I: pbuilder: network access will be disabled during build I: Current time: Fri Nov 14 19:36:25 +14 2025 I: pbuilder-time-stamp: 1763098585 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 [libgoby-java_3.3.1+dfsg2-11.dsc] I: copying [./libgoby-java_3.3.1+dfsg2.orig.tar.xz] I: copying [./libgoby-java_3.3.1+dfsg2-11.debian.tar.xz] I: Extracting source gpgv: Signature made Tue May 14 16:31:58 2024 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./libgoby-java_3.3.1+dfsg2-11.dsc: no acceptable signature found dpkg-source: info: extracting libgoby-java in libgoby-java-3.3.1+dfsg2 dpkg-source: info: unpacking libgoby-java_3.3.1+dfsg2.orig.tar.xz dpkg-source: info: unpacking libgoby-java_3.3.1+dfsg2-11.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying protoc.patch dpkg-source: info: applying adding_dependencies.patch dpkg-source: info: applying using_jbzip2.patch dpkg-source: info: applying adapting_to_old_fastutil.patch dpkg-source: info: applying using_GeneratedMessageV3.patch dpkg-source: info: applying using_commons-cli.patch dpkg-source: info: applying using_correct_SamReader_api.patch dpkg-source: info: applying inclusions_in_SplitTranscriptsMode.patch dpkg-source: info: applying catch_IOException_LineIterator.patch dpkg-source: info: applying computing_fisher_pvalue_hypergeom.patch dpkg-source: info: applying exclude_not_runnable_tests.patch dpkg-source: info: applying goby_script.patch dpkg-source: info: applying path_of_goby_jar_for_Debian.patch dpkg-source: info: applying jaxb_dependency.patch dpkg-source: info: applying using_pcre2.patch dpkg-source: info: applying omit_test_failing_randomly.patch dpkg-source: info: applying adding_opens_arg_for_tests.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1730115/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Nov 14 05:36 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/1730115/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1730115/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=57834cd097a548aa8464a3e7aa0343bc LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1730115 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ONmzhG9r/pbuilderrc_HiaN --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ONmzhG9r/b2 --logfile b2/build.log libgoby-java_3.3.1+dfsg2-11.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.10.11+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.11-1~bpo12+1 (2024-10-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1730115/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 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), maven-debian-helper, javahelper, default-jdk, ant, ant-contrib, libjbzip2-java, libcommons-collections3-java, libcommons-configuration-java, libcommons-exec-java, libcommons-io-java, libcommons-lang-java, libcommons-logging-java, libcommons-math-java, libcommons-cli-java, libdistlib-java, liblog4j1.2-java, libexec-maven-plugin-java, libjaxb-api-java, libmaven-assembly-plugin-java, libmaven-antrun-plugin-java, libbuild-helper-maven-plugin-java, libmaven-dependency-plugin-java, libmaven-source-plugin-java, libmaven-javadoc-plugin-java, libprotobuf-java, libhtsjdk-java, libfastutil-java, protobuf-compiler, libjsap-java, libdsiutils-java, libicb-utils-java, libreflections-java, libpj-java, libprotobuf-dev, pkgconf, r-cran-rjava, libeasymock-java, junit4, testng, libpicard-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 ... 19787 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 maven-debian-helper; however: Package maven-debian-helper is not installed. pbuilder-satisfydepends-dummy depends on javahelper; however: Package javahelper is not installed. pbuilder-satisfydepends-dummy depends on default-jdk; however: Package default-jdk is not installed. pbuilder-satisfydepends-dummy depends on ant; however: Package ant is not installed. pbuilder-satisfydepends-dummy depends on ant-contrib; however: Package ant-contrib is not installed. pbuilder-satisfydepends-dummy depends on libjbzip2-java; however: Package libjbzip2-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-collections3-java; however: Package libcommons-collections3-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-configuration-java; however: Package libcommons-configuration-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-exec-java; however: Package libcommons-exec-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-io-java; however: Package libcommons-io-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-lang-java; however: Package libcommons-lang-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-logging-java; however: Package libcommons-logging-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 libcommons-cli-java; however: Package libcommons-cli-java is not installed. pbuilder-satisfydepends-dummy depends on libdistlib-java; however: Package libdistlib-java is not installed. pbuilder-satisfydepends-dummy depends on liblog4j1.2-java; however: Package liblog4j1.2-java is not installed. pbuilder-satisfydepends-dummy depends on libexec-maven-plugin-java; however: Package libexec-maven-plugin-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 libmaven-assembly-plugin-java; however: Package libmaven-assembly-plugin-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 libbuild-helper-maven-plugin-java; however: Package libbuild-helper-maven-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-source-plugin-java; however: Package libmaven-source-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 libprotobuf-java; however: Package libprotobuf-java is not installed. pbuilder-satisfydepends-dummy depends on libhtsjdk-java; however: Package libhtsjdk-java is not installed. pbuilder-satisfydepends-dummy depends on libfastutil-java; however: Package libfastutil-java is not installed. pbuilder-satisfydepends-dummy depends on protobuf-compiler; however: Package protobuf-compiler is not installed. pbuilder-satisfydepends-dummy depends on libjsap-java; however: Package libjsap-java is not installed. pbuilder-satisfydepends-dummy depends on libdsiutils-java; however: Package libdsiutils-java is not installed. pbuilder-satisfydepends-dummy depends on libicb-utils-java; however: Package libicb-utils-java is not installed. pbuilder-satisfydepends-dummy depends on libreflections-java; however: Package libreflections-java is not installed. pbuilder-satisfydepends-dummy depends on libpj-java; however: Package libpj-java is not installed. pbuilder-satisfydepends-dummy depends on libprotobuf-dev; however: Package libprotobuf-dev is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on r-cran-rjava; however: Package r-cran-rjava is not installed. pbuilder-satisfydepends-dummy depends on libeasymock-java; however: Package libeasymock-java is not installed. pbuilder-satisfydepends-dummy depends on junit4; however: Package junit4 is not installed. pbuilder-satisfydepends-dummy depends on testng; however: Package testng is not installed. pbuilder-satisfydepends-dummy depends on libpicard-java; however: Package libpicard-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-contrib{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-headless{a} default-jre{a} default-jre-headless{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} dwz{a} fastjar{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gpg{a} gpg-agent{a} gpgconf{a} gpgsm{a} groff-base{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} intltool-debian{a} jarwrapper{a} java-common{a} java-wrappers{a} javahelper{a} junit4{a} junit5{a} libactivation-java{a} libaopalliance-java{a} libapache-pom-java{a} libapiguardian-java{a} libapparmor1{a} libarchive-zip-perl{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} libbarclay-java{a} libbatik-java{a} libblas3{a} libbrotli1{a} libbsh-java{a} libbuild-helper-maven-plugin-java{a} libbyte-buddy-java{a} libcairo-gobject2{a} libcairo2{a} libcdi-api-java{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcloudproviders0{a} libcolord2{a} libcolt-free-java{a} libcom-err2{a} libcommons-beanutils-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-collections4-java{a} libcommons-compress-java{a} libcommons-configuration-java{a} libcommons-digester-java{a} libcommons-exec-java{a} libcommons-io-java{a} libcommons-jexl2-java{a} libcommons-lang-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-math-java{a} libcommons-math3-java{a} libcommons-parent-java{a} libcommons-text-java{a} libcommons-validator-java{a} libcups2t64{a} libcurl4t64{a} libdatrie1{a} libdbus-1-3{a} libdconf1{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdistlib-java{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} libdsiutils-java{a} libdynaloader-functions-perl{a} libeasymock-java{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} libfastutil-java{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} libfontbox2-java{a} libfontconfig1{a} libfop-java{a} libfreemarker-java{a} libfreetype6{a} libfribidi0{a} libgatk-native-bindings-java{a} libgbm1{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libgfortran5{a} libgif7{a} libgkl-java{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0t64{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgoogle-gson-java{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgtk-3-0t64{a} libgtk-3-common{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhtsjdk-java{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libhttpclient-java{a} libhttpcore-java{a} libicb-utils-java{a} libice6{a} libicu4j-java{a} libicu72{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libitext1-java{a} libjansi-java{a} libjavassist-java{a} libjaxb-api-java{a} libjaxen-java{a} libjaxp1.3-java{a} libjbig0{a} libjboss-logging-java{a} libjboss-vfs-java{a} libjbzip2-java{a} libjcommander-java{a} libjetty9-java{a} libjoptsimple-java{a} libjpeg62-turbo{a} libjsap-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} liblapack3{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblightcouch-java{a} libllvm19{a} liblog4j1.2-java{a} liblog4j2-java{a} liblogback-