Wed Feb 19 14:18:07 UTC 2025 I: starting to build biojava6-live/trixie/amd64 on jenkins on '2025-02-19 14:18'
Wed Feb 19 14:18:07 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_38/47560/console.log
Wed Feb 19 14:18:07 UTC 2025 I: Downloading source for trixie/biojava6-live=6.1.0+dfsg-5
--2025-02-19 14:18:08-- http://deb.debian.org/debian/pool/main/b/biojava6-live/biojava6-live_6.1.0%2bdfsg-5.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 3360 (3.3K) [text/prs.lines.tag]
Saving to: ‘biojava6-live_6.1.0+dfsg-5.dsc’
0K ... 100% 445M=0s
2025-02-19 14:18:08 (445 MB/s) - ‘biojava6-live_6.1.0+dfsg-5.dsc’ saved [3360/3360]
Wed Feb 19 14:18:08 UTC 2025 I: biojava6-live_6.1.0+dfsg-5.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: biojava6-live
Binary: libbiojava6-java, libbiojava6-java-doc
Architecture: all
Version: 6.1.0+dfsg-5
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Pierre Gruet <pgt@debian.org>
Homepage: https://www.biojava.org
Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/biojava6-live
Vcs-Git: https://salsa.debian.org/med-team/biojava6-live.git
Build-Depends: debhelper-compat (= 13), javahelper, maven-debian-helper
Build-Depends-Indep: default-jdk, default-jdk-doc, junit4 <!nocheck>, 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 <!nocheck>
Package-List:
libbiojava6-java deb java optional arch=all
libbiojava6-java-doc deb doc optional arch=all
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352d378215ef762c6c4cf1b6f6cbe0e443024a881c3c642a88040c7b71859914 27540 biojava6-live_6.1.0+dfsg-5.debian.tar.xz
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Wed Feb 19 14:18:08 UTC 2025 I: Checking whether the package is not for us
Wed Feb 19 14:18:08 UTC 2025 I: Starting 1st build on remote node infom02-amd64.debian.net.
Wed Feb 19 14:18:08 UTC 2025 I: Preparing to do remote build '1' on infom02-amd64.debian.net.
Wed Feb 19 16:23:41 UTC 2025 I: Deleting $TMPDIR on infom02-amd64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Tue Mar 24 08:41:10 -12 2026
I: pbuilder-time-stamp: 1774384870
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [biojava6-live_6.1.0+dfsg-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
dpkg-source: warning: cannot verify inline signature for ./biojava6-live_6.1.0+dfsg-5.dsc: unsupported subcommand
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/309805/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='amd64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
DISTRIBUTION='trixie'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='4a5f73575aec4496b9d2c19cf6d97e98'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='309805'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.MtIEMJB1/pbuilderrc_dmKa --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MtIEMJB1/b1 --logfile b1/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+12'
USER='root'
_='/usr/bin/systemd-run'
I: uname -a
Linux infom02-amd64 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/309805/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <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 ... 19809 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} gpgv{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-intel1{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} libffi8{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} libgcrypt20{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} libgnutls30t64{a} libgoogle-gson-java{a} libgpg-error0{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} libidn2-0{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} libldap2{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} libnspr4{a} libnss3{a} libopentest4j-java{a} libopentest4j-reporting-java{a} liboro-java{a} libp11-kit0{a} libpam-systemd{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libparams-classify-perl{a} libpciaccess0{a} libpcsclite1{a} libpicocli-java{a} libpipeline1{a} libpixman-1-0{a} libplexus-ant-factory-java{a} libplexus-archiver-java{a} libplexus-bsh-factory-java{a} libplexus-build-api-java{a} libplexus-cipher-java{a} libplexus-classworlds-java{a} libplexus-compiler-java{a} libplexus-component-annotations-java{a} libplexus-container-default-java{a} libplexus-container-default1.5-java{a} libplexus-i18n-java{a} libplexus-interactivity-api-java{a} libplexus-interpolation-java{a} libplexus-io-java{a} libplexus-languages-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libplexus-velocity-java{a} libplexus-xml-java{a} libpng16-16t64{a} libproc2-0{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-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} libtasn1-6{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libtxw2-java{a} libuchardet0{a} libunistring5{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-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-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} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} sopv-gpgv{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 libgpg-error-l10n 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-argcomplete python3-debian python3-magic python3-requests python3-unidiff python3-xdg strace systemd-cryptsetup systemd-timesyncd wget xdg-user-dirs
0 packages upgraded, 430 newly installed, 0 to remove and 0 not upgraded.
Need to get 345 MB of archives. After unpacking 1187 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main amd64 libsystemd-shared amd64 257.3-1 [2138 kB]
Get: 2 http://deb.debian.org/debian trixie/main amd64 libapparmor1 amd64 3.1.7-2 [42.0 kB]
Get: 3 http://deb.debian.org/debian trixie/main amd64 systemd amd64 257.3-1 [3092 kB]
Get: 4 http://deb.debian.org/debian trixie/main amd64 systemd-sysv amd64 257.3-1 [61.4 kB]
Get: 5 http://deb.debian.org/debian trixie/main amd64 libdbus-1-3 amd64 1.16.0-1 [177 kB]
Get: 6 http://deb.debian.org/debian trixie/main amd64 dbus-bin amd64 1.16.0-1 [78.9 kB]
Get: 7 http://deb.debian.org/debian trixie/main amd64 dbus-session-bus-common all 1.16.0-1 [51.1 kB]
Get: 8 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB]
Get: 9 http://deb.debian.org/debian trixie/main amd64 dbus-daemon amd64 1.16.0-1 [157 kB]
Get: 10 http://deb.debian.org/debian trixie/main amd64 dbus-system-bus-common all 1.16.0-1 [52.2 kB]
Get: 11 http://deb.debian.org/debian trixie/main amd64 dbus amd64 1.16.0-1 [70.5 kB]
Get: 12 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 13 http://deb.debian.org/debian trixie/main amd64 binfmt-support amd64 2.2.2-7 [64.3 kB]
Get: 14 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB]
Get: 15 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB]
Get: 16 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB]
Get: 17 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB]
Get: 18 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB]
Get: 19 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024b-6 [257 kB]
Get: 20 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB]
Get: 21 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB]
Get: 22 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB]
Get: 23 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB]
Get: 24 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.2-1 [745 kB]
Get: 25 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B]
Get: 26 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.1-2 [28.0 kB]
Get: 27 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB]
Get: 28 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB]
Get: 29 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-7 [878 kB]
Get: 30 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 31 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.4.0-2 [1422 kB]
Get: 32 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20241223 [164 kB]
Get: 33 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 34 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 35 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 36 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 37 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 38 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 39 http://deb.debian.org/debian trixie/main amd64 libpam-systemd amd64 257.3-1 [293 kB]
Get: 40 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-3 [92.1 kB]
Get: 41 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 42 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [311 kB]
Get: 43 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.83.3-2 [1511 kB]
Get: 44 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 45 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB]
Get: 46 http://deb.debian.org/debian trixie/main amd64 shared-mime-info amd64 2.4-5+b2 [760 kB]
Get: 47 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB]
Get: 48 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.46-4 [284 kB]
Get: 49 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB]
Get: 50 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB]
Get: 51 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB]
Get: 52 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB]
Get: 53 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB]
Get: 54 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB]
Get: 55 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-2 [140 kB]
Get: 56 http://deb.debian.org/debian trixie/main amd64 gtk-update-icon-cache amd64 4.17.4+ds-4 [51.3 kB]
Get: 57 http://deb.debian.org/debian trixie/main amd64 hicolor-icon-theme all 0.18-2 [11.8 kB]
Get: 58 http://deb.debian.org/debian trixie/main amd64 adwaita-icon-theme all 47.0-2 [463 kB]
Get: 59 http://deb.debian.org/debian trixie/main amd64 ca-certificates-java all 20240118 [11.6 kB]
Get: 60 http://deb.debian.org/debian trixie/main amd64 java-common all 0.76 [6776 B]
Get: 61 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB]
Get: 62 http://deb.debian.org/debian trixie/main amd64 libnspr4 amd64 2:4.36-1 [110 kB]
Get: 63 http://deb.debian.org/debian trixie/main amd64 libnss3 amd64 2:3.107-1 [1390 kB]
Get: 64 http://deb.debian.org/debian trixie/main amd64 libpcsclite1 amd64 2.3.1-1 [56.0 kB]
Get: 65 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jre-headless amd64 21.0.6+7-1 [41.7 MB]
Get: 66 http://deb.debian.org/debian trixie/main amd64 default-jre-headless amd64 2:1.21-76 [3192 B]
Get: 67 http://deb.debian.org/debian trixie/main amd64 ant all 1.10.15-1 [2163 kB]
Get: 68 http://deb.debian.org/debian trixie/main amd64 ant-optional all 1.10.15-1 [456 kB]
Get: 69 http://deb.debian.org/debian trixie/main amd64 at-spi2-common all 2.55.2-1 [170 kB]
Get: 70 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB]
Get: 71 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB]
Get: 72 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 73 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB]
Get: 74 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 75 http://deb.debian.org/debian trixie/main amd64 dbus-user-session amd64 1.16.0-1 [51.0 kB]
Get: 76 http://deb.debian.org/debian trixie/main amd64 libdconf1 amd64 0.40.0-5 [41.8 kB]
Get: 77 http://deb.debian.org/debian trixie/main amd64 dconf-service amd64 0.40.0-5 [32.4 kB]
Get: 78 http://deb.debian.org/debian trixie/main amd64 dconf-gsettings-backend amd64 0.40.0-5 [28.6 kB]
Get: 79 http://deb.debian.org/debian trixie/main amd64 dctrl-tools amd64 2.24-3+b1 [104 kB]
Get: 80 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 81 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB]
Get: 82 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 83 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 84 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 85 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 86 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 87 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 88 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 89 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 90 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 91 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 92 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB]
Get: 93 http://deb.debian.org/debian trixie/main amd64 libatk1.0-0t64 amd64 2.55.2-1 [51.4 kB]
Get: 94 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB]
Get: 95 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB]
Get: 96 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB]
Get: 97 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB]
Get: 98 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB]
Get: 99 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB]
Get: 100 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB]
