apidocs/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-java-doc/apidocs/index.html
> dpkg --search /usr/share/doc/libjgrapht-java/api/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libjgrapht-java/api/index.html
> dpkg --search /usr/share/doc/libjgrapht-java-doc/api/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libjgrapht-java-doc/api/index.html
> dpkg --search /usr/share/doc/libjgrapht-java/apidocs/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libjgrapht-java/apidocs/index.html
> dpkg --search /usr/share/doc/libjgrapht-java-doc/apidocs/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libjgrapht-java-doc/apidocs/index.html
> dpkg --search /usr/share/doc/libjmol-java/api/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libjmol-java/api/index.html
> dpkg --search /usr/share/doc/libjmol-java-doc/api/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libjmol-java-doc/api/index.html
> dpkg --search /usr/share/doc/libjmol-java/apidocs/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libjmol-java/apidocs/index.html
> dpkg --search /usr/share/doc/libjmol-java-doc/apidocs/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libjmol-java-doc/apidocs/index.html
> dpkg --search /usr/share/doc/libjson-simple-java/api/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libjson-simple-java/api/index.html
> dpkg --search /usr/share/doc/libjson-simple-java-doc/api/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libjson-simple-java-doc/api/index.html
> dpkg --search /usr/share/doc/libjson-simple-java/apidocs/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libjson-simple-java/apidocs/index.html
> dpkg --search /usr/share/doc/libjson-simple-java-doc/apidocs/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libjson-simple-java-doc/apidocs/index.html
> dpkg --search /usr/share/doc/libmmtf-java/api/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libmmtf-java/api/index.html
> dpkg --search /usr/share/doc/libmmtf-java-doc/api/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libmmtf-java-doc/api/index.html
> dpkg --search /usr/share/doc/libmmtf-java/apidocs/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libmmtf-java/apidocs/index.html
> dpkg --search /usr/share/doc/libmmtf-java-doc/apidocs/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libmmtf-java-doc/apidocs/index.html
> dpkg --search /usr/share/doc/libslf4j-java/api/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libslf4j-java/api/index.html
> dpkg --search /usr/share/doc/libslf4j-java-doc/api/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libslf4j-java-doc/api/index.html
> dpkg --search /usr/share/doc/libslf4j-java/apidocs/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libslf4j-java/apidocs/index.html
> dpkg --search /usr/share/doc/libslf4j-java-doc/apidocs/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libslf4j-java-doc/apidocs/index.html
> dpkg --search /usr/share/doc/libvecmath-java/api/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libvecmath-java/api/index.html
> dpkg --search /usr/share/doc/libvecmath-java-doc/api/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libvecmath-java-doc/api/index.html
> dpkg --search /usr/share/doc/libvecmath-java/apidocs/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libvecmath-java/apidocs/index.html
> dpkg --search /usr/share/doc/libvecmath-java-doc/apidocs/index.html 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libvecmath-java-doc/apidocs/index.html
	bash -c "rm -f target/apidocs/*.sh target/apidocs/options"
	mh_unpatchpoms -plibbiojava6-java
   dh_install
   jh_installjavadoc
   debian/rules override_dh_installdocs
make[1]: Entering directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg'
dpkg: warning: --compare-versions used with obsolete relation operator '>'
dh_installdocs
# Deleting calls to urchinTracker to enhance privacy.
for F in $(find . -name "*.html"); do \
        sed -i 's/^<div.*urchinTracker.*div>$//' $F; \
done
make[1]: Leaving directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg'
   dh_installchangelogs
   dh_lintian
   dh_perl
   dh_link
   jh_installlibs
   jh_classpath
Duplicate specification "version|V" for option "V"
Duplicate specification "V:s" for option "V"
Duplicate specification "version|V" for option "V"
Duplicate specification "V:s" for option "V"
Duplicate specification "version|V" for option "V"
Duplicate specification "V:s" for option "V"
Duplicate specification "V:s" for option "V"
Duplicate specification "V:s" for option "V"
Duplicate specification "version|V" for option "V"
Duplicate specification "version|V" for option "V"
Duplicate specification "V:s" for option "V"
Duplicate specification "V:s" for option "V"
   jh_manifest
   jh_depends
   dh_strip_nondeterminism
   dh_compress
   dh_fixperms
   dh_missing
   dh_installdeb
   dh_gencontrol
dpkg-gencontrol: warning: package libbiojava6-java: substitution variable ${maven:CompileDepends} unused, but is defined
dpkg-gencontrol: warning: package libbiojava6-java: substitution variable ${maven:Depends} unused, but is defined
dpkg-gencontrol: warning: package libbiojava6-java: substitution variable ${maven:DocDepends} unused, but is defined
dpkg-gencontrol: warning: package libbiojava6-java-doc: substitution variable ${maven:CompileDepends} unused, but is defined
dpkg-gencontrol: warning: package libbiojava6-java-doc: substitution variable ${maven:Depends} unused, but is defined
dpkg-gencontrol: warning: package libbiojava6-java-doc: substitution variable ${maven:DocDepends} unused, but is defined
   dh_md5sums
   dh_builddeb
dpkg-deb: building package 'libbiojava6-java' in '../libbiojava6-java_6.1.0+dfsg-5_all.deb'.
dpkg-deb: building package 'libbiojava6-java-doc' in '../libbiojava6-java-doc_6.1.0+dfsg-5_all.deb'.
 dpkg-genbuildinfo --build=binary -O../biojava6-live_6.1.0+dfsg-5_arm64.buildinfo
 dpkg-genchanges --build=binary -O../biojava6-live_6.1.0+dfsg-5_arm64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/2957838/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/2957838/tmp/hooks/B01_cleanup finished
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env 
I: removing directory /srv/workspace/pbuilder/2957838 and its subdirectories
I: Current time: Wed Nov  6 09:41:45 +14 2024
I: pbuilder-time-stamp: 1730835705