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-file-management-java{a} libmaven-filtering-java{a} libmaven-invoker-java{a} libmaven-jar-plugin-java{a} libmaven-javadoc-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} libmaven-source-plugin-java{a} libmaven3-core-java{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libmjson-java{a} libmodule-runtime-perl{a} libmongodb-java{a} libmoo-perl{a} libncbi-ngs3{a} libncbi-vdb3{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnghttp2-14{a} libngs-java{a} libngs-jni{a} libnpth0t64{a} libnsl2{a} libnspr4{a} libnss3{a} libobjenesis-java{a} libopentest4j-java{a} libopentest4j-reporting-java{a} liboro-java{a} libpam-systemd{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libparams-classify-perl{a} libpciaccess0{a} libpcsclite1{a} libpicard-java{a} libpicocli-java{a} libpipeline1{a} libpixman-1-0{a} libpj-java{a} libpkgconf3{a} libplexus-ant-factory-java{a} libplexus-archiver-java{a} libplexus-bsh-factory-java{a} libplexus-build-api-java{a} libplexus-cipher-java{a} libplexus-classworlds-java{a} libplexus-compiler-java{a} libplexus-component-annotations-java{a} libplexus-container-default-java{a} libplexus-container-default1.5-java{a} libplexus-i18n-java{a} libplexus-interactivity-api-java{a} libplexus-interpolation-java{a} libplexus-io-java{a} libplexus-languages-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libplexus-velocity-java{a} libpng16-16t64{a} libproc2-0{a} libprotobuf-dev{a} libprotobuf-java{a} libprotobuf-lite32t64{a} libprotobuf32t64{a} libprotoc32t64{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libqdox-java{a} libqdox2-java{a} libreadline8t64{a} libreflections-java{a} librhino-java{a} librole-tiny-perl{a} librtmp1{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} libsm6{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libssh2-1t64{a} libsub-quote-perl{a} libsurefire-java{a} libsystemd-shared{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} libunivocity-parsers-java{a} liburi-perl{a} libvelocity-tools-java{a} libvulkan1{a} libwagon-file-java{a} libwagon-http-shaded-java{a} libwagon-provider-api-java{a} libwayland-client0{a} libwayland-cursor0{a} libwayland-egl1{a} libwayland-server0{a} libwebp7{a} libwebsocket-api-java{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxalan2-java{a} libxau6{a} libxbean-reflect-java{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxerces2-java{a} libxext6{a} libxfixes3{a} libxft2{a} libxi6{a} libxinerama1{a} libxkbcommon0{a} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxml2-utils{a} libxmlgraphics-commons-java{a} libxpp3-java{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxss1{a} libxstream-java{a} libxt6t64{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} ncbi-vdb-data{a} netbase{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} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} protobuf-compiler{a} python3{a} python3-minimal{a} python3.12{a} python3.12-minimal{a} r-base-core{a} r-cran-rjava{a} readline-common{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} systemd{a} systemd-sysv{a} testng{a} tzdata{a} ucf{a} unzip{a} velocity{a} wdiff{a} x11-common{a} xdg-utils{a} xkb-data{a} zip{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf ant-optional at-spi2-core chrony curl debian-keyring dput dput-ng dupload equivs fonts-dejavu-extra gnupg-utils gpg-wks-client icc-profiles-free krb5-locales libarchive-cpio-perl libatk-wrapper-java-jni libdata-dump-perl libdistro-info-perl libfile-mimeinfo-perl libgdk-pixbuf2.0-bin libgit-wrapper-perl libgitlab-api-v4-perl libgkl-jni libglib2.0-data libgtk-3-bin libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjson-perl libkmod2 libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl libnet-dbus-perl libnss-systemd librsvg2-common libsasl2-modules libsaxon-java libsoap-lite-perl libstring-shellquote-perl libx11-protocol-perl libxstring-perl libxt-dev libyaml-snake-java licensecheck lintian linux-sysctl-defaults lynx mesa-vulkan-drivers ntpsec openntpd pristine-tar psmisc publicsuffix python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg r-base-dev r-doc-html r-recommended strace systemd-cryptsetup systemd-timesyncd wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 464 newly installed, 0 to remove and 0 not upgraded. Need to get 404 MB of archives. After unpacking 1033 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libapparmor1 amd64 3.1.7-1+b1 [42.0 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libsystemd-shared amd64 256.6-1 [2061 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 systemd amd64 256.6-1 [3488 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 systemd-sysv amd64 256.6-1 [58.2 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libdbus-1-3 amd64 1.14.10-4+b1 [203 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 dbus-bin amd64 1.14.10-4+b1 [106 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 dbus-session-bus-common all 1.14.10-4 [79.0 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.3-1 [105 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 dbus-daemon amd64 1.14.10-4+b1 [185 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 dbus-system-bus-common all 1.14.10-4 [80.1 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 dbus amd64 1.14.10-4+b1 [98.6 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 libpython3.12-minimal amd64 3.12.6-1 [814 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.6-1 [2168 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 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 2024a-4 [255 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 24 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b2 [40.3 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.6-1 [1963 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.6-1 [669 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get: 34 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-1 [1381 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libpam-systemd amd64 256.6-1 [278 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-9 [97.2 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [311 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.1-1 [1499 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.1 [699 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 shared-mime-info amd64 2.4-5+b1 [759 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-1 [139 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 gtk-update-icon-cache amd64 4.16.3+ds-1 [49.7 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 hicolor-icon-theme all 0.18-1 [12.0 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 adwaita-icon-theme all 47.0-1 [463 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 java-common all 0.76 [6776 B] Get: 70 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libnspr4 amd64 2:4.35-1.1+b1 [109 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libnss3 amd64 2:3.105-2 [1393 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libpcsclite1 amd64 2.3.0-1 [55.4 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jre-headless amd64 21.0.5~8ea-1 [41.8 MB] Get: 75 http://deb.debian.org/debian trixie/main amd64 default-jre-headless amd64 2:1.21-76 [3192 B] Get: 76 http://deb.debian.org/debian trixie/main amd64 ant all 1.10.15-1 [2163 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 ant-contrib all 1.0~b3+svn177-12 [262 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 at-spi2-common all 2.54.0-1 [170 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 dbus-user-session amd64 1.14.10-4+b1 [79.1 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libdconf1 amd64 0.40.0-4+b2 [41.9 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 dconf-service amd64 0.40.0-4+b2 [32.4 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 dconf-gsettings-backend amd64 0.40.0-4+b2 [28.7 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 dctrl-tools amd64 2.24-3+b1 [104 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 95 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libatk1.0-0t64 amd64 2.54.0-1 [51.2 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2 [144 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libatspi2.0-0t64 amd64 2.54.0-1 [76.4 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libatk-bridge2.0-0t64 amd64 2.54.0-1 [67.6 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b4 [300 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2 [115 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2 [105 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libcairo-gobject2 amd64 1.18.2-2 [130 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libcloudproviders0 amd64 0.3.6-1 [28.9 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libcolord2 amd64 1.4.7-1+b1 [139 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libavahi-common-data amd64 0.8-13+b2 [112 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libavahi-common3 amd64 0.8-13+b2 [43.3 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libavahi-client3 amd64 0.8-13+b2 [47.0 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libcups2t64 amd64 2.4.10-2 [251 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libepoxy0 amd64 1.5.10-2 [193 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 9.0.0-1 [474 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.54.0+ds-2 [223 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-2 [54.4 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-2 [35.2 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libwayland-client0 amd64 1.23.0-1 [26.4 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libwayland-cursor0 amd64 1.23.0-1 [11.3 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libwayland-egl1 amd64 1.23.0-1 [5392 B] Get: 143 http://deb.debian.org/debian trixie/main amd64 libxcomposite1 amd64 1:0.4.5-1+b1 [14.9 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libxfixes3 amd64 1:6.0.0-2+b1 [20.3 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libxcursor1 amd64 1:1.2.2-1 [37.1 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libxdamage1 amd64 1:1.1.6-1+b1 [15.5 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libxinerama1 amd64 2:1.1.4-3+b1 [16.0 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 xkb-data all 2.42-1 [790 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 libxkbcommon0 amd64 1.6.0-1+b1 [109 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 libxrandr2 amd64 2:1.5.4-1 [36.1 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 libgtk-3-common all 3.24.43-4 [4657 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 libgtk-3-0t64 amd64 3.24.43-4 [2754 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libglvnd0 amd64 1.7.0-1+b1 [56.3 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.123-1 [8084 B] Get: 155 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 libglapi-mesa amd64 24.2.4-1 [37.9 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 libx11-xcb1 amd64 2:1.8.7-1+b1 [232 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 libxcb-dri2-0 amd64 1.17.0-2 [106 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 libxcb-dri3-0 amd64 1.17.0-2 [107 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 libxcb-glx0 amd64 1.17.0-2 [122 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 libxcb-present0 amd64 1.17.0-2 [105 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 libxcb-randr0 amd64 1.17.0-2 [116 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 libxcb-sync1 amd64 1.17.0-2 [108 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 libxcb-xfixes0 amd64 1.17.0-2 [109 kB] Get: 165 http://deb.debian.org/debian trixie/main amd64 libxshmfence1 amd64 1.3-1+b1 [8852 B] Get: 166 http://deb.debian.org/debian trixie/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 libdrm-intel1 amd64 2.4.123-1 [63.7 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 libdrm-radeon1 amd64 2.4.123-1 [22.3 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get: 172 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 libllvm19 amd64 1:19.1.1-1 [26.0 MB] Get: 174 http://deb.debian.org/debian trixie/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 libsensors5 amd64 1:3.6.0-10 [34.7 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 mesa-libgallium amd64 24.2.4-1 [9182 kB] Get: 177 http://deb.debian.org/debian trixie/main amd64 libvulkan1 amd64 1.3.290.0-1 [126 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 libwayland-server0 amd64 1.23.0-1 [34.0 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 libgbm1 amd64 24.2.4-1 [42.7 kB] Get: 180 http://deb.debian.org/debian trixie/main amd64 libgl1-mesa-dri amd64 24.2.4-1 [43.8 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 libglx-mesa0 amd64 24.2.4-1 [154 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 libglx0 amd64 1.7.0-1+b1 [35.0 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 libgl1 amd64 1.7.0-1+b1 [89.8 kB] Get: 184 http://deb.debian.org/debian trixie/main amd64 libasound2-data all 1.2.12-1 [21.0 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 libasound2t64 amd64 1.2.12-1 [369 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 libgif7 amd64 5.2.2-1 [43.9 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get: 188 http://deb.debian.org/debian trixie/main amd64 libxtst6 amd64 2:1.2.3-1.1+b1 [25.9 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jre amd64 21.0.5~8ea-1 [205 kB] Get: 190 http://deb.debian.org/debian trixie/main amd64 default-jre amd64 2:1.21-76 [1068 B] Get: 191 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jdk-headless amd64 21.0.5~8ea-1 [82.8 MB] Get: 192 http://deb.debian.org/debian trixie/main amd64 default-jdk-headless amd64 2:1.21-76 [1124 B] Get: 193 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jdk amd64 21.0.5~8ea-1 [4346 kB] Get: 194 http://deb.debian.org/debian trixie/main amd64 default-jdk amd64 2:1.21-76 [1076 B] Get: 195 http://deb.debian.org/debian trixie/main amd64 libassuan9 amd64 3.0.1-2 [60.6 kB] Get: 196 http://deb.debian.org/debian trixie/main amd64 gpgconf amd64 2.2.43-8+b1 [120 kB] Get: 197 http://deb.debian.org/debian trixie/main amd64 libksba8 amd64 1.6.7-2 [132 kB] Get: 198 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 199 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 200 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3 [187 kB] Get: 201 http://deb.debian.org/debian trixie/main amd64 libnpth0t64 amd64 1.6-3.1 [17.9 kB] Get: 202 http://deb.debian.org/debian trixie/main amd64 dirmngr amd64 2.2.43-8+b1 [367 kB] Get: 203 http://deb.debian.org/debian trixie/main amd64 gnupg-l10n all 2.2.43-8 [696 kB] Get: 204 http://deb.debian.org/debian trixie/main amd64 gpg amd64 2.2.43-8+b1 [527 kB] Get: 205 http://deb.debian.org/debian trixie/main amd64 pinentry-curses amd64 1.2.1-4+b1 [79.7 kB] Get: 206 http://deb.debian.org/debian trixie/main amd64 gpg-agent amd64 2.2.43-8+b1 [250 kB] Get: 207 http://deb.debian.org/debian trixie/main amd64 gpgsm amd64 2.2.43-8+b1 [252 kB] Get: 208 http://deb.debian.org/debian trixie/main amd64 gnupg all 2.2.43-8 [375 kB] Get: 209 http://deb.debian.org/debian trixie/main amd64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 210 http://deb.debian.org/debian trixie/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 211 http://deb.debian.org/debian trixie/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 212 http://deb.debian.org/debian trixie/main amd64 libfile-touch-perl all 0.12-2 [8816 B] Get: 213 http://deb.debian.org/debian trixie/main amd64 libio-pty-perl amd64 1:1.20-1+b1 [34.4 kB] Get: 214 http://deb.debian.org/debian trixie/main amd64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 215 http://deb.debian.org/debian trixie/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 216 http://deb.debian.org/debian trixie/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b3 [36.2 kB] Get: 217 http://deb.debian.org/debian trixie/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b1 [10.6 kB] Get: 218 http://deb.debian.org/debian trixie/main amd64 libdynaloader-functions-perl all 0.004-1 [12.1 kB] Get: 219 http://deb.debian.org/debian trixie/main amd64 libdevel-callchecker-perl amd64 0.009-1 [15.9 kB] Get: 220 http://deb.debian.org/debian trixie/main amd64 libparams-classify-perl amd64 0.015-2+b3 [22.4 kB] Get: 221 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 222 http://deb.debian.org/debian trixie/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 223 http://deb.debian.org/debian trixie/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 224 http://deb.debian.org/debian trixie/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 225 http://deb.debian.org/debian trixie/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 226 http://deb.debian.org/debian trixie/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 227 http://deb.debian.org/debian trixie/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 228 http://deb.debian.org/debian trixie/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 229 http://deb.debian.org/debian trixie/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 230 http://deb.debian.org/debian trixie/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 231 http://deb.debian.org/debian trixie/main amd64 liburi-perl all 5.29-1 [103 kB] Get: 232 http://deb.debian.org/debian trixie/main amd64 libhtml-parser-perl amd64 3.83-1 [99.4 kB] Get: 233 http://deb.debian.org/debian trixie/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 234 http://deb.debian.org/debian trixie/main amd64 libclone-perl amd64 0.47-1 [13.5 kB] Get: 235 http://deb.debian.org/debian trixie/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 236 http://deb.debian.org/debian trixie/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 237 http://deb.debian.org/debian trixie/main amd64 libhttp-message-perl all 6.46-1 [79.7 kB] Get: 238 http://deb.debian.org/debian trixie/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 239 http://deb.debian.org/debian trixie/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 240 http://deb.debian.org/debian trixie/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get: 241 http://deb.debian.org/debian trixie/main amd64 libnet-ssleay-perl amd64 1.94-1+b1 [339 kB] Get: 242 http://deb.debian.org/debian trixie/main amd64 libio-socket-ssl-perl all 2.089-1 [223 kB] Get: 243 http://deb.debian.org/debian trixie/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 244 http://deb.debian.org/debian trixie/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 245 http://deb.debian.org/debian trixie/main amd64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 246 http://deb.debian.org/debian trixie/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 247 http://deb.debian.org/debian trixie/main amd64 libwww-perl all 6.77-1 [183 kB] Get: 248 http://deb.debian.org/debian trixie/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get: 249 http://deb.debian.org/debian trixie/main amd64 wdiff amd64 1.2.2-6 [119 kB] Get: 250 http://deb.debian.org/debian trixie/main amd64 devscripts all 2.24.1 [1071 kB] Get: 251 http://deb.debian.org/debian trixie/main amd64 fastjar amd64 2:0.98-7 [80.1 kB] Get: 252 http://deb.debian.org/debian trixie/main amd64 jarwrapper all 0.80 [9692 B] Get: 253 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get: 254 http://deb.debian.org/debian trixie/main amd64 java-wrappers all 0.5 [8848 B] Get: 255 http://deb.debian.org/debian trixie/main amd64 javahelper all 0.80 [80.4 kB] Get: 256 http://deb.debian.org/debian trixie/main amd64 libhamcrest-java all 2.2-2 [121 kB] Get: 257 http://deb.debian.org/debian trixie/main amd64 junit4 all 4.13.2-4 [349 kB] Get: 258 http://deb.debian.org/debian trixie/main amd64 libapiguardian-java all 1.1.2-1 [4656 B] Get: 259 http://deb.debian.org/debian trixie/main amd64 libopentest4j-java all 1.2.0-4 [9516 B] Get: 260 http://deb.debian.org/debian trixie/main amd64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 261 http://deb.debian.org/debian trixie/main amd64 libpicocli-java all 4.6.2-2 [390 kB] Get: 262 http://deb.debian.org/debian