Get: 101 http://deb.debian.org/debian trixie/main amd64 libatspi2.0-0t64 amd64 2.55.2-1 [77.0 kB]
Get: 102 http://deb.debian.org/debian trixie/main amd64 libatk-bridge2.0-0t64 amd64 2.55.2-1 [68.1 kB]
Get: 103 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB]
Get: 104 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB]
Get: 105 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get: 106 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB]
Get: 107 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB]
Get: 108 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-2 [391 kB]
Get: 109 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB]
Get: 110 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB]
Get: 111 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB]
Get: 112 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b4 [27.8 kB]
Get: 113 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB]
Get: 114 http://deb.debian.org/debian trixie/main amd64 libcairo-gobject2 amd64 1.18.2-2 [130 kB]
Get: 115 http://deb.debian.org/debian trixie/main amd64 libcloudproviders0 amd64 0.3.6-1+b1 [29.2 kB]
Get: 116 http://deb.debian.org/debian trixie/main amd64 libcolord2 amd64 1.4.7-1+b2 [140 kB]
Get: 117 http://deb.debian.org/debian trixie/main amd64 libavahi-common-data amd64 0.8-16 [112 kB]
Get: 118 http://deb.debian.org/debian trixie/main amd64 libavahi-common3 amd64 0.8-16 [44.2 kB]
Get: 119 http://deb.debian.org/debian trixie/main amd64 libavahi-client3 amd64 0.8-16 [48.4 kB]
Get: 120 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB]
Get: 121 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB]
Get: 122 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB]
Get: 123 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB]
Get: 124 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB]
Get: 125 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB]
Get: 126 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB]
Get: 127 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B]
Get: 128 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB]
Get: 129 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB]
Get: 130 http://deb.debian.org/debian trixie/main amd64 libcups2t64 amd64 2.4.10-2+b1 [251 kB]
Get: 131 http://deb.debian.org/debian trixie/main amd64 libepoxy0 amd64 1.5.10-2 [193 kB]
Get: 132 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB]
Get: 133 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB]
Get: 134 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.2.0-1 [479 kB]
Get: 135 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-2 [463 kB]
Get: 136 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB]
Get: 137 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB]
Get: 138 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB]
Get: 139 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.56.1-1 [226 kB]
Get: 140 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.56.1-1 [55.3 kB]
Get: 141 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.56.1-1 [35.8 kB]
Get: 142 http://deb.debian.org/debian trixie/main amd64 libwayland-client0 amd64 1.23.1-1 [26.5 kB]
Get: 143 http://deb.debian.org/debian trixie/main amd64 libwayland-cursor0 amd64 1.23.1-1 [11.4 kB]
Get: 144 http://deb.debian.org/debian trixie/main amd64 libwayland-egl1 amd64 1.23.1-1 [5452 B]
Get: 145 http://deb.debian.org/debian trixie/main amd64 libxcomposite1 amd64 1:0.4.6-1 [16.3 kB]
Get: 146 http://deb.debian.org/debian trixie/main amd64 libxfixes3 amd64 1:6.0.0-2+b4 [20.2 kB]
Get: 147 http://deb.debian.org/debian trixie/main amd64 libxcursor1 amd64 1:1.2.3-1 [39.7 kB]
Get: 148 http://deb.debian.org/debian trixie/main amd64 libxdamage1 amd64 1:1.1.6-1+b2 [15.5 kB]
Get: 149 http://deb.debian.org/debian trixie/main amd64 libxinerama1 amd64 2:1.1.4-3+b3 [16.0 kB]
Get: 150 http://deb.debian.org/debian trixie/main amd64 xkb-data all 2.42-1 [790 kB]
Get: 151 http://deb.debian.org/debian trixie/main amd64 libxkbcommon0 amd64 1.7.0-2 [113 kB]
Get: 152 http://deb.debian.org/debian trixie/main amd64 libxrandr2 amd64 2:1.5.4-1+b3 [36.3 kB]
Get: 153 http://deb.debian.org/debian trixie/main amd64 libgtk-3-common all 3.24.48-4 [4873 kB]
Get: 154 http://deb.debian.org/debian trixie/main amd64 libgtk-3-0t64 amd64 3.24.48-4 [2767 kB]
Get: 155 http://deb.debian.org/debian trixie/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB]
Get: 156 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.123-1 [8084 B]
Get: 157 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB]
Get: 158 http://deb.debian.org/debian trixie/main amd64 libglapi-mesa amd64 24.3.4-3 [38.5 kB]
Get: 159 http://deb.debian.org/debian trixie/main amd64 libx11-xcb1 amd64 2:1.8.10-2 [241 kB]
Get: 160 http://deb.debian.org/debian trixie/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB]
Get: 161 http://deb.debian.org/debian trixie/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB]
Get: 162 http://deb.debian.org/debian trixie/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB]
Get: 163 http://deb.debian.org/debian trixie/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB]
Get: 164 http://deb.debian.org/debian trixie/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b4 [19.3 kB]
Get: 165 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB]
Get: 166 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB]
Get: 167 http://deb.debian.org/debian trixie/main amd64 libdrm-intel1 amd64 2.4.123-1 [63.7 kB]
Get: 168 http://deb.debian.org/debian trixie/main amd64 libdrm-radeon1 amd64 2.4.123-1 [22.3 kB]
Get: 169 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB]
Get: 170 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB]
Get: 171 http://deb.debian.org/debian trixie/main amd64 libllvm19 amd64 1:19.1.7-1+b1 [26.0 MB]
Get: 172 http://deb.debian.org/debian trixie/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB]
Get: 173 http://deb.debian.org/debian trixie/main amd64 libsensors5 amd64 1:3.6.0-10+b1 [35.1 kB]
Get: 174 http://deb.debian.org/debian trixie/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB]
Get: 175 http://deb.debian.org/debian trixie/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB]
Get: 176 http://deb.debian.org/debian trixie/main amd64 libxshmfence1 amd64 1.3-1+b3 [8852 B]
Get: 177 http://deb.debian.org/debian trixie/main amd64 mesa-libgallium amd64 24.3.4-3 [9492 kB]
Get: 178 http://deb.debian.org/debian trixie/main amd64 libwayland-server0 amd64 1.23.1-1 [34.0 kB]
Get: 179 http://deb.debian.org/debian trixie/main amd64 libgbm1 amd64 24.3.4-3 [43.7 kB]
Get: 180 http://deb.debian.org/debian trixie/main amd64 libvulkan1 amd64 1.4.304.0-1 [129 kB]
Get: 181 http://deb.debian.org/debian trixie/main amd64 libgl1-mesa-dri amd64 24.3.4-3 [45.2 kB]
Get: 182 http://deb.debian.org/debian trixie/main amd64 libglx-mesa0 amd64 24.3.4-3 [143 kB]
Get: 183 http://deb.debian.org/debian trixie/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB]
Get: 184 http://deb.debian.org/debian trixie/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB]
Get: 185 http://deb.debian.org/debian trixie/main amd64 libasound2-data all 1.2.13-1 [21.1 kB]
Get: 186 http://deb.debian.org/debian trixie/main amd64 libasound2t64 amd64 1.2.13-1+b1 [373 kB]
Get: 187 http://deb.debian.org/debian trixie/main amd64 libgif7 amd64 5.2.2-1+b1 [44.2 kB]
Get: 188 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+24 [217 kB]
Get: 189 http://deb.debian.org/debian trixie/main amd64 libxtst6 amd64 2:1.2.5-1 [25.8 kB]
Get: 190 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jre amd64 21.0.6+7-1 [205 kB]
Get: 191 http://deb.debian.org/debian trixie/main amd64 default-jre amd64 2:1.21-76 [1068 B]
Get: 192 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jdk-headless amd64 21.0.6+7-1 [82.8 MB]
Get: 193 http://deb.debian.org/debian trixie/main amd64 default-jdk-headless amd64 2:1.21-76 [1124 B]
Get: 194 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jdk amd64 21.0.6+7-1 [3434 kB]
Get: 195 http://deb.debian.org/debian trixie/main amd64 default-jdk amd64 2:1.21-76 [1076 B]
Get: 196 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 197 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get: 198 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui-theme-base all 1.12.1+dfsg-1.1 [44.3 kB]
Get: 199 http://deb.debian.org/debian trixie/main amd64 openjdk-21-doc all 21.0.6+7-1 [13.2 MB]
Get: 200 http://deb.debian.org/debian trixie/main amd64 default-jdk-doc amd64 2:1.21-76 [3264 B]
Get: 201 http://deb.debian.org/debian trixie/main amd64 libgpg-error0 amd64 1.51-3 [82.2 kB]
Get: 202 http://deb.debian.org/debian trixie/main amd64 libassuan9 amd64 3.0.1-2 [60.6 kB]
Get: 203 http://deb.debian.org/debian trixie/main amd64 libgcrypt20 amd64 1.11.0-7 [843 kB]
Get: 204 http://deb.debian.org/debian trixie/main amd64 gpgconf amd64 2.2.46-1+b1 [121 kB]
Get: 205 http://deb.debian.org/debian trixie/main amd64 libksba8 amd64 1.6.7-2+b1 [136 kB]
Get: 206 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8+b1 [19.9 kB]
Get: 207 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8+b1 [57.6 kB]
Get: 208 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB]
Get: 209 http://deb.debian.org/debian trixie/main amd64 libnpth0t64 amd64 1.8-2 [22.9 kB]
Get: 210 http://deb.debian.org/debian trixie/main amd64 dirmngr amd64 2.2.46-1+b1 [369 kB]
Get: 211 http://deb.debian.org/debian trixie/main amd64 gnupg-l10n all 2.2.46-1 [702 kB]
Get: 212 http://deb.debian.org/debian trixie/main amd64 gpg amd64 2.2.46-1+b1 [532 kB]
Get: 213 http://deb.debian.org/debian trixie/main amd64 pinentry-curses amd64 1.3.1-2 [86.4 kB]
Get: 214 http://deb.debian.org/debian trixie/main amd64 gpg-agent amd64 2.2.46-1+b1 [252 kB]
Get: 215 http://deb.debian.org/debian trixie/main amd64 gpgsm amd64 2.2.46-1+b1 [255 kB]
Get: 216 http://deb.debian.org/debian trixie/main amd64 gnupg all 2.2.46-1 [376 kB]
Get: 217 http://deb.debian.org/debian trixie/main amd64 gpgv amd64 2.2.46-1+b1 [219 kB]
Get: 218 http://deb.debian.org/debian trixie/main amd64 sopv-gpgv all 0.1.1-1 [10.7 kB]
Get: 219 http://deb.debian.org/debian trixie/main amd64 libfile-dirlist-perl all 0.05-3 [7600 B]
Get: 220 http://deb.debian.org/debian trixie/main amd64 libfile-which-perl all 1.27-2 [15.1 kB]
Get: 221 http://deb.debian.org/debian trixie/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB]
Get: 222 http://deb.debian.org/debian trixie/main amd64 libfile-touch-perl all 0.12-2 [8816 B]
Get: 223 http://deb.debian.org/debian trixie/main amd64 libio-pty-perl amd64 1:1.20-1+b3 [34.3 kB]
Get: 224 http://deb.debian.org/debian trixie/main amd64 libipc-run-perl all 20231003.0-2 [101 kB]
Get: 225 http://deb.debian.org/debian trixie/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB]
Get: 226 http://deb.debian.org/debian trixie/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b4 [36.1 kB]
Get: 227 http://deb.debian.org/debian trixie/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b2 [10.6 kB]
Get: 228 http://deb.debian.org/debian trixie/main amd64 libdynaloader-functions-perl all 0.004-1 [12.1 kB]
Get: 229 http://deb.debian.org/debian trixie/main amd64 libdevel-callchecker-perl amd64 0.009-1+b1 [16.2 kB]
Get: 230 http://deb.debian.org/debian trixie/main amd64 libparams-classify-perl amd64 0.015-2+b4 [22.5 kB]
Get: 231 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB]
Get: 232 http://deb.debian.org/debian trixie/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB]
Get: 233 http://deb.debian.org/debian trixie/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB]
Get: 234 http://deb.debian.org/debian trixie/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB]
Get: 235 http://deb.debian.org/debian trixie/main amd64 libmoo-perl all 2.005005-1 [58.0 kB]
Get: 236 http://deb.debian.org/debian trixie/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB]
Get: 237 http://deb.debian.org/debian trixie/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB]
Get: 238 http://deb.debian.org/debian trixie/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB]
Get: 239 http://deb.debian.org/debian trixie/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB]
Get: 240 http://deb.debian.org/debian trixie/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB]
Get: 241 http://deb.debian.org/debian trixie/main amd64 liburi-perl all 5.30-1 [105 kB]
Get: 242 http://deb.debian.org/debian trixie/main amd64 libhtml-parser-perl amd64 3.83-1+b2 [99.7 kB]
Get: 243 http://deb.debian.org/debian trixie/main amd64 libhtml-tree-perl all 5.07-3 [211 kB]
Get: 244 http://deb.debian.org/debian trixie/main amd64 libclone-perl amd64 0.47-1+b1 [13.9 kB]
Get: 245 http://deb.debian.org/debian trixie/main amd64 libio-html-perl all 1.004-3 [16.2 kB]
Get: 246 http://deb.debian.org/debian trixie/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB]
Get: 247 http://deb.debian.org/debian trixie/main amd64 libhttp-message-perl all 7.00-2 [79.8 kB]
Get: 248 http://deb.debian.org/debian trixie/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB]
Get: 249 http://deb.debian.org/debian trixie/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB]
Get: 250 http://deb.debian.org/debian trixie/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B]
Get: 251 http://deb.debian.org/debian trixie/main amd64 libnet-ssleay-perl amd64 1.94-2 [339 kB]
Get: 252 http://deb.debian.org/debian trixie/main amd64 libio-socket-ssl-perl all 2.089-1 [223 kB]
Get: 253 http://deb.debian.org/debian trixie/main amd64 libnet-http-perl all 6.23-1 [23.9 kB]
Get: 254 http://deb.debian.org/debian trixie/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB]
Get: 255 http://deb.debian.org/debian trixie/main amd64 libtry-tiny-perl all 0.32-1 [22.9 kB]
Get: 256 http://deb.debian.org/debian trixie/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB]
Get: 257 http://deb.debian.org/debian trixie/main amd64 libwww-perl all 6.77-1 [183 kB]
Get: 258 http://deb.debian.org/debian trixie/main amd64 patchutils amd64 0.4.2-1 [77.5 kB]
Get: 259 http://deb.debian.org/debian trixie/main amd64 wdiff amd64 1.2.2-7 [122 kB]
Get: 260 http://deb.debian.org/debian trixie/main amd64 devscripts all 2.25.2 [1058 kB]
Get: 261 http://deb.debian.org/debian trixie/main amd64 fastjar amd64 2:0.98-7 [80.1 kB]
Get: 262 http://deb.debian.org/debian trixie/main amd64 jarwrapper all 0.80 [9692 B]
Get: 263 http://deb.debian.org/debian trixie/main amd64 javahelper all 0.80 [80.4 kB]
Get: 264 http://deb.debian.org/debian trixie/main amd64 junit all 3.8.2-10 [108 kB]
Get: 265 http://deb.debian.org/debian trixie/main amd64 libhamcrest-java all 2.2-2 [121 kB]
Get: 266 http://deb.debian.org/debian trixie/main amd64 junit4 all 4.13.2-5 [350 kB]
Get: 267 http://deb.debian.org/debian trixie/main amd64 libapiguardian-java all 1.1.2-1 [4656 B]
Get: 268 http://deb.debian.org/debian trixie/main amd64 libopentest4j-java all 1.2.0-4 [9516 B]
Get: 269 http://deb.debian.org/debian trixie/main amd64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB]
Get: 270 http://deb.debian.org/debian trixie/main amd64 libpicocli-java all 4.6.2-2 [390 kB]
Get: 271 http://deb.debian.org/debian trixie/main amd64 libunivocity-parsers-java all 2.9.1-1 [397 kB]
Get: 272 http://deb.debian.org/debian trixie/main amd64 junit5 all 5.10.3-1 [2459 kB]
Get: 273 http://deb.debian.org/debian trixie/main amd64 libactivation-java all 1.2.0-2 [84.7 kB]
Get: 274 http://deb.debian.org/debian trixie/main amd64 libantlr4-runtime-java all 4.9.2-2 [317 kB]
Get: 275 http://deb.debian.org/debian trixie/main amd64 libaopalliance-java all 20070526-7 [8572 B]
Get: 276 http://deb.debian.org/debian trixie/main amd64 libapache-pom-java all 33-2 [5852 B]
Get: 277 http://deb.debian.org/debian trixie/main amd64 libapfloat-java all 1.14.0-2 [725 kB]
Get: 278 http://deb.debian.org/debian trixie/main amd64 libargs4j-java all 2.33-2 [138 kB]
Get: 279 http://deb.debian.org/debian trixie/main amd64 libasm-java all 9.7.1-1 [391 kB]
Get: 280 http://deb.debian.org/debian trixie/main amd64 libatinject-jsr330-api-java all 1.0+ds1-6 [5112 B]
Get: 281 http://deb.debian.org/debian trixie/main amd64 libbsh-java all 2.0b4-20 [291 kB]
Get: 282 http://deb.debian.org/debian trixie/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-5 [8444 B]
Get: 283 http://deb.debian.org/debian trixie/main amd64 libcdi-api-java all 1.2-4 [55.3 kB]
Get: 284 http://deb.debian.org/debian trixie/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB]
Get: 285 http://deb.debian.org/debian trixie/main amd64 libgoogle-gson-java all 2.10.1-1 [262 kB]
Get: 286 http://deb.debian.org/debian trixie/main amd64 libciftools-java all 6.0.0-1 [2211 kB]
Get: 287 http://deb.debian.org/debian trixie/main amd64 libjaxen-java all 1.1.6-5 [214 kB]
Get: 288 http://deb.debian.org/debian trixie/main amd64 libdom4j-java all 2.1.4-1 [312 kB]
Get: 289 http://deb.debian.org/debian trixie/main amd64 libcommons-parent-java all 56-1 [10.8 kB]
Get: 290 http://deb.debian.org/debian trixie/main amd64 libcommons-io-java all 2.18.0-1 [509 kB]
Get: 291 http://deb.debian.org/debian trixie/main amd64 libslf4j-java all 1.7.32-1 [144 kB]
Get: 292 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-utils-java all 3.4.2-1 [137 kB]
Get: 293 http://deb.debian.org/debian trixie/main amd64 libcommons-cli-java all 1.6.0-1 [60.4 kB]
Get: 294 http://deb.debian.org/debian trixie/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB]
Get: 295 http://deb.debian.org/debian trixie/main amd64 libjsr305-java all 0.1~+svn49-12 [26.6 kB]
Get: 296 http://deb.debian.org/debian trixie/main amd64 libguava-java all 32.0.1-1 [2708 kB]
Get: 297 http://deb.debian.org/debian trixie/main amd64 libguice-java all 5.1.0-1 [932 kB]
Get: 298 http://deb.debian.org/debian trixie/main amd64 libmaven-parent-java all 43-2 [6252 B]
Get: 299 http://deb.debian.org/debian trixie/main amd64 libcommons-lang3-java all 3.17.0-1 [641 kB]
Get: 300 http://deb.debian.org/debian trixie/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB]
Get: 301 http://deb.debian.org/debian trixie/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB]
Get: 302 http://deb.debian.org/debian trixie/main amd64 libmaven-resolver-java all 1.9.22-1 [729 kB]
Get: 303 http://deb.debian.org/debian trixie/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB]
Get: 304 http://deb.debian.org/debian trixie/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB]
Get: 305 http://deb.debian.org/debian trixie/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B]
Get: 306 http://deb.debian.org/debian trixie/main amd64 libplexus-interpolation-java all 1.27-1 [76.8 kB]
Get: 307 http://deb.debian.org/debian trixie/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB]
Get: 308 http://deb.debian.org/debian trixie/main amd64 libsisu-inject-java all 0.3.5-1 [352 kB]
Get: 309 http://deb.debian.org/debian trixie/main amd64 libsisu-plexus-java all 0.3.5-1 [183 kB]
Get: 310 http://deb.debian.org/debian trixie/main amd64 libmaven3-core-java all 3.9.9-1 [1661 kB]
Get: 311 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB]
Get: 312 http://deb.debian.org/debian trixie/main amd64 libmaven-file-management-java all 3.0.0-2 [35.1 kB]
Get: 313 http://deb.debian.org/debian trixie/main amd64 libcommons-codec-java all 1.17.1-1 [303 kB]
Get: 314 http://deb.debian.org/debian trixie/main amd64 libcommons-compress-java all 1.27.1-2 [641 kB]
Get: 315 http://deb.debian.org/debian trixie/main amd64 libplexus-io-java all 3.3.1-2 [65.3 kB]
Get: 316 http://deb.debian.org/debian trixie/main amd64 libsnappy1v5 amd64 1.2.1-1+b1 [29.6 kB]
Get: 317 http://deb.debian.org/debian trixie/main amd64 libsnappy-jni amd64 1.1.10.7-1 [6492 B]
Get: 318 http://deb.debian.org/debian trixie/main amd64 libsnappy-java all 1.1.10.7-1 [87.6 kB]
Get: 319 http://deb.debian.org/debian trixie/main amd64 libxz-java all 1.9-1 [143 kB]
Get: 320 http://deb.debian.org/debian trixie/main amd64 libplexus-archiver-java all 4.6.1-1 [187 kB]
Get: 321 http://deb.debian.org/debian trixie/main amd64 libhttpcore-java all 4.4.16-1 [636 kB]
Get: 322 http://deb.debian.org/debian trixie/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB]
Get: 323 http://deb.debian.org/debian trixie/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB]
Get: 324 http://deb.debian.org/debian trixie/main amd64 libjsoup-java all 1.15.3-1 [431 kB]
Get: 325 http://deb.debian.org/debian trixie/main amd64 libwagon-http-java all 3.5.3-1 [49.5 kB]
Get: 326 http://deb.debian.org/debian trixie/main amd64 libistack-commons-java all 3.0.6-5 [145 kB]
Get: 327 http://deb.debian.org/debian trixie/main amd64 libcodemodel-java all 2.6+jaxb2.3.0.1-11 [164 kB]
Get: 328 http://deb.debian.org/debian trixie/main amd64 libcommons-collections3-java all 3.2.2-3 [530 kB]
Get: 329 http://deb.debian.org/debian trixie/main amd64 libcommons-beanutils-java all 1.9.4-2 [233 kB]
Get: 330 http://deb.debian.org/debian trixie/main amd64 libcommons-digester-java all 1.8.1-7 [138 kB]
Get: 331 http://deb.debian.org/debian trixie/main amd64 libcommons-exec-java all 1.3-2 [48.1 kB]
Get: 332 http://deb.debian.org/debian trixie/main amd64 libcommons-lang-java all 2.6-10 [273 kB]
Get: 333 http://deb.debian.org/debian trixie/main amd64 libcommons-math-java all 2.2-9 [933 kB]
Get: 334 http://deb.debian.org/debian trixie/main amd64 libmaven-archiver-java all 3.6.2-1 [26.1 kB]
Get: 335 http://deb.debian.org/debian trixie/main amd64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB]
Get: 336 http://deb.debian.org/debian trixie/main amd64 libcommons-text-java all 1.12.0-1 [222 kB]
Get: 337 http://deb.debian.org/debian trixie/main amd64 libcommons-validator-java all 1:1.9.0-1 [191 kB]
Get: 338 http://deb.debian.org/debian trixie/main amd64 libdoxia-core-java all 2.0.0-1 [149 kB]
Get: 339 http://deb.debian.org/debian trixie/main amd64 libplexus-xml-java all 3.0.1-2 [93.7 kB]
Get: 340 http://deb.debian.org/debian trixie/main amd64 libdoxia-java all 2.0.0-1 [113 kB]
Get: 341 http://deb.debian.org/debian trixie/main amd64 libmaven-reporting-api-java all 4.0.0-1 [6724 B]
Get: 342 http://deb.debian.org/debian trixie/main amd64 libxbean-reflect-java all 4.5-9 [132 kB]
Get: 343 http://deb.debian.org/debian trixie/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB]
Get: 344 http://deb.debian.org/debian trixie/main amd64 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB]
Get: 345 http://deb.debian.org/debian trixie/main amd64 velocity all 1.7-7 [431 kB]
Get: 346 http://deb.debian.org/debian trixie/main amd64 libplexus-velocity-java all 1.2-4 [9676 B]
Get: 347 http://deb.debian.org/debian trixie/main amd64 liboro-java all 2.0.8a-14 [70.5 kB]
Get: 348 http://deb.debian.org/debian trixie/main amd64 libvelocity-tools-java all 2.0-9 [311 kB]
Get: 349 http://deb.debian.org/debian trixie/main amd64 libdoxia-sitetools-java all 2.0.0-1 [176 kB]
Get: 350 http://deb.debian.org/debian trixie/main amd64 libdtd-parser-java all 1.2-1 [64.9 kB]
Get: 351 http://deb.debian.org/debian trixie/main amd64 libel-api-java all 3.0.0-3 [64.9 kB]
Get: 352 http://deb.debian.org/debian trixie/main amd64 libexec-maven-plugin-java all 3.1.0-2 [66.7 kB]
Get: 353 http://deb.debian.org/debian trixie/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB]
Get: 354 http://deb.debian.org/debian trixie/main amd64 libstax-ex-java all 1.7.8-3 [40.9 kB]
Get: 355 http://deb.debian.org/debian trixie/main amd64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB]
Get: 356 http://deb.debian.org/debian trixie/main amd64 librelaxng-datatype-java all 1.0+ds1-4 [11.8 kB]
Get: 357 http://deb.debian.org/debian trixie/main amd64 libxsom-java all 2.3.0.1-11 [401 kB]
Get: 358 http://deb.debian.org/debian trixie/main amd64 libfastinfoset-java all 1.2.12-4 [347 kB]
Get: 359 http://deb.debian.org/debian trixie/main amd64 libfastutil-java all 8.5.15+dfsg-1 [20.0 MB]
Get: 360 http://deb.debian.org/debian trixie/main amd64 libinchi1.07 amd64 1.07.2+dfsg-1 [556 kB]
Get: 361 http://deb.debian.org/debian trixie/main amd64 libitext5-java all 5.5.13.3-4 [2667 kB]
Get: 362 http://deb.debian.org/debian trixie/main amd64 libjackson2-annotations-java all 2.14.0-1 [68.8 kB]
Get: 363 http://deb.debian.org/debian trixie/main amd64 libjackson2-core-java all 2.14.1-1 [447 kB]
Get: 364 http://deb.debian.org/debian trixie/main amd64 libjackson2-databind-java all 2.14.0+ds-1 [1532 kB]
Get: 365 http://deb.debian.org/debian trixie/main amd64 libjakarta-activation-java all 2.0.0-1 [59.8 kB]
Get: 366 http://deb.debian.org/debian trixie/main amd64 libjansi-java all 2.4.1-2 [100 kB]
Get: 367 http://deb.debian.org/debian trixie/main amd64 librngom-java all 2.3.0.1-11 [292 kB]
Get: 368 http://deb.debian.org/debian trixie/main amd64 libtxw2-java all 2.3.0.1-11 [134 kB]
Get: 369 http://deb.debian.org/debian trixie/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB]
Get: 370 http://deb.debian.org/debian trixie/main amd64 libjaxb-java all 2.3.0.1-11 [1980 kB]
Get: 371 http://deb.debian.org/debian trixie/main amd64 libjsp-api-java all 2.3.4-3 [53.7 kB]
Get: 372 http://deb.debian.org/debian trixie/main amd64 libservlet-api-java all 4.0.1-2 [81.0 kB]
Get: 373 http://deb.debian.org/debian trixie/main amd64 libwebsocket-api-java all 1.1-2 [40.1 kB]
Get: 374 http://deb.debian.org/debian trixie/main amd64 libjetty9-java all 9.4.56-1 [2964 kB]
Get: 375 http://deb.debian.org/debian trixie/main amd64 libjheaps-java all 0.14-2 [144 kB]