trixie/main amd64 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 263 http://deb.debian.org/debian trixie/main amd64 junit5 all 5.10.3-1 [2459 kB] Get: 264 http://deb.debian.org/debian trixie/main amd64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 265 http://deb.debian.org/debian trixie/main amd64 libaopalliance-java all 20070526-7 [8572 B] Get: 266 http://deb.debian.org/debian trixie/main amd64 libapache-pom-java all 29-2 [5276 B] Get: 267 http://deb.debian.org/debian trixie/main amd64 libasm-java all 9.7-2 [390 kB] Get: 268 http://deb.debian.org/debian trixie/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 269 http://deb.debian.org/debian trixie/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 270 http://deb.debian.org/debian trixie/main amd64 libcommons-lang3-java all 3.14.0-1 [621 kB] Get: 271 http://deb.debian.org/debian trixie/main amd64 libfreemarker-java all 2.3.32-2 [1546 kB] Get: 272 http://deb.debian.org/debian trixie/main amd64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 273 http://deb.debian.org/debian trixie/main amd64 libjoptsimple-java all 5.0.4-4 [73.1 kB] Get: 274 http://deb.debian.org/debian trixie/main amd64 libcommons-codec-java all 1.16.0-1 [297 kB] Get: 275 http://deb.debian.org/debian trixie/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 276 http://deb.debian.org/debian trixie/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 277 http://deb.debian.org/debian trixie/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 278 http://deb.debian.org/debian trixie/main amd64 liblightcouch-java all 0.2.0-1 [75.0 kB] Get: 279 http://deb.debian.org/debian trixie/main amd64 libmongodb-java all 3.6.3-2 [1901 kB] Get: 280 http://deb.debian.org/debian trixie/main amd64 libslf4j-java all 1.7.32-1 [144 kB] Get: 281 http://deb.debian.org/debian trixie/main amd64 liblog4j2-java all 2.19.0-2 [2310 kB] Get: 282 http://deb.debian.org/debian trixie/main amd64 libbarclay-java all 5.0.0+dfsg-1 [108 kB] Get: 283 http://deb.debian.org/debian trixie/main amd64 libjaxp1.3-java all 1.3.05-6 [227 kB] Get: 284 http://deb.debian.org/debian trixie/main amd64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 285 http://deb.debian.org/debian trixie/main amd64 libcommons-io-java all 2.16.1-1 [480 kB] Get: 286 http://deb.debian.org/debian trixie/main amd64 libxmlgraphics-commons-java all 2.8-2 [623 kB] Get: 287 http://deb.debian.org/debian trixie/main amd64 libbatik-java all 1.17+dfsg-1 [3923 kB] Get: 288 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get: 289 http://deb.debian.org/debian trixie/main amd64 libbsh-java all 2.0b4-20 [291 kB] Get: 290 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-utils-java all 3.3.4-1 [138 kB] Get: 291 http://deb.debian.org/debian trixie/main amd64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 292 http://deb.debian.org/debian trixie/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 293 http://deb.debian.org/debian trixie/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 294 http://deb.debian.org/debian trixie/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 295 http://deb.debian.org/debian trixie/main amd64 libguava-java all 32.0.1-1 [2708 kB] Get: 296 http://deb.debian.org/debian trixie/main amd64 libguice-java all 4.2.3-2 [1435 kB] Get: 297 http://deb.debian.org/debian trixie/main amd64 libmaven-parent-java all 35-1 [6140 B] Get: 298 http://deb.debian.org/debian trixie/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 299 http://deb.debian.org/debian trixie/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 300 http://deb.debian.org/debian trixie/main amd64 libmaven-resolver-java all 1.6.3-1 [548 kB] Get: 301 http://deb.debian.org/debian trixie/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 302 http://deb.debian.org/debian trixie/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 303 http://deb.debian.org/debian trixie/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 304 http://deb.debian.org/debian trixie/main amd64 libplexus-interpolation-java all 1.26-1 [76.8 kB] Get: 305 http://deb.debian.org/debian trixie/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 306 http://deb.debian.org/debian trixie/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 307 http://deb.debian.org/debian trixie/main amd64 libcdi-api-java all 1.2-3 [54.3 kB] Get: 308 http://deb.debian.org/debian trixie/main amd64 libsisu-inject-java all 0.3.4-2 [347 kB] Get: 309 http://deb.debian.org/debian trixie/main amd64 libsisu-plexus-java all 0.3.4-3 [181 kB] Get: 310 http://deb.debian.org/debian trixie/main amd64 libmaven3-core-java all 3.8.8-1 [1579 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 3.0.0-1 [35.1 kB] Get: 313 http://deb.debian.org/debian trixie/main amd64 libbuild-helper-maven-plugin-java all 3.3.0-1 [59.5 kB] Get: 314 http://deb.debian.org/debian trixie/main amd64 libbyte-buddy-java all 1.14.19-1 [4756 kB] Get: 315 http://deb.debian.org/debian trixie/main amd64 libcolt-free-java all 1.2.0+dfsg-8 [440 kB] Get: 316 http://deb.debian.org/debian trixie/main amd64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 317 http://deb.debian.org/debian trixie/main amd64 libcommons-beanutils-java all 1.9.4-2 [233 kB] Get: 318 http://deb.debian.org/debian trixie/main amd64 libcommons-collections4-java all 4.4-2 [682 kB] Get: 319 http://deb.debian.org/debian trixie/main amd64 libcommons-compress-java all 1.25.0-1 [635 kB] Get: 320 http://deb.debian.org/debian trixie/main amd64 libcommons-lang-java all 2.6-10 [273 kB] Get: 321 http://deb.debian.org/debian trixie/main amd64 libcommons-configuration-java all 1.10-6 [347 kB] Get: 322 http://deb.debian.org/debian trixie/main amd64 libcommons-digester-java all 1.8.1-6 [137 kB] Get: 323 http://deb.debian.org/debian trixie/main amd64 libcommons-exec-java all 1.3-2 [48.1 kB] Get: 324 http://deb.debian.org/debian trixie/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get: 325 http://deb.debian.org/debian trixie/main amd64 libcommons-math-java all 2.2-8 [926 kB] Get: 326 http://deb.debian.org/debian trixie/main amd64 libcommons-math3-java all 3.6.1-3 [2018 kB] Get: 327 http://deb.debian.org/debian trixie/main amd64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 328 http://deb.debian.org/debian trixie/main amd64 libsnappy1v5 amd64 1.2.1-1 [29.1 kB] Get: 329 http://deb.debian.org/debian trixie/main amd64 libsnappy-jni amd64 1.1.10.5-2 [6396 B] Get: 330 http://deb.debian.org/debian trixie/main amd64 libsnappy-java all 1.1.10.5-2 [87.5 kB] Get: 331 http://deb.debian.org/debian trixie/main amd64 libxz-java all 1.9-1 [143 kB] Get: 332 http://deb.debian.org/debian trixie/main amd64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 333 http://deb.debian.org/debian trixie/main amd64 libmaven-archiver-java all 3.6.0-1 [25.1 kB] Get: 334 http://deb.debian.org/debian trixie/main amd64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 335 http://deb.debian.org/debian trixie/main amd64 libcommons-text-java all 1.11.0-1 [217 kB] Get: 336 http://deb.debian.org/debian trixie/main amd64 libcommons-validator-java all 1:1.7-1 [181 kB] Get: 337 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.63.0-1 [74.8 kB] Get: 338 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 339 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 340 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-7 [216 kB] Get: 341 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.10.1-1 [352 kB] Get: 342 http://deb.debian.org/debian trixie/main amd64 libdistlib-java all 1.0-5 [72.5 kB] Get: 343 http://deb.debian.org/debian trixie/main amd64 libjaxen-java all 1.1.6-4 [214 kB] Get: 344 http://deb.debian.org/debian trixie/main amd64 libdom4j-java all 2.1.4-1 [312 kB] Get: 345 http://deb.debian.org/debian trixie/main amd64 libdoxia-core-java all 1.12.0-1 [213 kB] Get: 346 http://deb.debian.org/debian trixie/main amd64 libfontbox2-java all 2.0.29-1 [1510 kB] Get: 347 http://deb.debian.org/debian trixie/main amd64 libqdox-java all 1.12.1-3 [172 kB] Get: 348 http://deb.debian.org/debian trixie/main amd64 libfop-java all 1:2.8-3 [10.1 MB] Get: 349 http://deb.debian.org/debian trixie/main amd64 libitext1-java all 1.4-7 [1257 kB] Get: 350 http://deb.debian.org/debian trixie/main amd64 libxbean-reflect-java all 4.5-8 [133 kB] Get: 351 http://deb.debian.org/debian trixie/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 352 http://deb.debian.org/debian trixie/main amd64 libdoxia-java all 1.12.0-1 [459 kB] Get: 353 http://deb.debian.org/debian trixie/main amd64 libmaven-reporting-api-java all 3.1.1-1 [7240 B] Get: 354 http://deb.debian.org/debian trixie/main amd64 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB] Get: 355 http://deb.debian.org/debian trixie/main amd64 velocity all 1.7-7 [431 kB] Get: 356 http://deb.debian.org/debian trixie/main amd64 libplexus-velocity-java all 1.2-3.1 [10.5 kB] Get: 357 http://deb.debian.org/debian trixie/main amd64 liboro-java all 2.0.8a-14 [70.5 kB] Get: 358 http://deb.debian.org/debian trixie/main amd64 libvelocity-tools-java all 2.0-9 [311 kB] Get: 359 http://deb.debian.org/debian trixie/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 360 http://deb.debian.org/debian trixie/main amd64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 361 http://deb.debian.org/debian trixie/main amd64 libxalan2-java all 2.7.2-4 [3419 kB] Get: 362 http://deb.debian.org/debian trixie/main amd64 libdoxia-sitetools-java all 1.11.1-1 [202 kB] Get: 363 http://deb.debian.org/debian trixie/main amd64 libfastutil-java all 8.5.14+dfsg-1 [19.8 MB] Get: 364 http://deb.debian.org/debian trixie/main amd64 libxpp3-java all 1.1.4c-3 [292 kB] Get: 365 http://deb.debian.org/debian trixie/main amd64 libxstream-java all 1.4.20-1 [565 kB] Get: 366 http://deb.debian.org/debian trixie/main amd64 libjsap-java all 2.1-5 [102 kB] Get: 367 http://deb.debian.org/debian trixie/main amd64 liblogback-java all 1:1.2.11-5 [701 kB] Get: 368 http://deb.debian.org/debian trixie/main amd64 libdsiutils-java all 2.7.3+dfsg-1 [524 kB] Get: 369 http://deb.debian.org/debian trixie/main amd64 