Get: 376 http://deb.debian.org/debian trixie/main amd64 libxml-commons-external-java all 1.4.01-6 [240 kB]
Get: 377 http://deb.debian.org/debian trixie/main amd64 libxerces2-java all 2.12.2-1 [1440 kB]
Get: 378 http://deb.debian.org/debian trixie/main amd64 libjgraphx-java all 2.1.0.7-5 [809 kB]
Get: 379 http://deb.debian.org/debian trixie/main amd64 libjgrapht-java all 1.5.2-1 [1610 kB]
Get: 380 http://deb.debian.org/debian trixie/main amd64 libjni-inchi-jni amd64 0.8+dfsg-8 [9188 B]
Get: 381 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-incremental-java all 1.1-6 [9916 B]
Get: 382 http://deb.debian.org/debian trixie/main amd64 libplexus-compiler-java all 2.13.0-1 [99.5 kB]
Get: 383 http://deb.debian.org/debian trixie/main amd64 libqdox2-java all 2.0.3-1 [296 kB]
Get: 384 http://deb.debian.org/debian trixie/main amd64 libplexus-languages-java all 1.1.1-2 [47.3 kB]
Get: 385 http://deb.debian.org/debian trixie/main amd64 libmaven-compiler-plugin-java all 3.13.0-1 [78.8 kB]
Get: 386 http://deb.debian.org/debian trixie/main amd64 liblog4j1.2-java all 1.2.17-11 [444 kB]
Get: 387 http://deb.debian.org/debian trixie/main amd64 libjni-inchi-java all 0.8+dfsg-8 [33.6 kB]
Get: 388 http://deb.debian.org/debian trixie/main amd64 libnaga-java all 3.0+svn80-5 [43.5 kB]
Get: 389 http://deb.debian.org/debian trixie/main amd64 libjmol-java all 16.2.33+dfsg-1 [10.4 MB]
Get: 390 http://deb.debian.org/debian trixie/main amd64 libjson-simple-java all 2.3.0-1 [63.8 kB]
Get: 391 http://deb.debian.org/debian trixie/main amd64 libjtidy-java all 7+svn20110807-6 [251 kB]
Get: 392 http://deb.debian.org/debian trixie/main amd64 liblightcouch-java all 0.2.0-1 [75.0 kB]
Get: 393 http://deb.debian.org/debian trixie/main amd64 libmongodb-java all 3.6.3-2 [1901 kB]
Get: 394 http://deb.debian.org/debian trixie/main amd64 liblog4j2-java all 2.19.0-2 [2310 kB]
Get: 395 http://deb.debian.org/debian trixie/main amd64 libmaven-antrun-plugin-java all 3.1.0-1 [36.9 kB]
Get: 396 http://deb.debian.org/debian trixie/main amd64 libmaven-common-artifact-filters-java all 3.4.0-1 [47.7 kB]
Get: 397 http://deb.debian.org/debian trixie/main amd64 libmaven-artifact-transfer-java all 0.13.1-2 [158 kB]
Get: 398 http://deb.debian.org/debian trixie/main amd64 libplexus-build-api-java all 0.0.7-4 [10.3 kB]
Get: 399 http://deb.debian.org/debian trixie/main amd64 libmaven-filtering-java all 3.4.0-1 [51.4 kB]
Get: 400 http://deb.debian.org/debian trixie/main amd64 libmaven-assembly-plugin-java all 3.4.2-2 [242 kB]
Get: 401 http://deb.debian.org/debian trixie/main amd64 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB]
Get: 402 http://deb.debian.org/debian trixie/main amd64 libmaven-dependency-analyzer-java all 1.15.1-1 [38.5 kB]
Get: 403 http://deb.debian.org/debian trixie/main amd64 libmaven-dependency-tree-java all 3.3.0-1 [35.0 kB]
Get: 404 http://deb.debian.org/debian trixie/main amd64 libmaven-reporting-impl-java all 4.0.0-1 [17.6 kB]
Get: 405 http://deb.debian.org/debian trixie/main amd64 libmaven-dependency-plugin-java all 3.8.1-1 [191 kB]
Get: 406 http://deb.debian.org/debian trixie/main amd64 libmaven-deploy-plugin-java all 3.1.3-1 [37.1 kB]
Get: 407 http://deb.debian.org/debian trixie/main amd64 libmaven-enforcer-plugin-java all 3.5.0-1 [178 kB]
Get: 408 http://deb.debian.org/debian trixie/main amd64 libmaven-install-plugin-java all 3.1.3-1 [30.2 kB]
Get: 409 http://deb.debian.org/debian trixie/main amd64 libmaven-invoker-java all 3.3.0-1 [29.1 kB]
Get: 410 http://deb.debian.org/debian trixie/main amd64 libplexus-interactivity-api-java all 1.3-1 [11.6 kB]
Get: 411 http://deb.debian.org/debian trixie/main amd64 libmaven-javadoc-plugin-java all 3.10.1-2 [451 kB]
Get: 412 http://deb.debian.org/debian trixie/main amd64 libplexus-container-default1.5-java all 2.1.1-1 [4476 B]
Get: 413 http://deb.debian.org/debian trixie/main amd64 libplexus-ant-factory-java all 1.0~alpha2.1-4 [11.4 kB]
Get: 414 http://deb.debian.org/debian trixie/main amd64 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B]
Get: 415 http://deb.debian.org/debian trixie/main amd64 libmaven-plugin-tools-java all 3.10.2-1 [245 kB]
Get: 416 http://deb.debian.org/debian trixie/main amd64 libmaven-jaxb2-plugin-java all 0.15.1-1 [118 kB]
Get: 417 http://deb.debian.org/debian trixie/main amd64 libmaven-reporting-exec-java all 2.0.0-1 [23.9 kB]
Get: 418 http://deb.debian.org/debian trixie/main amd64 libmaven-resources-plugin-java all 3.3.1-1 [27.5 kB]
Get: 419 http://deb.debian.org/debian trixie/main amd64 libmaven-site-plugin-java all 3.21.0-1 [106 kB]
Get: 420 http://deb.debian.org/debian trixie/main amd64 libmsgpack-java all 0.9.6-1 [161 kB]
Get: 421 http://deb.debian.org/debian trixie/main amd64 libmmtf-java all 1.0.11-1 [187 kB]
Get: 422 http://deb.debian.org/debian trixie/main amd64 libsurefire-java all 2.22.3-3 [1284 kB]
Get: 423 http://deb.debian.org/debian trixie/main amd64 libvecmath-java all 1.5.2-7 [97.0 kB]
Get: 424 http://deb.debian.org/debian trixie/main amd64 libwagon-file-java all 3.5.3-1 [8388 B]
Get: 425 http://deb.debian.org/debian trixie/main amd64 libxml2-utils amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [99.4 kB]
Get: 426 http://deb.debian.org/debian trixie/main amd64 libxmlunit-java all 1.6-2 [100 kB]
Get: 427 http://deb.debian.org/debian trixie/main amd64 maven all 3.9.9-1 [19.7 kB]
Get: 428 http://deb.debian.org/debian trixie/main amd64 maven-repo-helper all 1.11 [142 kB]
Get: 429 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB]
Get: 430 http://deb.debian.org/debian trixie/main amd64 maven-debian-helper all 2.6.7 [108 kB]
Fetched 345 MB in 7s (51.3 MB/s)
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Unpacking libapparmor1:amd64 (3.1.7-2) ...
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Unpacking systemd (257.3-1) ...
Setting up libapparmor1:amd64 (3.1.7-2) ...
Setting up systemd (257.3-1) ...
Created symlink '/etc/systemd/system/getty.target.wants/getty@tty1.service' -> '/usr/lib/systemd/system/getty@.service'.
Created symlink '/etc/systemd/system/multi-user.target.wants/remote-fs.target' -> '/usr/lib/systemd/system/remote-fs.target'.
Created symlink '/etc/systemd/system/sysinit.target.wants/systemd-pstore.service' -> '/usr/lib/systemd/system/systemd-pstore.service'.
Initializing machine ID from random generator.
Creating group 'systemd-journal' with GID 999.
Creating group 'systemd-network' with GID 998.
Creating user 'systemd-network' (systemd Network Management) with UID 998 and GID 998.
[0;1;39m/usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring.[0m
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Unpacking libpipeline1:amd64 (1.5.8-1) ...
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Unpacking binfmt-support (2.2.2-7) ...
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Setting up libpython3.13-minimal:amd64 (3.13.2-1) ...
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Selecting previously unselected package python3-minimal.
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Unpacking readline-common (8.2-6) ...
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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
Unpacking libreadline8t64:amd64 (8.2-6) ...
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Setting up libldap2:amd64 (2.6.9+dfsg-1) ...
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Setting up dbus-bin (1.16.0-1) ...
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:amd64 (1.7.0-2) ...
Setting up libnaga-java (3.0+svn80-5) ...
Setting up libwayland-client0:amd64 (1.23.1-1) ...
Setting up libnet-ssleay-perl:amd64 (1.94-2) ...
Setting up automake (1:1.17-3) ...
update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
Setting up libksba8:amd64 (1.6.7-2+b1) ...
Setting up pinentry-curses (1.3.1-2) ...
Setting up libdom4j-java (2.1.4-1) ...
Setting up libjaxb-api-java (2.3.1-1) ...
Setting up libfile-stripnondeterminism-perl (1.14.1-2) ...
Setting up libxcb-dri3-0:amd64 (1.17.0-2+b1) ...
Setting up libwagon-provider-api-java (3.5.3-1) ...
Setting up libllvm19:amd64 (1:19.1.7-1+b1) ...
Setting up libwayland-server0:amd64 (1.23.1-1) ...
Setting up libx11-xcb1:amd64 (2:1.8.10-2) ...
Setting up libhttp-date-perl (6.06-1) ...
Setting up gettext (0.23.1-1) ...
Setting up libjetty9-java (9.4.56-1) ...
Setting up libxdamage1:amd64 (1:1.1.6-1+b2) ...
Setting up libfile-listing-perl (6.16-1) ...
Setting up libplexus-languages-java (1.1.1-2) ...
Setting up libxrender1:amd64 (1:0.9.10-1.1+b4) ...
Setting up jarwrapper (0.80) ...
Setting up libtool (2.5.4-3) ...
Setting up fontconfig-config (2.15.0-2) ...
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:amd64 (0.8-16) ...
Setting up libcommons-logging-java (1.3.0-1) ...
Setting up libxext6:amd64 (2:1.3.4-1+b3) ...
Setting up libnet-http-perl (6.23-1) ...
Setting up libsisu-inject-java (0.3.5-1) ...
Setting up libidn2-0:amd64 (2.3.7-2+b1) ...
Setting up libnss3:amd64 (2:3.107-1) ...
Setting up libciftools-java (6.0.0-1) ...
Setting up dbus-daemon (1.16.0-1) ...
Setting up libdevel-callchecker-perl:amd64 (0.009-1+b1) ...
Setting up libcommons-lang-java (2.6-10) ...
Setting up libmaven-dependency-analyzer-java (1.15.1-1) ...
Setting up libjackson2-databind-java (2.14.0+ds-1) ...
Setting up libplexus-cipher-java (2.0-1) ...
Setting up libxxf86vm1:amd64 (1:1.1.4-1+b4) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libxmlunit-java (1.6-2) ...
Setting up dh-autoreconf (20) ...
Setting up patchutils (0.4.2-1) ...
Setting up libthai0:amd64 (0.1.29-2+b1) ...
Setting up ca-certificates (20241223) ...
Updating certificates in /etc/ssl/certs...
152 added, 0 removed; done.
Setting up libsisu-plexus-java (0.3.5-1) ...
Setting up libglib2.0-0t64:amd64 (2.83.3-2) ...
Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ...
Setting up libxfixes3:amd64 (1:6.0.0-2+b4) ...
Setting up dbus (1.16.0-1) ...
Running in chroot, ignoring request.
invoke-rc.d: policy-rc.d denied execution of start.
Setting up shared-mime-info (2.4-5+b2) ...
Setting up libp11-kit0:amd64 (0.25.5-3) ...
Setting up libxinerama1:amd64 (2:1.1.4-3+b3) ...
Setting up libstreambuffer-java (1.5.4-1.1) ...
Setting up libgssapi-krb5-2:amd64 (1.21.3-4) ...
Setting up libxrandr2:amd64 (2:1.5.4-1+b3) ...
Setting up libcommons-lang3-java (3.17.0-1) ...
Setting up libreadline8t64:amd64 (8.2-6) ...
Setting up dh-strip-nondeterminism (1.14.1-2) ...
Setting up libwww-robotrules-perl (6.02-1) ...
Setting up librngom-java (2.3.0.1-11) ...
Setting up libdrm2:amd64 (2.4.123-1) ...
Setting up libjni-inchi-jni (0.8+dfsg-8) ...
Setting up libjgraphx-java (2.1.0.7-5) ...
Setting up groff-base (1.23.0-7) ...
Setting up libwayland-cursor0:amd64 (1.23.1-1) ...
Setting up libhtml-parser-perl:amd64 (3.83-1+b2) ...
Setting up gpgconf (2.2.46-1+b1) ...
Setting up libpam-systemd:amd64 (257.3-1) ...
Setting up libcommons-beanutils-java (1.9.4-2) ...
Setting up libplexus-sec-dispatcher-java (2.0-3) ...
Setting up libharfbuzz0b:amd64 (10.2.0-1) ...
Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-2) ...
Setting up libsnappy-java (1.1.10.7-1) ...
Setting up libfontconfig1:amd64 (2.15.0-2) ...
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+really2.9.14-0.2+b1) ...
Setting up libcommons-codec-java (1.17.1-1) ...
Setting up libpython3.13-stdlib:amd64 (3.13.2-1) ...
Setting up libavahi-client3:amd64 (0.8-16) ...
Setting up libio-socket-ssl-perl (2.089-1) ...
Setting up gpg (2.2.46-1+b1) ...
Setting up libpython3-stdlib:amd64 (3.13.1-2) ...
Setting up libhttp-message-perl (7.00-2) ...
Setting up libdrm-amdgpu1:amd64 (2.4.123-1) ...
Setting up libgnutls30t64:amd64 (3.8.9-2) ...
Setting up gtk-update-icon-cache (4.17.4+ds-4) ...
Setting up libhttp-negotiate-perl (6.01-2) ...
Setting up velocity (1.7-7) ...
Setting up fontconfig (2.15.0-2) ...
Regenerating fonts cache... done.
Setting up gpg-agent (2.2.46-1+b1) ...
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 libatk1.0-0t64:amd64 (2.55.2-1) ...
Setting up openjdk-21-jre-headless:amd64 (21.0.6+7-1) ...
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
Setting up libxi6:amd64 (2:1.8.2-1) ...
Setting up libhttp-cookies-perl (6.11-1) ...
Setting up python3.13 (3.13.2-1) ...
Setting up libcommons-io-java (2.18.0-1) ...
Setting up libdrm-radeon1:amd64 (2.4.123-1) ...
Setting up libcommons-digester-java (1.8.1-7) ...
Setting up libxtst6:amd64 (2:1.2.5-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libhtml-tree-perl (5.07-3) ...
Setting up libxcursor1:amd64 (1:1.2.3-1) ...
Setting up libparams-classify-perl:amd64 (0.015-2+b4) ...
Setting up gpgsm (2.2.46-1+b1) ...
Setting up libpango-1.0-0:amd64 (1.56.1-1) ...
Setting up libdrm-intel1:amd64 (2.4.123-1) ...
Setting up libcloudproviders0:amd64 (0.3.6-1+b1) ...
Setting up python3 (3.13.1-2) ...