libobjenesis-java all 3.3-3 [41.3 kB] Get: 370 http://deb.debian.org/debian trixie/main amd64 libeasymock-java all 5.2.0-1 [131 kB] Get: 371 http://deb.debian.org/debian trixie/main amd64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 372 http://deb.debian.org/debian trixie/main amd64 libexec-maven-plugin-java all 3.1.0-2 [66.7 kB] Get: 373 http://deb.debian.org/debian trixie/main amd64 libgatk-native-bindings-java all 1.0.0+dfsg-2 [8024 B] Get: 374 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-3 [837 kB] Get: 375 http://deb.debian.org/debian trixie/main amd64 libmjson-java all 1.4.0-3 [60.4 kB] Get: 376 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB] Get: 377 http://deb.debian.org/debian trixie/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB] Get: 378 http://deb.debian.org/debian trixie/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB] Get: 379 http://deb.debian.org/debian trixie/main amd64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB] Get: 380 http://deb.debian.org/debian trixie/main amd64 libncbi-vdb3 amd64 3.0.2+dfsg-2+b1 [1049 kB] Get: 381 http://deb.debian.org/debian trixie/main amd64 libncbi-ngs3 amd64 3.0.3+dfsg-9 [155 kB] Get: 382 http://deb.debian.org/debian trixie/main amd64 libngs-jni amd64 3.0.3+dfsg-9 [23.8 kB] Get: 383 http://deb.debian.org/debian trixie/main amd64 libngs-java amd64 3.0.3+dfsg-9 [110 kB] Get: 384 http://deb.debian.org/debian trixie/main amd64 librhino-java all 1.7.14-2.1 [1357 kB] Get: 385 http://deb.debian.org/debian trixie/main amd64 libhtsjdk-java all 4.1.0+dfsg-2 [1833 kB] Get: 386 http://deb.debian.org/debian trixie/main amd64 libgkl-java all 0.8.11+dfsg-2 [24.7 kB] Get: 387 http://deb.debian.org/debian trixie/main amd64 libicu4j-java all 73.2-1 [16.4 MB] Get: 388 http://deb.debian.org/debian trixie/main amd64 liblog4j1.2-java all 1.2.17-11 [444 kB] Get: 389 http://deb.debian.org/debian trixie/main amd64 libicb-utils-java all 2.0.1+git20161002.afee1d9-5 [81.5 kB] Get: 390 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.0.10-1+b1 [56.7 kB] Get: 391 http://deb.debian.org/debian trixie/main amd64 libjansi-java all 2.4.1-2 [100 kB] Get: 392 http://deb.debian.org/debian trixie/main amd64 libjavassist-java all 1:3.27.0-1 [731 kB] Get: 393 http://deb.debian.org/debian trixie/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 394 http://deb.debian.org/debian trixie/main amd64 libjboss-logging-java all 3.5.3-1 [56.2 kB] Get: 395 http://deb.debian.org/debian trixie/main amd64 libjboss-vfs-java all 3.2.15.Final-3 [130 kB] Get: 396 http://deb.debian.org/debian trixie/main amd64 libjbzip2-java all 0.9.1-8 [42.7 kB] Get: 397 http://deb.debian.org/debian trixie/main amd64 libjcommander-java all 1.71-4 [73.0 kB] Get: 398 http://deb.debian.org/debian trixie/main amd64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 399 http://deb.debian.org/debian trixie/main amd64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 400 http://deb.debian.org/debian trixie/main amd64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 401 http://deb.debian.org/debian trixie/main amd64 libjetty9-java all 9.4.55-1 [2980 kB] Get: 402 http://deb.debian.org/debian trixie/main amd64 libjsoup-java all 1.15.3-1 [431 kB] Get: 403 http://deb.debian.org/debian trixie/main amd64 libjtidy-java all 7+svn20110807-5 [250 kB] Get: 404 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 405 http://deb.debian.org/debian trixie/main amd64 libmaven-antrun-plugin-java all 3.1.0-1 [36.9 kB] Get: 406 http://deb.debian.org/debian trixie/main amd64 libmaven-common-artifact-filters-java all 3.3.2-1 [48.2 kB] Get: 407 http://deb.debian.org/debian trixie/main amd64 libmaven-artifact-transfer-java all 0.13.1-2 [158 kB] Get: 408 http://deb.debian.org/debian trixie/main amd64 libplexus-build-api-java all 0.0.7-4 [10.3 kB] Get: 409 http://deb.debian.org/debian trixie/main amd64 libmaven-filtering-java all 3.3.0-1 [50.2 kB] Get: 410 http://deb.debian.org/debian trixie/main amd64 libmaven-assembly-plugin-java all 3.4.2-1 [242 kB] Get: 411 http://deb.debian.org/debian trixie/main amd64 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB] Get: 412 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-incremental-java all 1.1-4 [9924 B] Get: 413 http://deb.debian.org/debian trixie/main amd64 libplexus-compiler-java all 2.12.1-3 [99.3 kB] Get: 414 http://deb.debian.org/debian trixie/main amd64 libqdox2-java all 2.0.3-1 [296 kB] Get: 415 http://deb.debian.org/debian trixie/main amd64 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 416 http://deb.debian.org/debian trixie/main amd64 libmaven-compiler-plugin-java all 3.10.1-2 [59.0 kB] Get: 417 http://deb.debian.org/debian trixie/main amd64 libmaven-dependency-analyzer-java all 1.14.1-1 [35.2 kB] Get: 418 http://deb.debian.org/debian trixie/main amd64 libmaven-dependency-tree-java all 3.2.1-1 [34.7 kB] Get: 419 http://deb.debian.org/debian trixie/main amd64 libmaven-reporting-impl-java all 3.2.0-2 [15.2 kB] Get: 420 http://deb.debian.org/debian trixie/main amd64 libmaven-dependency-plugin-java all 3.5.0-1 [173 kB] Get: 421 http://deb.debian.org/debian trixie/main amd64 libmaven-invoker-java all 3.2.0-1 [28.1 kB] Get: 422 http://deb.debian.org/debian trixie/main amd64 libplexus-interactivity-api-java all 1.1-2 [11.0 kB] Get: 423 http://deb.debian.org/debian trixie/main amd64 libmaven-javadoc-plugin-java all 3.4.1-3 [454 kB] Get: 424 http://deb.debian.org/debian trixie/main amd64 libplexus-container-default1.5-java all 2.1.1-1 [4476 B] Get: 425 http://deb.debian.org/debian trixie/main amd64 libplexus-ant-factory-java all 1.0~alpha2.1-4 [11.4 kB] Get: 426 http://deb.debian.org/debian trixie/main amd64 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B] Get: 427 http://deb.debian.org/debian trixie/main amd64 libmaven-plugin-tools-java all 3.7.1-1 [265 kB] Get: 428 http://deb.debian.org/debian trixie/main amd64 libmaven-reporting-exec-java all 1.6.0-1 [26.8 kB] Get: 429 http://deb.debian.org/debian trixie/main amd64 libmaven-resources-plugin-java all 3.3.1-1 [27.5 kB] Get: 430 http://deb.debian.org/debian trixie/main amd64 libmaven-site-plugin-java all 3.12.1-2 [107 kB] Get: 431 http://deb.debian.org/debian trixie/main amd64 libmaven-source-plugin-java all 3.2.1-2 [27.6 kB] Get: 432 http://deb.debian.org/debian trixie/main amd64 libpaper1 amd64 1.1.29+b1 [12.9 kB] Get: 433 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 1.1.29+b1 [9176 B] Get: 434 http://deb.debian.org/debian trixie/main amd64 libpicard-java all 3.1.1+dfsg-1 [1743 kB] Get: 435 http://deb.debian.org/debian trixie/main amd64 libpj-java all 0.0~20150107+dfsg-5 [1389 kB] Get: 436 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-3 [36.2 kB] Get: 437 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get: 438 http://deb.debian.org/debian trixie/main amd64 libprotobuf32t64 amd64 3.21.12-9 [982 kB] Get: 439 http://deb.debian.org/debian trixie/main amd64 libprotobuf-lite32t64 amd64 3.21.12-9 [274 kB] Get: 440 http://deb.debian.org/debian trixie/main amd64 libprotobuf-dev amd64 3.21.12-9 [1329 kB] Get: 441 http://deb.debian.org/debian trixie/main amd64 libprotobuf-java all 3.21.12-9 [1260 kB] Get: 442 http://deb.debian.org/debian trixie/main amd64 libprotoc32t64 amd64 3.21.12-9 [920 kB] Get: 443 http://deb.debian.org/debian trixie/main amd64 libreflections-java all 0.10.2+dfsg-2 [125 kB] Get: 444 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.3-1+b1 [33.6 kB] Get: 445 http://deb.debian.org/debian trixie/main amd64 libsurefire-java all 2.22.3-2 [1169 kB] Get: 446 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB] Get: 447 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get: 448 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b1 [17.0 kB] Get: 449 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB] Get: 450 http://deb.debian.org/debian trixie/main amd64 libwagon-file-java all 3.5.3-1 [8388 B] Get: 451 http://deb.debian.org/debian trixie/main amd64 libwagon-http-shaded-java all 3.5.3-1 [1341 kB] Get: 452 http://deb.debian.org/debian trixie/main amd64 libxml2-utils amd64 2.12.7+dfsg+really2.9.14-0.1 [99.1 kB] Get: 453 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get: 454 http://deb.debian.org/debian trixie/main amd64 maven all 3.8.8-1 [19.3 kB] Get: 455 http://deb.debian.org/debian trixie/main amd64 maven-repo-helper all 1.11 [142 kB] Get: 456 http://deb.debian.org/debian trixie/main amd64 maven-debian-helper all 2.6.4 [108 kB] Get: 457 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-3 [29.9 kB] Get: 458 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-3 [26.1 kB] Get: 459 http://deb.debian.org/debian trixie/main amd64 protobuf-compiler amd64 3.21.12-9 [84.5 kB] Get: 460 http://deb.debian.org/debian trixie/main amd64 zip amd64 3.0-14 [233 kB] Get: 461 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 462 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.4.1-3 [28.3 MB] Get: 463 http://deb.debian.org/debian trixie/main amd64 r-cran-rjava amd64 1.0-11-1 [702 kB] Get: 464 http://deb.debian.org/debian trixie/main amd64 testng all 6.9.12-4 [795 kB] Fetched 404 MB in 9s (46.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libapparmor1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19787 files and directories currently installed.) Preparing to unpack .../libapparmor1_3.1.7-1+b1_amd64.deb ... Unpacking libapparmor1:amd64 (3.1.7-1+b1) ... Selecting previously unselected package libsystemd-shared:amd64. Preparing to unpack .../libsystemd-shared_256.6-1_amd64.deb ... Unpacking libsystemd-shared:amd64 (256.6-1) ... Selecting previously unselected package systemd. Preparing to unpack .../systemd_256.6-1_amd64.deb ... Unpacking systemd (256.6-1) ... Setting up libapparmor1:amd64 (3.1.7-1+b1) ... Setting up libsystemd-shared:amd64 (256.6-1) ... Setting up systemd (256.6-1) ... 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. /usr/lib/tmpfiles.d/legacy.conf:13: Duplicate line for path "/run/lock", ignoring. Selecting previously unselected package systemd-sysv. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20750 files and directories currently installed.) Preparing to unpack .../00-systemd-sysv_256.6-1_amd64.deb ... Unpacking systemd-sysv (256.6-1) ... Selecting previously unselected package libdbus-1-3:amd64. Preparing to unpack .../01-libdbus-1-3_1.14.10-4+b1_amd64.deb ... Unpacking libdbus-1-3:amd64 (1.14.10-4+b1) ... Selecting previously unselected package dbus-bin. Preparing to unpack .../02-dbus-bin_1.14.10-4+b1_amd64.deb ... Unpacking dbus-bin (1.14.10-4+b1) ... Selecting previously unselected package dbus-session-bus-common. Preparing to unpack .../03-dbus-session-bus-common_1.14.10-4_all.deb ... Unpacking dbus-session-bus-common (1.14.10-4) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../04-libexpat1_2.6.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.3-1) ... Selecting previously unselected package dbus-daemon. Preparing to unpack .../05-dbus-daemon_1.14.10-4+b1_amd64.deb ... Unpacking dbus-daemon (1.14.10-4+b1) ... Selecting previously unselected package dbus-system-bus-common. Preparing to unpack .../06-dbus-system-bus-common_1.14.10-4_all.deb ... Unpacking dbus-system-bus-common (1.14.10-4) ... Selecting previously unselected package dbus. Preparing to unpack .../07-dbus_1.14.10-4+b1_amd64.deb ... Unpacking dbus (1.14.10-4+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package binfmt-support. Preparing to unpack .../09-binfmt-support_2.2.2-7_amd64.deb ... Unpacking binfmt-support (2.2.2-7) ... Selecting previously unselected package libpython3.12-minimal:amd64. Preparing to unpack .../10-libpython3.12-minimal_3.12.6-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.6-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../11-python3.12-minimal_3.12.6-1_amd64.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:amd64 (3.12.6-1) ... Setting up libexpat1:amd64 (2.6.3-1) ... Setting up python3.12-minimal (3.12.6-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21188 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_amd64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.1-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../07-libkeyutils1_1.6.3-3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b2) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... 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 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.6-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.6-1_amd64.deb ... Unpacking python3.12 (3.12.6-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 22260 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_amd64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../002-libproc2-0_2%3a4.0.4-6_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.4-6_amd64.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../005-openssl_3.3.2-1_amd64.deb ... Unpacking openssl (3.3.2-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../006-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../007-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../008-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../009-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../010-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../011-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../012-groff-base_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package libpam-systemd:amd64. Preparing to unpack .../013-libpam-systemd_256.6-1_amd64.deb ... Unpacking libpam-systemd:amd64 (256.6-1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../014-bsdextrautils_2.40.2-9_amd64.deb ... Unpacking bsdextrautils (2.40.2-9) ... Selecting previously unselected package man-db. Preparing to unpack .../015-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package ucf. Preparing to unpack .../016-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package libgdk-pixbuf2.0-common. Preparing to unpack .../017-libgdk-pixbuf2.0-common_2.42.12+dfsg-1_all.deb ... Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ... Selecting previously unselected package libglib2.0-0t64:amd64. Preparing to unpack .../018-libglib2.0-0t64_2.82.1-1_amd64.deb ... Unpacking libglib2.0-0t64:amd64 (2.82.1-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../019-libicu72_72.1-5_amd64.deb ... Unpacking libicu72:amd64 (72.1-5) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../020-libxml2_2.12.7+dfsg+really2.9.14-0.1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... Selecting previously unselected package shared-mime-info. Preparing to unpack .../021-shared-mime-info_2.4-5+b1_amd64.deb ... Unpacking shared-mime-info (2.4-5+b1) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../022-libjpeg62-turbo_1%3a2.1.5-3_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-3) ... Selecting previously unselected package libpng16-16t64:amd64. Preparing to unpack .../023-libpng16-16t64_1.6.44-2_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.44-2) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../024-libdeflate0_1.22-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.22-1) ... Selecting previously unselected package libjbig0:amd64. Preparing to unpack .../025-libjbig0_2.1-6.1+b1_amd64.deb ... Unpacking libjbig0:amd64 (2.1-6.1+b1) ... Selecting previously unselected package liblerc4:amd64. Preparing to unpack .../026-liblerc4_4.0.0+ds-4+b1_amd64.deb ... Unpacking liblerc4:amd64 (4.0.0+ds-4+b1) ... Selecting previously unselected package libsharpyuv0:amd64. Preparing to unpack .../027-libsharpyuv0_1.4.0-0.1_amd64.deb ... Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... Selecting previously unselected package libwebp7:amd64. Preparing to unpack .../028-libwebp7_1.4.0-0.1_amd64.deb ... Unpacking libwebp7:amd64 (1.4.0-0.1) ... Selecting previously unselected package libtiff6:amd64. Preparing to unpack .../029-libtiff6_4.5.1+git230720-5_amd64.deb ... Unpacking libtiff6:amd64 (4.5.1+git230720-5) ... Selecting previously unselected package libgdk-pixbuf-2.0-0:amd64. Preparing to unpack .../030-libgdk-pixbuf-2.0-0_2.42.12+dfsg-1_amd64.deb ... Unpacking libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-1) ... Selecting previously unselected package gtk-update-icon-cache. Preparing to unpack .../031-gtk-update-icon-cache_4.16.3+ds-1_amd64.deb ... No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. No diversion 'diversion of /usr/share/man/man8/update-icon-caches.8.gz to /usr/share/man/man8/update-icon-caches.gtk2.8.gz by libgtk-3-bin', none removed. Unpacking gtk-update-icon-cache (4.16.3+ds-1) ... Selecting previously unselected package hicolor-icon-theme. Preparing to unpack .../032-hicolor-icon-theme_0.18-1_all.deb ... Unpacking hicolor-icon-theme (0.18-1) ... Selecting previously unselected package adwaita-icon-theme. Preparing to unpack .../033-adwaita-icon-theme_47.0-1_all.deb ... Unpacking adwaita-icon-theme (47.0-1) ... Selecting previously unselected package ca-certificates-java. Preparing to unpack .../034-ca-certificates-java_20240118_all.deb ... Unpacking ca-certificates-java (20240118) ... Selecting previously unselected package java-common. Preparing to unpack .../035-java-common_0.76_all.deb ... Unpacking java-common (0.76) ... Selecting previously unselected package liblcms2-2:amd64. Preparing to unpack .../036-liblcms2-2_2.14-2+b1_amd64.deb ... Unpacking liblcms2-2:amd64 (2.14-2+b1) ... Selecting previously unselected package libnspr4:amd64. Preparing to unpack .../037-libnspr4_2%3a4.35-1.1+b1_amd64.deb ... Unpacking libnspr4:amd64 (2:4.35-1.1+b1) ... Selecting previously unselected package libnss3:amd64. Preparing to unpack .../038-libnss3_2%3a3.105-2_amd64.deb ... Unpacking libnss3:amd64 (2:3.105-2) ... Selecting previously unselected package libpcsclite1:amd64. Preparing to unpack .../039-libpcsclite1_2.3.0-1_amd64.deb ... Unpacking libpcsclite1:amd64 (2.3.0-1) ... Selecting previously unselected package openjdk-21-jre-headless:amd64. Preparing to unpack .../040-openjdk-21-jre-headless_21.0.5~8ea-1_amd64.deb ... Unpacking openjdk-21-jre-headless:amd64 (21.0.5~8ea-1) ... Selecting previously unselected package default-jre-headless. Preparing to unpack .../041-default-jre-headless_2%3a1.21-76_amd64.deb ... Unpacking default-jre-headless (2:1.21-76) ... Selecting previously unselected package ant. Preparing to unpack .../042-ant_1.10.15-1_all.deb ... Unpacking ant (1.10.15-1) ... Selecting previously unselected package ant-contrib. Preparing to unpack .../043-ant-contrib_1.0~b3+svn177-12_all.deb ... Unpacking ant-contrib (1.0~b3+svn177-12) ... Selecting previously unselected package at-spi2-common. Preparing to unpack .../044-at-spi2-common_2.54.0-1_all.deb ... Unpacking at-spi2-common (2.54.