Setting up sopv-gpgv (0.1.1-1) ...
update-alternatives: using /usr/bin/sopv-gpgv to provide /usr/bin/sopv (sopv) in auto mode
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:amd64 (1.18.2-2) ...
Setting up libcolord2:amd64 (1.4.7-1+b2) ...
Setting up libdconf1:amd64 (0.40.0-5) ...
Setting up dirmngr (2.2.46-1+b1) ...
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 (21.0.6+7-1) ...
Setting up dbus-user-session (1.16.0-1) ...
Setting up libmaven-resolver-java (1.9.22-1) ...
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:amd64 (2.55.2-1) ...
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 gnupg (2.2.46-1) ...
Setting up liblightcouch-java (0.2.0-1) ...
Setting up libwagon-http-java (3.5.3-1) ...
Setting up libcairo-gobject2:amd64 (1.18.2-2) ...
Setting up libmaven-shared-utils-java (3.4.2-1) ...
Setting up libfastinfoset-java (1.2.12-4) ...
Setting up libpangoft2-1.0-0:amd64 (1.56.1-1) ...
Setting up libmaven-resources-plugin-java (3.3.1-1) ...
Setting up libcups2t64:amd64 (2.4.10-2+b1) ...
Setting up libpangocairo-1.0-0:amd64 (1.56.1-1) ...
Setting up libatk-bridge2.0-0t64:amd64 (2.55.2-1) ...
Setting up mesa-libgallium:amd64 (24.3.4-3) ...
Setting up libplexus-io-java (3.3.1-2) ...
Setting up libmaven-install-plugin-java (3.1.3-1) ...
Setting up libcommons-compress-java (1.27.1-2) ...
Setting up libcommons-validator-java (1:1.9.0-1) ...
Setting up libgbm1:amd64 (24.3.4-3) ...
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 libgl1-mesa-dri:amd64 (24.3.4-3) ...
Setting up libmaven-invoker-java (3.3.0-1) ...
Setting up debhelper (13.24.1) ...
Setting up dconf-service (0.40.0-5) ...
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 libglx-mesa0:amd64 (24.3.4-3) ...
Setting up libglx0:amd64 (1.7.0-1+b2) ...
Setting up dconf-gsettings-backend:amd64 (0.40.0-5) ...
Setting up libmaven-archiver-java (3.6.2-1) ...
Setting up libgl1:amd64 (1.7.0-1+b2) ...
Setting up libgtk-3-common (3.24.48-4) ...
Setting up libgtk-3-0t64:amd64 (3.24.48-4) ...
Setting up liberror-prone-java (2.18.0-1) ...
Setting up libwww-perl (6.77-1) ...
Setting up devscripts (2.25.2) ...
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 (5.1.0-1) ...
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 (3.9.9-1) ...
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 (3.0.0-2) ...
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 (2.40-6) ...
Processing triggers for systemd (257.3-1) ...
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:FIRMAPROFESIONAL_CA_ROOT-A_WEB.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:SecureSign_Root_CA12.pem
Adding debian:SecureSign_Root_CA14.pem
Adding debian:SecureSign_Root_CA15.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: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_CYBER_Root_CA.pem
Adding debian:TWCA_Global_Root_CA.pem
Adding debian:TWCA_Root_Certification_Authority.pem
Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem
Adding debian:Telekom_Security_TLS_RSA_Root_2023.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 (3.9.9-1) ...
update-alternatives: using /usr/share/maven/bin/mvn to provide /usr/bin/mvn (mvn) in auto mode
Setting up openjdk-21-jre:amd64 (21.0.6+7-1) ...
Setting up ant (1.10.15-1) ...
Setting up junit4 (4.13.2-5) ...
Setting up openjdk-21-jdk-headless:amd64 (21.0.6+7-1) ...
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jwebserver to provide /usr/bin/jwebserver (jwebserver) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/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:amd64 (21.0.6+7-1) ...
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/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 (2.6.7) ...
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 (20241223) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Processing triggers for ca-certificates-java (20240118) ...
done.
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/biojava6-live-6.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../biojava6-live_6.1.0+dfsg-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 amd64
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 POM for org.apache.maven.plugins:maven-assembly-plugin:jar:3.7.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:3.7.1: Plugin org.apache.maven.plugins:maven-assembly-plugin:3.7.1 or one of its dependencies could not be resolved:
Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:3.7.1 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:3.0.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:3.0.1: Plugin org.apache.maven.plugins:maven-release-plugin:3.0.1 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:3.0.1 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-assembly-plugin:jar:3.7.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:3.7.1: Plugin org.apache.maven.plugins:maven-assembly-plugin:3.7.1 or one of its dependencies could not be resolved:
Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:3.7.1 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:3.0.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:3.0.1: Plugin org.apache.maven.plugins:maven-release-plugin:3.0.1 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:3.0.1 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-assembly-plugin:jar:3.7.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:3.7.1: Plugin org.apache.maven.plugins:maven-assembly-plugin:3.7.1 or one of its dependencies could not be resolved:
Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:3.7.1 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:3.0.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:3.0.1: Plugin org.apache.maven.plugins:maven-release-plugin:3.0.1 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:3.0.1 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] --- javadoc: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-assembly-plugin:jar:3.7.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:3.7.1: Plugin org.apache.maven.plugins:maven-assembly-plugin:3.7.1 or one of its dependencies could not be resolved:
Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:3.7.1 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:3.0.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:3.0.1: Plugin org.apache.maven.plugins:maven-release-plugin:3.0.1 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:3.0.1 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] --- resources:3.3.1:resources (default-resources) @ biojava-core ---
[INFO] Copying 24 resources from src/main/resources to target/classes
[INFO]
[INFO] --- compiler: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] --- resources:3.3.1:testResources (default-testResources) @ biojava-core ---
[INFO] Copying 48 resources from src/test/resources to target/test-classes
[INFO]
[INFO] --- compiler: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] --- surefire:2.22.3:test (default-test) @ biojava-core ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- jar: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] --- javadoc: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-assembly-plugin:jar:3.7.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:3.7.1: Plugin org.apache.maven.plugins:maven-assembly-plugin:3.7.1 or one of its dependencies could not be resolved:
Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:3.7.1 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:3.0.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:3.0.1: Plugin org.apache.maven.plugins:maven-release-plugin:3.0.1 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:3.0.1 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] --- resources: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] --- compiler: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] --- resources: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] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-forester ---
[INFO] No sources to compile
[INFO]
[INFO] --- surefire:2.22.3:test (default-test) @ biojava-forester ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- jar: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] --- javadoc: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-assembly-plugin:jar:3.7.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:3.7.1: Plugin org.apache.maven.plugins:maven-assembly-plugin:3.7.1 or one of its dependencies could not be resolved:
Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:3.7.1 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:3.0.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:3.0.1: Plugin org.apache.maven.plugins:maven-release-plugin:3.0.1 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:3.0.1 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] --- resources:3.3.1:resources (default-resources) @ biojava-alignment ---
[INFO] Copying 2 resources from src/main/resources to target/classes
[INFO]
[INFO] --- compiler: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] --- resources:3.3.1:testResources (default-testResources) @ biojava-alignment ---
[INFO] Copying 11 resources from src/test/resources to target/test-classes
[INFO]
[INFO] --- compiler: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] --- surefire:2.22.3:test (default-test) @ biojava-alignment ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- jar: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] --- javadoc: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/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/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-assembly-plugin:jar:3.7.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:3.7.1: Plugin org.apache.maven.plugins:maven-assembly-plugin:3.7.1 or one of its dependencies could not be resolved:
Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:3.7.1 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:3.0.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:3.0.1: Plugin org.apache.maven.plugins:maven-release-plugin:3.0.1 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:3.0.1 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] --- resources: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] --- compiler: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] --- resources:3.3.1:testResources (default-testResources) @ biojava-structure ---
[INFO] Copying 55 resources from src/test/resources to target/test-classes
[INFO]
[INFO] --- compiler: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] --- surefire:2.22.3:test (default-test) @ biojava-structure ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- jar: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] --- javadoc: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-assembly-plugin:jar:3.7.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:3.7.1: Plugin org.apache.maven.plugins:maven-assembly-plugin:3.7.1 or one of its dependencies could not be resolved:
Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:3.7.1 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:3.0.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:3.0.1: Plugin org.apache.maven.plugins:maven-release-plugin:3.0.1 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:3.0.1 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] --- resources: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] --- compiler: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] --- resources: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] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-jcolorbrewer ---
[INFO] No sources to compile
[INFO]
[INFO] --- surefire:2.22.3:test (default-test) @ biojava-jcolorbrewer ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- jar: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] --- javadoc: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-assembly-plugin:jar:3.7.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:3.7.1: Plugin org.apache.maven.plugins:maven-assembly-plugin:3.7.1 or one of its dependencies could not be resolved:
Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:3.7.1 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:3.0.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:3.0.1: Plugin org.apache.maven.plugins:maven-release-plugin:3.0.1 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:3.0.1 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] --- resources:3.3.1:resources (default-resources) @ biojava-structure-gui ---
[INFO] Copying 49 resources from src/main/resources to target/classes
[INFO]
[INFO] --- compiler: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] --- resources: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] --- compiler: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] --- surefire:2.22.3:test (default-test) @ biojava-structure-gui ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- jar: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] --- javadoc: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-assembly-plugin:jar:3.7.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:3.7.1: Plugin org.apache.maven.plugins:maven-assembly-plugin:3.7.1 or one of its dependencies could not be resolved:
Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:3.7.1 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:3.0.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:3.0.1: Plugin org.apache.maven.plugins:maven-release-plugin:3.0.1 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:3.0.1 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] --- resources:3.3.1:resources (default-resources) @ biojava-genome ---
[INFO] Copying 1 resource from src/main/resources to target/classes
[INFO]
[INFO] --- compiler: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] --- resources:3.3.1:testResources (default-testResources) @ biojava-genome ---
[INFO] Copying 83 resources from src/test/resources to target/test-classes
[INFO]
[INFO] --- compiler: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] --- surefire:2.22.3:test (default-test) @ biojava-genome ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- jar: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] --- javadoc: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-assembly-plugin:jar:3.7.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:3.7.1: Plugin org.apache.maven.plugins:maven-assembly-plugin:3.7.1 or one of its dependencies could not be resolved:
Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:3.7.1 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:3.0.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:3.0.1: Plugin org.apache.maven.plugins:maven-release-plugin:3.0.1 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:3.0.1 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] --- resources:3.3.1:resources (default-resources) @ biojava-modfinder ---
[INFO] Copying 2 resources from src/main/resources to target/classes
[INFO]
[INFO] --- compiler: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] --- resources:3.3.1:testResources (default-testResources) @ biojava-modfinder ---
[INFO] Copying 2 resources from src/test/resources to target/test-classes
[INFO]
[INFO] --- compiler: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] --- surefire:2.22.3:test (default-test) @ biojava-modfinder ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- jar: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] --- javadoc: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-assembly-plugin:jar:3.7.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:3.7.1: Plugin org.apache.maven.plugins:maven-assembly-plugin:3.7.1 or one of its dependencies could not be resolved:
Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:3.7.1 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:3.0.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:3.0.1: Plugin org.apache.maven.plugins:maven-release-plugin:3.0.1 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:3.0.1 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] --- resources: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] --- compiler: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] --- resources: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] --- compiler: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] --- surefire:2.22.3:test (default-test) @ biojava-ws ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- jar: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] --- javadoc: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-assembly-plugin:jar:3.7.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:3.7.1: Plugin org.apache.maven.plugins:maven-assembly-plugin:3.7.1 or one of its dependencies could not be resolved:
Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:3.7.1 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:3.0.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:3.0.1: Plugin org.apache.maven.plugins:maven-release-plugin:3.0.1 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:3.0.1 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] Parameter 'descriptorRefs' is unknown for plugin 'maven-jar-plugin:3.3.0:jar (default-jar)'
[INFO]
[INFO] --- resources:3.3.1:resources (default-resources) @ biojava-protein-disorder ---
[INFO] Copying 11 resources from src/main/resources to target/classes
[INFO]
[INFO] --- compiler: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] --- resources:3.3.1:testResources (default-testResources) @ biojava-protein-disorder ---
[INFO] Copying 2 resources from src/test/resources to target/test-classes
[INFO]
[INFO] --- compiler: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] --- surefire:2.22.3:test (default-test) @ biojava-protein-disorder ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- jar: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] --- javadoc: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-assembly-plugin:jar:3.7.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:3.7.1: Plugin org.apache.maven.plugins:maven-assembly-plugin:3.7.1 or one of its dependencies could not be resolved:
Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:3.7.1 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:3.0.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:3.0.1: Plugin org.apache.maven.plugins:maven-release-plugin:3.0.1 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:3.0.1 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] --- resources:3.3.1:resources (default-resources) @ biojava-aa-prop ---
[INFO] Copying 11 resources from src/main/resources to target/classes
[INFO]
[INFO] --- compiler: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] --- resources:3.3.1:testResources (default-testResources) @ biojava-aa-prop ---
[INFO] Copying 7 resources from src/test/resources to target/test-classes
[INFO]
[INFO] --- compiler: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] --- surefire:2.22.3:test (default-test) @ biojava-aa-prop ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- jar: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] --- javadoc: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-assembly-plugin:jar:3.7.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:3.7.1: Plugin org.apache.maven.plugins:maven-assembly-plugin:3.7.1 or one of its dependencies could not be resolved:
Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:3.7.1 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:3.0.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:3.0.1: Plugin org.apache.maven.plugins:maven-release-plugin:3.0.1 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:3.0.1 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] --- resources:3.3.1:resources (default-resources) @ biojava-survival ---
[INFO] Copying 1 resource from src/main/resources to target/classes
[INFO]
[INFO] --- compiler: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] --- resources: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] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-survival ---
[INFO] No sources to compile
[INFO]
[INFO] --- surefire:2.22.3:test (default-test) @ biojava-survival ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- jar: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] --- javadoc: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-assembly-plugin:jar:3.7.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:3.7.1: Plugin org.apache.maven.plugins:maven-assembly-plugin:3.7.1 or one of its dependencies could not be resolved:
Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:3.7.1 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:3.0.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:3.0.1: Plugin org.apache.maven.plugins:maven-release-plugin:3.0.1 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:3.0.1 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] --- resources:3.3.1:resources (default-resources) @ biojava-ontology ---
[INFO] Copying 3 resources from src/main/resources to target/classes
[INFO]
[INFO] --- compiler: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] --- resources:3.3.1:testResources (default-testResources) @ biojava-ontology ---
[INFO] Copying 6 resources from src/test/resources to target/test-classes
[INFO]
[INFO] --- compiler: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] --- surefire:2.22.3:test (default-test) @ biojava-ontology ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- jar: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] --- javadoc: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-assembly-plugin:jar:3.7.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:3.7.1: Plugin org.apache.maven.plugins:maven-assembly-plugin:3.7.1 or one of its dependencies could not be resolved:
Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:3.7.1 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:3.0.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:3.0.1: Plugin org.apache.maven.plugins:maven-release-plugin:3.0.1 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:3.0.1 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] --- resources: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] --- compiler: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] --- resources: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] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-protein-comparison-tool ---
[INFO] No sources to compile
[INFO]
[INFO] --- surefire:2.22.3:test (default-test) @ biojava-protein-comparison-tool ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- jar: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] --- javadoc: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-assembly-plugin:jar:3.7.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:3.7.1: Plugin org.apache.maven.plugins:maven-assembly-plugin:3.7.1 or one of its dependencies could not be resolved:
Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:3.7.1 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:3.0.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:3.0.1: Plugin org.apache.maven.plugins:maven-release-plugin:3.0.1 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:3.0.1 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] >>> javadoc:3.10.1:aggregate (default-cli) > compile @ biojava >>>
[INFO]
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO] Forking biojava-core 6.1.0
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO]
[INFO] --- resources:3.3.1:resources (default-resources) @ biojava-core ---
[INFO] Copying 24 resources from src/main/resources to target/classes
[INFO]
[INFO] --- compiler: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] --- resources: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] --- compiler: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] --- resources:3.3.1:resources (default-resources) @ biojava-alignment ---
[INFO] Copying 2 resources from src/main/resources to target/classes
[INFO]
[INFO] --- compiler: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] --- resources: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] --- compiler: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]
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO] Forking biojava-jcolorbrewer 6.1.0
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO]
[INFO] --- resources: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] --- compiler: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] --- resources:3.3.1:resources (default-resources) @ biojava-structure-gui ---
[INFO] Copying 49 resources from src/main/resources to target/classes
[INFO]
[INFO] --- compiler: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]
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[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO]
[INFO] --- resources:3.3.1:resources (default-resources) @ biojava-genome ---
[INFO] Copying 1 resource from src/main/resources to target/classes
[INFO]
[INFO] --- compiler: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]
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[INFO] Forking biojava-modfinder 6.1.0
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO]
[INFO] --- resources:3.3.1:resources (default-resources) @ biojava-modfinder ---
[INFO] Copying 2 resources from src/main/resources to target/classes
[INFO]
[INFO] --- compiler: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] --- resources: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] --- compiler: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] --- resources:3.3.1:resources (default-resources) @ biojava-protein-disorder ---
[INFO] Copying 11 resources from src/main/resources to target/classes
[INFO]
[INFO] --- compiler: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] --- resources:3.3.1:resources (default-resources) @ biojava-aa-prop ---
[INFO] Copying 11 resources from src/main/resources to target/classes
[INFO]
[INFO] --- compiler: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]
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[INFO] Forking biojava-survival 6.1.0
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO]
[INFO] --- resources:3.3.1:resources (default-resources) @ biojava-survival ---
[INFO] Copying 1 resource from src/main/resources to target/classes
[INFO]
[INFO] --- compiler: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]
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[INFO] Forking biojava-ontology 6.1.0
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[INFO]
[INFO] --- resources:3.3.1:resources (default-resources) @ biojava-ontology ---
[INFO] Copying 3 resources from src/main/resources to target/classes
[INFO]
[INFO] --- compiler: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]
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[INFO] Forking biojava-protein-comparison-tool 6.1.0
[INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[INFO]
[INFO] --- resources: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] --- compiler: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] <<< javadoc: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] --- javadoc: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 [ 16.804 s]
[INFO] biojava-core ....................................... SUCCESS [ 11.324 s]
[INFO] biojava-forester ................................... SUCCESS [ 9.798 s]
[INFO] biojava-alignment .................................. SUCCESS [ 3.449 s]
[INFO] biojava-structure .................................. SUCCESS [ 10.222 s]
[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 1.918 s]
[INFO] biojava-structure-gui .............................. SUCCESS [ 4.972 s]
[INFO] biojava-genome ..................................... SUCCESS [ 2.880 s]
[INFO] biojava-modfinder .................................. SUCCESS [ 2.350 s]
[INFO] biojava-ws ......................................... SUCCESS [ 1.912 s]
[INFO] biojava-protein-disorder ........................... SUCCESS [ 1.783 s]
[INFO] biojava-aa-prop .................................... SUCCESS [ 2.663 s]
[INFO] biojava-survival ................................... SUCCESS [ 3.034 s]
[INFO] biojava-ontology ................................... SUCCESS [ 2.511 s]
[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 1.271 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 01:17 min
[INFO] Finished at: 2026-03-24T08:47:53-12:00
[INFO] ------------------------------------------------------------------------
make[1]: Leaving directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg'
dh_auto_test
/usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/biojava6-live-6.1.0\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf -Dproperties.file.manual=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven.properties org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven-repo --batch-mode test
OpenJDK 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] --- resources:3.3.1:resources (default-resources) @ biojava-core ---
[INFO] Copying 24 resources from src/main/resources to target/classes
[INFO]
[INFO] --- compiler:3.13.0:compile (default-compile) @ biojava-core ---
[INFO] Nothing to compile - all classes are up to date.
[INFO]
[INFO] --- resources:3.3.1:testResources (default-testResources) @ biojava-core ---
[INFO] Copying 48 resources from src/test/resources to target/test-classes
[INFO]
[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-core ---
[INFO] Nothing to compile - all classes are up to date.
[INFO]
[INFO] --- surefire: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.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: 0.015 s - in org.biojava.nbio.core.sequence.EditSequenceTest
[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: 0.162 s - in org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest
[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: 0.297 s - in org.biojava.nbio.core.sequence.TranslationTest
[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: 0.051 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: 0.02 s - in org.biojava.nbio.core.sequence.SequenceViewTest
[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: 0.019 s - in org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest
[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: 0.079 s - in org.biojava.nbio.core.sequence.io.FastaReaderTest
[INFO] Running org.biojava.nbio.core.sequence.io.FastaWriterTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojava.nbio.core.sequence.io.FastaWriterTest
[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: 0.38 s - in org.biojava.nbio.core.sequence.io.ABITracerTest
[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: 0.065 s - in org.biojava.nbio.core.sequence.io.GenbankCookbookTest
[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: 0.06 s - in org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest
[INFO] Running org.biojava.nbio.core.sequence.io.GenbankWriterTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.114 s - in org.biojava.nbio.core.sequence.io.GenbankWriterTest
[INFO] Running org.biojava.nbio.core.sequence.io.embl.EmblReaderTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojava.nbio.core.sequence.io.embl.EmblReaderTest
[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: 0.061 s - in org.biojava.nbio.core.sequence.io.FastaGeneWriterTest
[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: 0.09 s - in org.biojava.nbio.core.sequence.io.GenbankReaderTest
[INFO] Running org.biojava.nbio.core.sequence.location.LocationParserTest
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.009 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: 0.148 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: 0.028 s - in 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] Running org.biojava.nbio.core.sequence.location.TargetedLocationParserTest
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojava.nbio.core.sequence.location.TargetedLocationParserTest
[INFO] Running org.biojava.nbio.core.sequence.TaxonomyIDTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 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: 0.064 s - in org.biojava.nbio.core.sequence.StrandTest
[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: 0.021 s - in org.biojava.nbio.core.sequence.views.WindowViewTests
[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: 0.08 s - in org.biojava.nbio.core.sequence.RNASequenceTest
[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: 0.025 s - in org.biojava.nbio.core.sequence.JoiningSequenceReaderTest
[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: 0.019 s - in org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest
[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: 0.146 s - in org.biojava.nbio.core.sequence.ChromosomeSequenceTest
[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: 0.055 s - in org.biojava.nbio.core.sequence.ExonSequenceTest
[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: 0.02 s - in org.biojava.nbio.core.sequence.TestSequenceEquals
[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: 0.079 s - in 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.
[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: 0.249 s - in org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest
[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: 0.08 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: 0.049 s - in org.biojava.nbio.core.sequence.ProteinSequenceTest
[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: 0.101 s - in org.biojava.nbio.core.sequence.TranscriptSequenceTest
[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: 0.041 s - in org.biojava.nbio.core.search.io.HspTest
[INFO] Running org.biojava.nbio.core.search.io.blast.BlastTabularParserTest
createObjects
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
getFileExtensions
setFile
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.609 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: 0.019 s - in org.biojava.nbio.core.search.io.blast.BlastXMLParserTest
[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: 0.038 s - in org.biojava.nbio.core.search.io.SearchIOTest
[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: 0.077 s - in org.biojava.nbio.core.TestAmbiguityCompoundSet
[INFO] Running org.biojava.nbio.core.util.EqualsTest
[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.065 s - in org.biojava.nbio.core.util.EqualsTest
[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: 0.16 s - in org.biojava.nbio.core.util.StringManipulationHelperTest
[INFO] Running org.biojava.nbio.core.util.CRC64ChecksumTest
[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 s - in org.biojava.nbio.core.util.CRC64ChecksumTest
[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: 0.42 s - in org.biojava.nbio.core.util.SequenceToolsTest
[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: 0.061 s - in org.biojava.nbio.core.util.PrettyXMLWriterTest
[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: 0.15 s - in org.biojava.nbio.core.util.FlatFileCacheTest
[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: 0.017 s - in org.biojava.nbio.core.util.TestUncompressInputStream
[INFO] Running org.biojava.nbio.core.util.SingleLinkageClustererTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s - in org.biojava.nbio.core.util.SingleLinkageClustererTest
[INFO] Running org.biojava.nbio.core.util.HashcoderTest
[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.109 s - in org.biojava.nbio.core.util.HashcoderTest
[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: 0.269 s - in org.biojava.nbio.core.util.FileDownloadUtilsTest
[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: 0.196 s - in org.biojava.nbio.core.util.XMLHelperTest
[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: 0.049 s - in org.biojava.nbio.core.util.SoftHashMapTest
[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: 0.03 s - in org.biojava.nbio.core.fasta.TestFASTAReader
[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: 0.043 s - in org.biojava.nbio.core.alignment.SimpleSequencePairTest
[INFO] Running org.biojava.nbio.core.alignment.SimpleProfileTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.086 s - in org.biojava.nbio.core.alignment.SimpleProfileTest
[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: 0.038 s - in org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest
[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: 0.08 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: 0.149 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: 0.147 s - in org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest
[INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.185 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest
[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] --- resources: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] --- compiler:3.13.0:compile (default-compile) @ biojava-forester ---
[INFO] Nothing to compile - all classes are up to date.
[INFO]
[INFO] --- resources: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] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-forester ---
[INFO] No sources to compile
[INFO]
[INFO] --- surefire: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] --- resources:3.3.1:resources (default-resources) @ biojava-alignment ---
[INFO] Copying 2 resources from src/main/resources to target/classes
[INFO]
[INFO] --- compiler:3.13.0:compile (default-compile) @ biojava-alignment ---
[INFO] Nothing to compile - all classes are up to date.
[INFO]
[INFO] --- resources:3.3.1:testResources (default-testResources) @ biojava-alignment ---
[INFO] Copying 11 resources from src/test/resources to target/test-classes
[INFO]
[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-alignment ---
[INFO] Nothing to compile - all classes are up to date.
[INFO]
[INFO] --- surefire:2.22.3:test (default-test) @ biojava-alignment ---
[INFO]
[INFO] -------------------------------------------------------
[INFO] T E S T S
[INFO] -------------------------------------------------------
[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: 0.077 s - in org.biojava.nbio.phylo.TestDistanceTreeEvaluator
[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: 0.074 s - in org.biojava.nbio.phylo.TestForesterWrapper
[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: 0.166 s - in org.biojava.nbio.alignment.FractionalIdentityScorerTest
[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: 0.094 s - in org.biojava.nbio.alignment.LocalAlignmentTest
[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: 0.084 s - in org.biojava.nbio.alignment.FractionalSimilarityScorerTest
[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: 0.11 s - in org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest
[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: 0.104 s - in org.biojava.nbio.alignment.io.TestStockholmParser
[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: 0.208 s - in org.biojava.nbio.alignment.NeedlemanWunschTest
[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: 0.112 s - in org.biojava.nbio.alignment.SmithWatermanTest
[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: 1.295 s - in org.biojava.nbio.alignment.TestDNAAlignment
[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: 0.087 s - in org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest
[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: 0.087 s - in org.biojava.nbio.alignment.SimpleProfilePairTest
[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: 0.137 s - in org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading
[INFO] Running org.biojava.nbio.alignment.routines.AlignerHelperTest
[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.biojava.nbio.alignment.routines.AlignerHelperTest
[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: 0.1 s - in org.biojava.nbio.alignment.routines.GuanUberbacherTest
[INFO] Running org.biojava.nbio.alignment.SimpleGapPenaltyTest
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 s - in org.biojava.nbio.alignment.SimpleGapPenaltyTest
[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: 0.12 s - in org.biojava.nbio.alignment.GuideTreeTest
[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: 0.134 s - in org.biojava.nbio.alignment.TestSubOptimalMSA
[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] --- resources: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] --- compiler:3.13.0:compile (default-compile) @ biojava-structure ---
[INFO] Nothing to compile - all classes are up to date.