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../045-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../046-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../047-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../048-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../049-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package dbus-user-session. Preparing to unpack .../050-dbus-user-session_1.14.10-4+b1_amd64.deb ... Unpacking dbus-user-session (1.14.10-4+b1) ... Selecting previously unselected package libdconf1:amd64. Preparing to unpack .../051-libdconf1_0.40.0-4+b2_amd64.deb ... Unpacking libdconf1:amd64 (0.40.0-4+b2) ... Selecting previously unselected package dconf-service. Preparing to unpack .../052-dconf-service_0.40.0-4+b2_amd64.deb ... Unpacking dconf-service (0.40.0-4+b2) ... Selecting previously unselected package dconf-gsettings-backend:amd64. Preparing to unpack .../053-dconf-gsettings-backend_0.40.0-4+b2_amd64.deb ... Unpacking dconf-gsettings-backend:amd64 (0.40.0-4+b2) ... Selecting previously unselected package dctrl-tools. Preparing to unpack .../054-dctrl-tools_2.24-3+b1_amd64.deb ... Unpacking dctrl-tools (2.24-3+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../055-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../056-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../057-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../058-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../059-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../060-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../061-libelf1t64_0.191-2_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-2) ... Selecting previously unselected package dwz. Preparing to unpack .../062-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../063-gettext_0.22.5-2_amd64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../064-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../065-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../066-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package libatk1.0-0t64:amd64. Preparing to unpack .../067-libatk1.0-0t64_2.54.0-1_amd64.deb ... Unpacking libatk1.0-0t64:amd64 (2.54.0-1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../068-libxau6_1%3a1.0.9-1+b1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.9-1+b1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../069-libxdmcp6_1%3a1.1.2-3+b1_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3+b1) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../070-libxcb1_1.17.0-2_amd64.deb ... Unpacking libxcb1:amd64 (1.17.0-2) ... Selecting previously unselected package libx11-data. Preparing to unpack .../071-libx11-data_2%3a1.8.7-1_all.deb ... Unpacking libx11-data (2:1.8.7-1) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../072-libx11-6_2%3a1.8.7-1+b1_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.7-1+b1) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../073-libxext6_2%3a1.3.4-1+b1_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.4-1+b1) ... Selecting previously unselected package libxi6:amd64. Preparing to unpack .../074-libxi6_2%3a1.8.2-1_amd64.deb ... Unpacking libxi6:amd64 (2:1.8.2-1) ... Selecting previously unselected package libatspi2.0-0t64:amd64. Preparing to unpack .../075-libatspi2.0-0t64_2.54.0-1_amd64.deb ... Unpacking libatspi2.0-0t64:amd64 (2.54.0-1) ... Selecting previously unselected package libatk-bridge2.0-0t64:amd64. Preparing to unpack .../076-libatk-bridge2.0-0t64_2.54.0-1_amd64.deb ... Unpacking libatk-bridge2.0-0t64:amd64 (2.54.0-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../077-libbrotli1_1.1.0-2+b4_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b4) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../078-libfreetype6_2.13.3+dfsg-1_amd64.deb ... Unpacking libfreetype6:amd64 (2.13.3+dfsg-1) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../079-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../080-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../081-fontconfig-config_2.15.0-1.1_amd64.deb ... Unpacking fontconfig-config (2.15.0-1.1) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../082-libfontconfig1_2.15.0-1.1_amd64.deb ... Unpacking libfontconfig1:amd64 (2.15.0-1.1) ... Selecting previously unselected package libpixman-1-0:amd64. Preparing to unpack .../083-libpixman-1-0_0.42.2-1+b1_amd64.deb ... Unpacking libpixman-1-0:amd64 (0.42.2-1+b1) ... Selecting previously unselected package libxcb-render0:amd64. Preparing to unpack .../084-libxcb-render0_1.17.0-2_amd64.deb ... Unpacking libxcb-render0:amd64 (1.17.0-2) ... Selecting previously unselected package libxcb-shm0:amd64. Preparing to unpack .../085-libxcb-shm0_1.17.0-2_amd64.deb ... Unpacking libxcb-shm0:amd64 (1.17.0-2) ... Selecting previously unselected package libxrender1:amd64. Preparing to unpack .../086-libxrender1_1%3a0.9.10-1.1+b1_amd64.deb ... Unpacking libxrender1:amd64 (1:0.9.10-1.1+b1) ... Selecting previously unselected package libcairo2:amd64. Preparing to unpack .../087-libcairo2_1.18.2-2_amd64.deb ... Unpacking libcairo2:amd64 (1.18.2-2) ... Selecting previously unselected package libcairo-gobject2:amd64. Preparing to unpack .../088-libcairo-gobject2_1.18.2-2_amd64.deb ... Unpacking libcairo-gobject2:amd64 (1.18.2-2) ... Selecting previously unselected package libcloudproviders0:amd64. Preparing to unpack .../089-libcloudproviders0_0.3.6-1_amd64.deb ... Unpacking libcloudproviders0:amd64 (0.3.6-1) ... Selecting previously unselected package libcolord2:amd64. Preparing to unpack .../090-libcolord2_1.4.7-1+b1_amd64.deb ... Unpacking libcolord2:amd64 (1.4.7-1+b1) ... Selecting previously unselected package libavahi-common-data:amd64. Preparing to unpack .../091-libavahi-common-data_0.8-13+b2_amd64.deb ... Unpacking libavahi-common-data:amd64 (0.8-13+b2) ... Selecting previously unselected package libavahi-common3:amd64. Preparing to unpack .../092-libavahi-common3_0.8-13+b2_amd64.deb ... Unpacking libavahi-common3:amd64 (0.8-13+b2) ... Selecting previously unselected package libavahi-client3:amd64. Preparing to unpack .../093-libavahi-client3_0.8-13+b2_amd64.deb ... Unpacking libavahi-client3:amd64 (0.8-13+b2) ... Selecting previously unselected package libcups2t64:amd64. Preparing to unpack .../094-libcups2t64_2.4.10-2_amd64.deb ... Unpacking libcups2t64:amd64 (2.4.10-2) ... Selecting previously unselected package libepoxy0:amd64. Preparing to unpack .../095-libepoxy0_1.5.10-2_amd64.deb ... Unpacking libepoxy0:amd64 (1.5.10-2) ... Selecting previously unselected package libfribidi0:amd64. Preparing to unpack .../096-libfribidi0_1.0.15-1_amd64.deb ... Unpacking libfribidi0:amd64 (1.0.15-1) ... Selecting previously unselected package libgraphite2-3:amd64. Preparing to unpack .../097-libgraphite2-3_1.3.14-2_amd64.deb ... Unpacking libgraphite2-3:amd64 (1.3.14-2) ... Selecting previously unselected package libharfbuzz0b:amd64. Preparing to unpack .../098-libharfbuzz0b_9.0.0-1_amd64.deb ... Unpacking libharfbuzz0b:amd64 (9.0.0-1) ... Selecting previously unselected package fontconfig. Preparing to unpack .../099-fontconfig_2.15.0-1.1_amd64.deb ... Unpacking fontconfig (2.15.0-1.1) ... Selecting previously unselected package libthai-data. Preparing to unpack .../100-libthai-data_0.1.29-2_all.deb ... Unpacking libthai-data (0.1.29-2) ... Selecting previously unselected package libdatrie1:amd64. Preparing to unpack .../101-libdatrie1_0.2.13-3_amd64.deb ... Unpacking libdatrie1:amd64 (0.2.13-3) ... Selecting previously unselected package libthai0:amd64. Preparing to unpack .../102-libthai0_0.1.29-2_amd64.deb ... Unpacking libthai0:amd64 (0.1.29-2) ... Selecting previously unselected package libpango-1.0-0:amd64. Preparing to unpack .../103-libpango-1.0-0_1.54.0+ds-2_amd64.deb ... Unpacking libpango-1.0-0:amd64 (1.54.0+ds-2) ... Selecting previously unselected package libpangoft2-1.0-0:amd64. Preparing to unpack .../104-libpangoft2-1.0-0_1.54.0+ds-2_amd64.deb ... Unpacking libpangoft2-1.0-0:amd64 (1.54.0+ds-2) ... Selecting previously unselected package libpangocairo-1.0-0:amd64. Preparing to unpack .../105-libpangocairo-1.0-0_1.54.0+ds-2_amd64.deb ... Unpacking libpangocairo-1.0-0:amd64 (1.54.0+ds-2) ... Selecting previously unselected package libwayland-client0:amd64. Preparing to unpack .../106-libwayland-client0_1.23.0-1_amd64.deb ... Unpacking libwayland-client0:amd64 (1.23.0-1) ... Selecting previously unselected package libwayland-cursor0:amd64. Preparing to unpack .../107-libwayland-cursor0_1.23.0-1_amd64.deb ... Unpacking libwayland-cursor0:amd64 (1.23.0-1) ... Selecting previously unselected package libwayland-egl1:amd64. Preparing to unpack .../108-libwayland-egl1_1.23.0-1_amd64.deb ... Unpacking libwayland-egl1:amd64 (1.23.0-1) ... Selecting previously unselected package libxcomposite1:amd64. Preparing to unpack .../109-libxcomposite1_1%3a0.4.5-1+b1_amd64.deb ... Unpacking libxcomposite1:amd64 (1:0.4.5-1+b1) ... Selecting previously unselected package libxfixes3:amd64. Preparing to unpack .../110-libxfixes3_1%3a6.0.0-2+b1_amd64.deb ... Unpacking libxfixes3:amd64 (1:6.0.0-2+b1) ... Selecting previously unselected package libxcursor1:amd64. Preparing to unpack .../111-libxcursor1_1%3a1.2.2-1_amd64.deb ... Unpacking libxcursor1:amd64 (1:1.2.2-1) ... Selecting previously unselected package libxdamage1:amd64. Preparing to unpack .../112-libxdamage1_1%3a1.1.6-1+b1_amd64.deb ... Unpacking libxdamage1:amd64 (1:1.1.6-1+b1) ... Selecting previously unselected package libxinerama1:amd64. Preparing to unpack .../113-libxinerama1_2%3a1.1.4-3+b1_amd64.deb ... Unpacking libxinerama1:amd64 (2:1.1.4-3+b1) ... Selecting previously unselected package xkb-data. Preparing to unpack .../114-xkb-data_2.42-1_all.deb ... Unpacking xkb-data (2.42-1) ... Selecting previously unselected package libxkbcommon0:amd64. Preparing to unpack .../115-libxkbcommon0_1.6.0-1+b1_amd64.deb ... Unpacking libxkbcommon0:amd64 (1.6.0-1+b1) ... Selecting previously unselected package libxrandr2:amd64. Preparing to unpack .../116-libxrandr2_2%3a1.5.4-1_amd64.deb ... Unpacking libxrandr2:amd64 (2:1.5.4-1) ... Selecting previously unselected package libgtk-3-common. Preparing to unpack .../117-libgtk-3-common_3.24.43-4_all.deb ... Unpacking libgtk-3-common (3.24.43-4) ... Selecting previously unselected package libgtk-3-0t64:amd64. Preparing to unpack .../118-libgtk-3-0t64_3.24.43-4_amd64.deb ... Unpacking libgtk-3-0t64:amd64 (3.24.43-4) ... Selecting previously unselected package libglvnd0:amd64. Preparing to unpack .../119-libglvnd0_1.7.0-1+b1_amd64.deb ... Unpacking libglvnd0:amd64 (1.7.0-1+b1) ... Selecting previously unselected package libdrm-common. Preparing to unpack .../120-libdrm-common_2.4.123-1_all.deb ... Unpacking libdrm-common (2.4.123-1) ... Selecting previously unselected package libdrm2:amd64. Preparing to unpack .../121-libdrm2_2.4.123-1_amd64.deb ... Unpacking libdrm2:amd64 (2.4.123-1) ... Selecting previously unselected package libglapi-mesa:amd64. Preparing to unpack .../122-libglapi-mesa_24.2.4-1_amd64.deb ... Unpacking libglapi-mesa:amd64 (24.2.4-1) ... Selecting previously unselected package libx11-xcb1:amd64. Preparing to unpack .../123-libx11-xcb1_2%3a1.8.7-1+b1_amd64.deb ... Unpacking libx11-xcb1:amd64 (2:1.8.7-1+b1) ... Selecting previously unselected package libxcb-dri2-0:amd64. Preparing to unpack .../124-libxcb-dri2-0_1.17.0-2_amd64.deb ... Unpacking libxcb-dri2-0:amd64 (1.17.0-2) ... Selecting previously unselected package