[INFO]
[INFO] --- resources:3.3.1:testResources (default-testResources) @ biojava-structure ---
[INFO] Copying 55 resources from src/test/resources to target/test-classes
[INFO]
[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-structure ---
[INFO] Nothing to compile - all classes are up to date.
[INFO]
[INFO] --- surefire:2.22.3:test (default-test) @ biojava-structure ---
[INFO]
[INFO] -------------------------------------------------------
[INFO] T E S T S
[INFO] -------------------------------------------------------
[INFO] Running org.biojava.nbio.structure.TestCloning
[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestCloning
[INFO] Running org.biojava.nbio.structure.secstruc.TestDSSPParser
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 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: 0.007 s - in org.biojava.nbio.structure.secstruc.TestSecStrucCalc
[INFO] Running org.biojava.nbio.structure.TestLoadStructureFromURL
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.TestLoadStructureFromURL
[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: 0.879 s - in org.biojava.nbio.structure.Test4hhb
[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: 1.004 s - in org.biojava.nbio.structure.TestURLIdentifier
[INFO] Running org.biojava.nbio.structure.ResidueNumberTest
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojava.nbio.structure.ResidueNumberTest
[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: 1.161 s - in org.biojava.nbio.structure.TestStructureSerialization
[INFO] Running org.biojava.nbio.structure.TestParsingCalcium
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestParsingCalcium
[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: 0.063 s - in org.biojava.nbio.structure.TestCalc
[INFO] Running org.biojava.nbio.structure.TestChargeAdder
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.006 s - in org.biojava.nbio.structure.TestChargeAdder
[INFO] Running org.biojava.nbio.structure.ElementTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.nbio.structure.ElementTest
[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: 1.566 s - in org.biojava.nbio.structure.TestEntityHeuristics
[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: 0.133 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: 0.007 s - in org.biojava.nbio.structure.cluster.TestSubunitExtractor
[INFO] Running org.biojava.nbio.structure.AtomPositionMapTest
[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.007 s - in org.biojava.nbio.structure.AtomPositionMapTest
[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: 0.694 s - in org.biojava.nbio.structure.geometry.TestSuperPosition
[INFO] Running org.biojava.nbio.structure.geometry.TestUnitQuaternions
[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.014 s - in org.biojava.nbio.structure.geometry.TestUnitQuaternions
[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: 0.03 s - in org.biojava.nbio.structure.geometry.TestSuperPositionQCP
[INFO] Running org.biojava.nbio.structure.TestAtomIterator
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestAtomIterator
[INFO] Running org.biojava.nbio.structure.io.FastaAFPChainConverterTest
[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.013 s - in org.biojava.nbio.structure.io.FastaAFPChainConverterTest
[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: 1.348 s - in org.biojava.nbio.structure.io.TestDifficultMmCIFFiles
[INFO] Running org.biojava.nbio.structure.io.TestSiftsParsing
[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.015 s - in org.biojava.nbio.structure.io.TestSiftsParsing
[INFO] Running org.biojava.nbio.structure.io.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: 2.37 s - in org.biojava.nbio.structure.io.TestNonDepositedFiles
[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFLigands
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.015 s - in org.biojava.nbio.structure.io.TestParseMmCIFLigands
[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: 0.99 s - in org.biojava.nbio.structure.io.TestHeaderOnly
[INFO] Running org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.701 s - in org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest
[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: 0.097 s - in org.biojava.nbio.structure.io.TestDBRefParsing
[INFO] Running org.biojava.nbio.structure.io.TestQuaternaryStructureProviders
[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.008 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: 0.007 s - in org.biojava.nbio.structure.io.TestMMcifOrganismParsing
[INFO] Running org.biojava.nbio.structure.io.StructureSequenceMatcherTest
[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.StructureSequenceMatcherTest
[INFO] Running org.biojava.nbio.structure.io.TestParseOnAsymId
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.TestParseOnAsymId
[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: 0.346 s - in org.biojava.nbio.structure.io.mmcif.TestChemCompProvider
[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: 1.573 s - in org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader
[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: 0.866 s - in org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes
[INFO] Running org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType
[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId
[INFO] Running org.biojava.nbio.structure.io.TestHardBioUnits
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.TestHardBioUnits
[INFO] Running org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB
[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: 1.007 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader
[INFO] Running org.biojava.nbio.structure.io.mmtf.TestBondFinding
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.mmtf.TestBondFinding
[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: 0.073 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: 0.007 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip
[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: 1.06 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter
[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance
[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: 0.117 s - in org.biojava.nbio.structure.io.TestMMCIFWriting
[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: 0.14 s - in org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest
[INFO] Running org.biojava.nbio.structure.io.TestURLBasedFileParsing
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.015 s - in org.biojava.nbio.structure.io.TestURLBasedFileParsing
[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFFeatures
[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.012 s - in org.biojava.nbio.structure.io.TestParseMmCIFFeatures
[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: 0.744 s - in org.biojava.nbio.structure.io.TestShortLines
[INFO] Running org.biojava.nbio.structure.io.TestTitleParsing
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.TestTitleParsing
[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: 0.057 s - in org.biojava.nbio.structure.TestPdbId
[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: 0.135 s - in org.biojava.nbio.structure.ResidueRangeTest
[INFO] Running org.biojava.nbio.structure.TestBond
[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 15, Time elapsed: 0.009 s - in org.biojava.nbio.structure.TestBond
[INFO] Running org.biojava.nbio.structure.redmine.Test1DARSeqAlign
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.redmine.Test1DARSeqAlign
[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: 0.034 s - in org.biojava.nbio.structure.SiteTest
[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: 0.793 s - in org.biojava.nbio.structure.PdbFileFormat30Test
[INFO] Running org.biojava.nbio.structure.basepairs.TestBasePairParameters
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.basepairs.TestBasePairParameters
[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: 0.034 s - in org.biojava.nbio.structure.align.client.TestStructureName
[INFO] Running org.biojava.nbio.structure.align.TestAlignmentConsistency
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.align.TestAlignmentConsistency
[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: 0.046 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: 0.006 s - in org.biojava.nbio.structure.align.ce.TestSmallAlignment
[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: 0.023 s - in org.biojava.nbio.structure.align.util.RotationAxisTest
[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: 0.072 s - in org.biojava.nbio.structure.align.util.AtomCacheTest
[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: 0.032 s - in org.biojava.nbio.structure.align.multiple.TestAFPChainConversion
[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: 0.048 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer
[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.009 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser
[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter
[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.022 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter
[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools
[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: 0.051 s - in org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools
[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.018 s - in org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector
[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: 0.048 s - in org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner
[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestCeSymm
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.018 s - in org.biojava.nbio.structure.symmetry.internal.TestCeSymm
[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes
[INFO] Running org.biojava.nbio.structure.TestExperimentalTechniques
[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.017 s - in org.biojava.nbio.structure.TestExperimentalTechniques
[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: 0.149 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: 0.019 s - in org.biojava.nbio.structure.contact.TestContactCalc
[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: 0.773 s - in org.biojava.nbio.structure.TestAltLocs
[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: 0.065 s - in org.biojava.nbio.structure.asa.TestAsaCalc
[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: 0.082 s - in org.biojava.nbio.structure.TestVeryLongFileName
[INFO] Running org.biojava.nbio.structure.TestDNAAlignment
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.018 s - in org.biojava.nbio.structure.TestDNAAlignment
[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: 0.445 s - in org.biojava.nbio.structure.ChemCompTest
[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: 0.1 s - in org.biojava.nbio.structure.TestStructureImpl
[INFO] Running org.biojava.nbio.structure.TestStructureCrossReferences
[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.017 s - in org.biojava.nbio.structure.TestStructureCrossReferences
[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: 0.633 s - in org.biojava.nbio.structure.TestAtomCache
[INFO] Running org.biojava.nbio.structure.PDBStatusTest
[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.023 s - in org.biojava.nbio.structure.PDBStatusTest
[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: 1.865 s - in org.biojava.nbio.structure.SourceCompoundTest
[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.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: 0.081 s - in org.biojava.nbio.structure.HetatomImplTest
[INFO] Running org.biojava.nbio.structure.TestNucleotides
[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.011 s - in org.biojava.nbio.structure.TestNucleotides
[INFO] Running org.biojava.nbio.structure.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: 1.398 s - in org.biojava.nbio.structure.TestKeywords
[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalInfo
[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.009 s - in org.biojava.nbio.structure.xtal.TestCrystalInfo
[INFO] Running org.biojava.nbio.structure.xtal.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: 3.744 s - in org.biojava.nbio.structure.xtal.TestInterfaceClustering
[INFO] Running org.biojava.nbio.structure.xtal.TestSpaceGroup
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.744 s - in org.biojava.nbio.structure.xtal.TestSpaceGroup
[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalCell
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 s - in org.biojava.nbio.structure.xtal.TestCrystalCell
[INFO] Running org.biojava.nbio.structure.Test2JA5
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.016 s - in org.biojava.nbio.structure.Test2JA5
[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: 0.54 s - in org.biojava.nbio.structure.chem.TestDownloadChemCompProvider
[INFO] Running org.biojava.nbio.structure.TestEntityResIndexMapping
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.797 s - in org.biojava.nbio.structure.TestEntityResIndexMapping
[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] --- resources: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] --- compiler:3.13.0:compile (default-compile) @ biojava-jcolorbrewer ---
[INFO] Nothing to compile - all classes are up to date.
[INFO]
[INFO] --- resources: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] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-jcolorbrewer ---
[INFO] No sources to compile
[INFO]
[INFO] --- surefire: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] --- resources:3.3.1:resources (default-resources) @ biojava-structure-gui ---
[INFO] Copying 49 resources from src/main/resources to target/classes
[INFO]
[INFO] --- compiler:3.13.0:compile (default-compile) @ biojava-structure-gui ---
[INFO] Nothing to compile - all classes are up to date.
[INFO]
[INFO] --- resources: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] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-structure-gui ---
[INFO] Nothing to compile - all classes are up to date.
[INFO]
[INFO] --- surefire:2.22.3:test (default-test) @ biojava-structure-gui ---
[INFO]
[INFO] -------------------------------------------------------
[INFO] T E S T S
[INFO] -------------------------------------------------------
[INFO] Running org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.12 s - in org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator
[INFO] Running org.biojava.nbio.structure.gui.JmolViewerImplTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 s - in org.biojava.nbio.structure.gui.JmolViewerImplTest
[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: 0.117 s - in org.biojava.nbio.structure.gui.TestAtomInfo
[INFO] Running org.biojava.nbio.structure.gui.ViewerTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.106 s - in org.biojava.nbio.structure.gui.ViewerTest
[INFO] Running org.biojava.nbio.structure.gui.StructureViewerTest
[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.091 s - in org.biojava.nbio.structure.gui.StructureViewerTest
[INFO] Running org.biojava.nbio.structure.gui.RenderStyleTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.119 s - in org.biojava.nbio.structure.gui.RenderStyleTest
[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] --- resources:3.3.1:resources (default-resources) @ biojava-genome ---
[INFO] Copying 1 resource from src/main/resources to target/classes
[INFO]
[INFO] --- compiler:3.13.0:compile (default-compile) @ biojava-genome ---
[INFO] Nothing to compile - all classes are up to date.
[INFO]
[INFO] --- resources:3.3.1:testResources (default-testResources) @ biojava-genome ---
[INFO] Copying 83 resources from src/test/resources to target/test-classes
[INFO]
[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-genome ---
[INFO] Nothing to compile - all classes are up to date.
[INFO]
[INFO] --- surefire:2.22.3:test (default-test) @ biojava-genome ---
[INFO]
[INFO] -------------------------------------------------------
[INFO] T E S T S
[INFO] -------------------------------------------------------
[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: 0.12 s - in org.biojava.nbio.genome.TestChromosomeMappingTools
[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest
[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.269 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest
[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: 0.19 s - in org.biojava.nbio.genome.io.fastq.FastqToolsTest
[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest
[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.286 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest
[INFO] Running org.biojava.nbio.genome.io.fastq.FastqBuilderTest
[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.126 s - in org.biojava.nbio.genome.io.fastq.FastqBuilderTest
[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest
[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.161 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest
[INFO] Running org.biojava.nbio.genome.io.fastq.ConvertTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.231 s - in org.biojava.nbio.genome.io.fastq.ConvertTest
[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest
[INFO] Tests run: 29, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.268 s - in org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest
[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest
[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.161 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: 0.11 s - in org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest
[INFO] Running org.biojava.nbio.genome.io.fastq.FastqTest
[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.125 s - in org.biojava.nbio.genome.io.fastq.FastqTest
[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest
[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.157 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: 0.114 s - in org.biojava.nbio.genome.io.fastq.FastqVariantTest
[INFO] Running org.biojava.nbio.genome.TestGenomeMapping
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.078 s - in org.biojava.nbio.genome.TestGenomeMapping
[INFO] Running org.biojava.nbio.genome.FeatureListTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.112 s - in org.biojava.nbio.genome.FeatureListTest
[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: 1.118 s - in org.biojava.nbio.genome.GeneFeatureHelperTest
[INFO] Running org.biojava.nbio.genome.TestIssue355
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.096 s - in org.biojava.nbio.genome.TestIssue355
[INFO] Running org.biojava.nbio.genome.TestLocation
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.108 s - in org.biojava.nbio.genome.TestLocation
[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] --- resources:3.3.1:resources (default-resources) @ biojava-modfinder ---
[INFO] Copying 2 resources from src/main/resources to target/classes
[INFO]
[INFO] --- compiler:3.13.0:compile (default-compile) @ biojava-modfinder ---
[INFO] Nothing to compile - all classes are up to date.
[INFO]
[INFO] --- resources:3.3.1:testResources (default-testResources) @ biojava-modfinder ---
[INFO] Copying 2 resources from src/test/resources to target/test-classes
[INFO]
[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-modfinder ---
[INFO] Nothing to compile - all classes are up to date.
[INFO]
[INFO] --- surefire: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: 0.365 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: 0.406 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: 0.119 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: 0.094 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] --- resources: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] --- compiler:3.13.0:compile (default-compile) @ biojava-ws ---
[INFO] Nothing to compile - all classes are up to date.
[INFO]
[INFO] --- resources: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] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-ws ---
[INFO] Nothing to compile - all classes are up to date.
[INFO]
[INFO] --- surefire: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: 0.091 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] --- resources:3.3.1:resources (default-resources) @ biojava-protein-disorder ---
[INFO] Copying 11 resources from src/main/resources to target/classes
[INFO]
[INFO] --- compiler:3.13.0:compile (default-compile) @ biojava-protein-disorder ---
[INFO] Nothing to compile - all classes are up to date.
[INFO]
[INFO] --- resources:3.3.1:testResources (default-testResources) @ biojava-protein-disorder ---
[INFO] Copying 2 resources from src/test/resources to target/test-classes
[INFO]
[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-protein-disorder ---
[INFO] Nothing to compile - all classes are up to date.
[INFO]
[INFO] --- surefire: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: 6.095 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: 2.791 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] --- resources:3.3.1:resources (default-resources) @ biojava-aa-prop ---
[INFO] Copying 11 resources from src/main/resources to target/classes
[INFO]
[INFO] --- compiler:3.13.0:compile (default-compile) @ biojava-aa-prop ---
[INFO] Nothing to compile - all classes are up to date.
[INFO]
[INFO] --- resources:3.3.1:testResources (default-testResources) @ biojava-aa-prop ---
[INFO] Copying 7 resources from src/test/resources to target/test-classes
[INFO]
[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-aa-prop ---
[INFO] Nothing to compile - all classes are up to date.
[INFO]
[INFO] --- surefire:2.22.3:test (default-test) @ biojava-aa-prop ---
[INFO]
[INFO] -------------------------------------------------------
[INFO] T E S T S
[INFO] -------------------------------------------------------
[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: 0.872 s - in org.biojava.nbio.aaproperties.PeptidePropertiesImplTest
[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: 0.727 s - in org.biojava.nbio.aaproperties.CookBookTest
[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: 0.771 s - in org.biojava.nbio.aaproperties.GenbankCommandPromptTest
[INFO] Running org.biojava.nbio.aaproperties.CommandPromptTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint
SAOV_0114,53660.5723,41370.0,41370.0,4.986
SAOV_0094,45884.0164,57760.0,57760.0,8.5193
SAA6008_00126,95002.026,55240.0,55740.0,5.7263
SequenceName,A,N,MolecularWeight
SAOV_0114,0.101,0.0525,53660.5723
SAOV_0094,0.0537,0.0767,45884.0164
SAA6008_00126,0.0955,0.0414,95002.026
SequenceName,A,N,MolecularWeight
SAOV_0114,0.101,0.0525,53660.5723
SAOV_0094,0.0537,0.0767,45884.0164
SAA6008_00126,0.0955,0.0414,95002.026
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.756 s - in org.biojava.nbio.aaproperties.CommandPromptTest
[INFO] Running org.biojava.nbio.aaproperties.xml.AminoAcidTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.793 s - in org.biojava.nbio.aaproperties.xml.AminoAcidTest
[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: 0.788 s - in org.biojava.nbio.aaproperties.xml.ElementTest
[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: 0.085 s - in org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest
[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: 0.113 s - in org.biojava.nbio.aaproperties.profeat.CookBookTest
[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] --- resources:3.3.1:resources (default-resources) @ biojava-survival ---
[INFO] Copying 1 resource from src/main/resources to target/classes
[INFO]
[INFO] --- compiler:3.13.0:compile (default-compile) @ biojava-survival ---
[INFO] Nothing to compile - all classes are up to date.
[INFO]
[INFO] --- resources: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] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-survival ---
[INFO] No sources to compile
[INFO]
[INFO] --- surefire: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] --- resources:3.3.1:resources (default-resources) @ biojava-ontology ---
[INFO] Copying 3 resources from src/main/resources to target/classes
[INFO]
[INFO] --- compiler:3.13.0:compile (default-compile) @ biojava-ontology ---
[INFO] Nothing to compile - all classes are up to date.
[INFO]
[INFO] --- resources:3.3.1:testResources (default-testResources) @ biojava-ontology ---
[INFO] Copying 6 resources from src/test/resources to target/test-classes
[INFO]
[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-ontology ---
[INFO] Nothing to compile - all classes are up to date.
[INFO]
[INFO] --- surefire:2.22.3:test (default-test) @ biojava-ontology ---
[INFO]
[INFO] -------------------------------------------------------
[INFO] T E S T S
[INFO] -------------------------------------------------------
[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: 0.273 s - in org.biojava.nbio.ontology.TestParseSBO
[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: 0.185 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: 0.379 s - in org.biojava.nbio.ontology.TestOboFileParsing
[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] --- resources: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] --- compiler:3.13.0:compile (default-compile) @ biojava-protein-comparison-tool ---
[INFO] Nothing to compile - all classes are up to date.
[INFO]
[INFO] --- resources: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] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-protein-comparison-tool ---
[INFO] No sources to compile
[INFO]
[INFO] --- surefire: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 [ 0.002 s]
[INFO] biojava-core ....................................... SUCCESS [30:27 min]
[INFO] biojava-forester ................................... SUCCESS [ 0.045 s]
[INFO] biojava-alignment .................................. SUCCESS [09:13 min]
[INFO] biojava-structure .................................. SUCCESS [51:16 min]
[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.050 s]
[INFO] biojava-structure-gui .............................. SUCCESS [03:05 min]
[INFO] biojava-genome ..................................... SUCCESS [09:17 min]
[INFO] biojava-modfinder .................................. SUCCESS [02:04 min]
[INFO] biojava-ws ......................................... SUCCESS [ 30.873 s]
[INFO] biojava-protein-disorder ........................... SUCCESS [01:10 min]
[INFO] biojava-aa-prop .................................... SUCCESS [04:11 min]
[INFO] biojava-survival ................................... SUCCESS [ 0.031 s]
[INFO] biojava-ontology ................................... SUCCESS [01:32 min]
[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 0.081 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 01:52 h
[INFO] Finished at: 2026-03-24T10:40:44-12:00
[INFO] ------------------------------------------------------------------------
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install
/usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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 [ 0.567 s]
[INFO] biojava-core ....................................... SUCCESS [ 0.069 s]
[INFO] biojava-forester ................................... SUCCESS [ 0.055 s]
[INFO] biojava-alignment .................................. SUCCESS [ 0.043 s]
[INFO] biojava-structure .................................. SUCCESS [ 0.049 s]
[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.048 s]
[INFO] biojava-structure-gui .............................. SUCCESS [ 0.044 s]
[INFO] biojava-genome ..................................... SUCCESS [ 0.048 s]
[INFO] biojava-modfinder .................................. SUCCESS [ 0.040 s]
[INFO] biojava-ws ......................................... SUCCESS [ 0.048 s]
[INFO] biojava-protein-disorder ........................... SUCCESS [ 0.040 s]
[INFO] biojava-aa-prop .................................... SUCCESS [ 0.048 s]
[INFO] biojava-survival ................................... SUCCESS [ 0.043 s]
[INFO] biojava-ontology ................................... SUCCESS [ 0.041 s]
[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 0.042 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1.615 s
[INFO] Finished at: 2026-03-24T10:40:48-12:00
[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 "version|V" 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 "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"
Duplicate specification "V:s" for option "V"
Duplicate specification "V:s" for option "V"
Duplicate specification "version|V" 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_amd64.buildinfo
dpkg-genchanges --build=binary -O../biojava6-live_6.1.0+dfsg-5_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/309805 and its subdirectories
I: Current time: Tue Mar 24 10:46:40 -12 2026
I: pbuilder-time-stamp: 1774392400
Wed Feb 19 16:23:42 UTC 2025 I: 1st build successful. Starting 2nd build on remote node infom01-amd64.debian.net.
Wed Feb 19 16:23:42 UTC 2025 I: Preparing to do remote build '2' on infom01-amd64.debian.net.
Wed Feb 19 18:29:32 UTC 2025 I: Deleting $TMPDIR on infom01-amd64.debian.net.
Wed Feb 19 18:29:33 UTC 2025 I: biojava6-live_6.1.0+dfsg-5_amd64.changes:
Format: 1.8
Date: Thu, 31 Oct 2024 08:16:17 +0100
Source: biojava6-live
Binary: libbiojava6-java libbiojava6-java-doc
Architecture: all
Version: 6.1.0+dfsg-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Pierre Gruet <pgt@debian.org>
Description:
libbiojava6-java - Java API to biological data and applications (version 6)
libbiojava6-java-doc - [Biology] Documentation for BioJava 6
Closes: 1078612
Changes:
biojava6-live (6.1.0+dfsg-5) unstable; urgency=medium
.
* Raising Standards version to 4.7.0, no change
* Skipping test depending on certificate with foreseeable expiration
(Closes: #1078612)
* Updating the path to the javadoc files to install
Checksums-Sha1:
4e45d7b5a1e177788a643c256e7c4089f9431bca 18301 biojava6-live_6.1.0+dfsg-5_amd64.buildinfo
f05f60f595c85d8d9245671625930fd84feb0e7a 2255644 libbiojava6-java-doc_6.1.0+dfsg-5_all.deb
9b667bcf78994da3765dfb2662f6b2068868890b 5358880 libbiojava6-java_6.1.0+dfsg-5_all.deb
Checksums-Sha256:
d5c8555c3d07adbdeaa53f2797a98ed1cebfc46213799f77a94f4c930a8f7bfd 18301 biojava6-live_6.1.0+dfsg-5_amd64.buildinfo
81ceab010837e514646c214097990f3439636e7861b72b4449805b852a2a955b 2255644 libbiojava6-java-doc_6.1.0+dfsg-5_all.deb
baad814e3033837fed267b7914c38dcfc2afe5ceba72602c5f844b6ce21562b8 5358880 libbiojava6-java_6.1.0+dfsg-5_all.deb
Files:
07598f5916661960164eca0440425650 18301 java optional biojava6-live_6.1.0+dfsg-5_amd64.buildinfo
cab4ed4f0eeb9b596d67d8386ea22e2e 2255644 doc optional libbiojava6-java-doc_6.1.0+dfsg-5_all.deb
2d7b2ea2f66571699ab432473af01f78 5358880 java optional libbiojava6-java_6.1.0+dfsg-5_all.deb
Wed Feb 19 18:29:34 UTC 2025 I: diffoscope 288 will be used to compare the two builds:
Running as unit: rb-diffoscope-amd64_38-47560.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.MtIEMJB1/biojava6-live_6.1.0+dfsg-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.MtIEMJB1/biojava6-live_6.1.0+dfsg-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.MtIEMJB1/biojava6-live_6.1.0+dfsg-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.MtIEMJB1/b1/biojava6-live_6.1.0+dfsg-5_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.MtIEMJB1/b2/biojava6-live_6.1.0+dfsg-5_amd64.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call diffoscope.comparators.binary.FilesystemFile
## main (total time: 0.004s)
0.004s 2 calls outputs
0.000s 1 call cleanup
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 238ms
CPU time consumed: 240ms
Wed Feb 19 18:29:34 UTC 2025 I: diffoscope 288 found no differences in the changes files, and a .buildinfo file also exists.
Wed Feb 19 18:29:34 UTC 2025 I: biojava6-live from trixie built successfully and reproducibly on amd64.
Wed Feb 19 18:29:35 UTC 2025 I: Submitting .buildinfo files to external archives:
Wed Feb 19 18:29:35 UTC 2025 I: Submitting 20K b1/biojava6-live_6.1.0+dfsg-5_amd64.buildinfo.asc
Wed Feb 19 18:29:36 UTC 2025 I: Submitting 20K b2/biojava6-live_6.1.0+dfsg-5_amd64.buildinfo.asc
Wed Feb 19 18:29:37 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Wed Feb 19 18:29:37 UTC 2025 I: Done submitting .buildinfo files.
Wed Feb 19 18:29:37 UTC 2025 I: Removing signed biojava6-live_6.1.0+dfsg-5_amd64.buildinfo.asc files:
removed './b1/biojava6-live_6.1.0+dfsg-5_amd64.buildinfo.asc'
removed './b2/biojava6-live_6.1.0+dfsg-5_amd64.buildinfo.asc'