libxcb-dri3-0:amd64. Preparing to unpack .../125-libxcb-dri3-0_1.17.0-2_amd64.deb ... Unpacking libxcb-dri3-0:amd64 (1.17.0-2) ... Selecting previously unselected package libxcb-glx0:amd64. Preparing to unpack .../126-libxcb-glx0_1.17.0-2_amd64.deb ... Unpacking libxcb-glx0:amd64 (1.17.0-2) ... Selecting previously unselected package libxcb-present0:amd64. Preparing to unpack .../127-libxcb-present0_1.17.0-2_amd64.deb ... Unpacking libxcb-present0:amd64 (1.17.0-2) ... Selecting previously unselected package libxcb-randr0:amd64. Preparing to unpack .../128-libxcb-randr0_1.17.0-2_amd64.deb ... Unpacking libxcb-randr0:amd64 (1.17.0-2) ... Selecting previously unselected package libxcb-sync1:amd64. Preparing to unpack .../129-libxcb-sync1_1.17.0-2_amd64.deb ... Unpacking libxcb-sync1:amd64 (1.17.0-2) ... Selecting previously unselected package libxcb-xfixes0:amd64. Preparing to unpack .../130-libxcb-xfixes0_1.17.0-2_amd64.deb ... Unpacking libxcb-xfixes0:amd64 (1.17.0-2) ... Selecting previously unselected package libxshmfence1:amd64. Preparing to unpack .../131-libxshmfence1_1.3-1+b1_amd64.deb ... Unpacking libxshmfence1:amd64 (1.3-1+b1) ... Selecting previously unselected package libxxf86vm1:amd64. Preparing to unpack .../132-libxxf86vm1_1%3a1.1.4-1+b2_amd64.deb ... Unpacking libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Selecting previously unselected package libdrm-amdgpu1:amd64. Preparing to unpack .../133-libdrm-amdgpu1_2.4.123-1_amd64.deb ... Unpacking libdrm-amdgpu1:amd64 (2.4.123-1) ... Selecting previously unselected package libpciaccess0:amd64. Preparing to unpack .../134-libpciaccess0_0.17-3+b1_amd64.deb ... Unpacking libpciaccess0:amd64 (0.17-3+b1) ... Selecting previously unselected package libdrm-intel1:amd64. Preparing to unpack .../135-libdrm-intel1_2.4.123-1_amd64.deb ... Unpacking libdrm-intel1:amd64 (2.4.123-1) ... Selecting previously unselected package libdrm-radeon1:amd64. Preparing to unpack .../136-libdrm-radeon1_2.4.123-1_amd64.deb ... Unpacking libdrm-radeon1:amd64 (2.4.123-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../137-libedit2_3.1-20240808-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20240808-1) ... Selecting previously unselected package libz3-4:amd64. Preparing to unpack .../138-libz3-4_4.8.12-3.1+b2_amd64.deb ... Unpacking libz3-4:amd64 (4.8.12-3.1+b2) ... Selecting previously unselected package libllvm19:amd64. Preparing to unpack .../139-libllvm19_1%3a19.1.1-1_amd64.deb ... Unpacking libllvm19:amd64 (1:19.1.1-1) ... Selecting previously unselected package libsensors-config. Preparing to unpack .../140-libsensors-config_1%3a3.6.0-10_all.deb ... Unpacking libsensors-config (1:3.6.0-10) ... Selecting previously unselected package libsensors5:amd64. Preparing to unpack .../141-libsensors5_1%3a3.6.0-10_amd64.deb ... Unpacking libsensors5:amd64 (1:3.6.0-10) ... Selecting previously unselected package mesa-libgallium:amd64. Preparing to unpack .../142-mesa-libgallium_24.2.4-1_amd64.deb ... Unpacking mesa-libgallium:amd64 (24.2.4-1) ... Selecting previously unselected package libvulkan1:amd64. Preparing to unpack .../143-libvulkan1_1.3.290.0-1_amd64.deb ... Unpacking libvulkan1:amd64 (1.3.290.0-1) ... Selecting previously unselected package libwayland-server0:amd64. Preparing to unpack .../144-libwayland-server0_1.23.0-1_amd64.deb ... Unpacking libwayland-server0:amd64 (1.23.0-1) ... Selecting previously unselected package libgbm1:amd64. Preparing to unpack .../145-libgbm1_24.2.4-1_amd64.deb ... Unpacking libgbm1:amd64 (24.2.4-1) ... Selecting previously unselected package libgl1-mesa-dri:amd64. Preparing to unpack .../146-libgl1-mesa-dri_24.2.4-1_amd64.deb ... Unpacking libgl1-mesa-dri:amd64 (24.2.4-1) ... Selecting previously unselected package libglx-mesa0:amd64. Preparing to unpack .../147-libglx-mesa0_24.2.4-1_amd64.deb ... Unpacking libglx-mesa0:amd64 (24.2.4-1) ... Selecting previously unselected package libglx0:amd64. Preparing to unpack .../148-libglx0_1.7.0-1+b1_amd64.deb ... Unpacking libglx0:amd64 (1.7.0-1+b1) ... Selecting previously unselected package libgl1:amd64. Preparing to unpack .../149-libgl1_1.7.0-1+b1_amd64.deb ... Unpacking libgl1:amd64 (1.7.0-1+b1) ... Selecting previously unselected package libasound2-data. Preparing to unpack .../150-libasound2-data_1.2.12-1_all.deb ... Unpacking libasound2-data (1.2.12-1) ... Selecting previously unselected package libasound2t64:amd64. Preparing to unpack .../151-libasound2t64_1.2.12-1_amd64.deb ... Unpacking libasound2t64:amd64 (1.2.12-1) ... Selecting previously unselected package libgif7:amd64. Preparing to unpack .../152-libgif7_5.2.2-1_amd64.deb ... Unpacking libgif7:amd64 (5.2.2-1) ... Selecting previously unselected package x11-common. Preparing to unpack .../153-x11-common_1%3a7.7+23.1_all.deb ... Unpacking x11-common (1:7.7+23.1) ... Selecting previously unselected package libxtst6:amd64. Preparing to unpack .../154-libxtst6_2%3a1.2.3-1.1+b1_amd64.deb ... Unpacking libxtst6:amd64 (2:1.2.3-1.1+b1) ... Selecting previously unselected package openjdk-21-jre:amd64. Preparing to unpack .../155-openjdk-21-jre_21.0.5~8ea-1_amd64.deb ... Unpacking openjdk-21-jre:amd64 (21.0.5~8ea-1) ... Selecting previously unselected package default-jre. Preparing to unpack .../156-default-jre_2%3a1.21-76_amd64.deb ... Unpacking default-jre (2:1.21-76) ... Selecting previously unselected package openjdk-21-jdk-headless:amd64. Preparing to unpack .../157-openjdk-21-jdk-headless_21.0.5~8ea-1_amd64.deb ... Unpacking openjdk-21-jdk-headless:amd64 (21.0.5~8ea-1) ... Selecting previously unselected package default-jdk-headless. Preparing to unpack .../158-default-jdk-headless_2%3a1.21-76_amd64.deb ... Unpacking default-jdk-headless (2:1.21-76) ... Selecting previously unselected package openjdk-21-jdk:amd64. Preparing to unpack .../159-openjdk-21-jdk_21.0.5~8ea-1_amd64.deb ... Unpacking openjdk-21-jdk:amd64 (21.0.5~8ea-1) ... Selecting previously unselected package default-jdk. Preparing to unpack .../160-default-jdk_2%3a1.21-76_amd64.deb ... Unpacking default-jdk (2:1.21-76) ... Selecting previously unselected package libassuan9:amd64. Preparing to unpack .../161-libassuan9_3.0.1-2_amd64.deb ... Unpacking libassuan9:amd64 (3.0.1-2) ... Selecting previously unselected package gpgconf. Preparing to unpack .../162-gpgconf_2.2.43-8+b1_amd64.deb ... Unpacking gpgconf (2.2.43-8+b1) ... Selecting previously unselected package libksba8:amd64. Preparing to unpack .../163-libksba8_1.6.7-2_amd64.deb ... Unpacking libksba8:amd64 (1.6.7-2) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../164-libsasl2-modules-db_2.1.28+dfsg1-8_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../165-libsasl2-2_2.1.28+dfsg1-8_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../166-libldap-2.5-0_2.5.18+dfsg-3_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.18+dfsg-3) ... Selecting previously unselected package libnpth0t64:amd64. Preparing to unpack .../167-libnpth0t64_1.6-3.1_amd64.deb ... Unpacking libnpth0t64:amd64 (1.6-3.1) ... Selecting previously unselected package dirmngr. Preparing to unpack .../168-dirmngr_2.2.43-8+b1_amd64.deb ... Unpacking dirmngr (2.2.43-8+b1) ... Selecting previously unselected package gnupg-l10n. Preparing to unpack .../169-gnupg-l10n_2.2.43-8_all.deb ... Unpacking gnupg-l10n (2.2.43-8) ... Selecting previously unselected package gpg. Preparing to unpack .../170-gpg_2.2.43-8+b1_amd64.deb ... Unpacking gpg (2.2.43-8+b1) ... Selecting previously unselected package pinentry-curses. Preparing to unpack .../171-pinentry-curses_1.2.1-4+b1_amd64.deb ... Unpacking pinentry-curses (1.2.1-4+b1) ... Selecting previously unselected package gpg-agent. Preparing to unpack .../172-gpg-agent_2.2.43-8+b1_amd64.deb ... Unpacking gpg-agent (2.2.43-8+b1) ... Selecting previously unselected package gpgsm. Preparing to unpack .../173-gpgsm_2.2.43-8+b1_amd64.deb ... Unpacking gpgsm (2.2.43-8+b1) ... Selecting previously unselected package gnupg. Preparing to unpack .../174-gnupg_2.2.43-8_all.deb ... Unpacking gnupg (2.2.43-8) ... Selecting previously unselected package libfile-dirlist-perl. Preparing to unpack .../175-libfile-dirlist-perl_0.05-3_all.deb ... Unpacking libfile-dirlist-perl (0.05-3) ... Selecting previously unselected package libfile-which-perl. Preparing to unpack .../176-libfile-which-perl_1.27-2_all.deb ... Unpacking libfile-which-perl (1.27-2) ... Selecting previously unselected package libfile-homedir-perl. Preparing to unpack .../177-libfile-homedir-perl_1.006-2_all.deb ... Unpacking libfile-homedir-perl (1.006-2) ... Selecting previously unselected package libfile-touch-perl. Preparing to unpack .../178-libfile-touch-perl_0.12-2_all.deb ... Unpacking libfile-touch-perl (0.12-2) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../179-libio-pty-perl_1%3a1.20-1+b1_amd64.deb ... Unpacking libio-pty-perl (1:1.20-1+b1) ... Selecting previously unselected package libipc-run-perl. Preparing to unpack .../180-libipc-run-perl_20231003.0-2_all.deb ... Unpacking libipc-run-perl (20231003.0-2) ... Selecting previously unselected package libclass-method-modifiers-perl. Preparing to unpack .../181-libclass-method-modifiers-perl_2.15-1_all.deb ... Unpacking libclass-method-modifiers-perl (2.15-1) ... Selecting previously unselected package libclass-xsaccessor-perl. Preparing to unpack .../182-libclass-xsaccessor-perl_1.19-4+b3_amd64.deb ... Unpacking libclass-xsaccessor-perl (1.19-4+b3) ... Selecting previously unselected package libb-hooks-op-check-perl:amd64. Preparing to unpack .../183-libb-hooks-op-check-perl_0.22-3+b1_amd64.deb ... Unpacking libb-hooks-op-check-perl:amd64 (0.22-3+b1) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../184-libdynaloader-functions-perl_0.004-1_all.deb ... Unpacking libdynaloader-functions-perl (0.004-1) ... Selecting previously unselected package libdevel-callchecker-perl:amd64. Preparing to unpack .../185-libdevel-callchecker-perl_0.009-1_amd64.deb ... Unpacking libdevel-callchecker-perl:amd64 (0.009-1) ... Selecting previously unselected package libparams-classify-perl:amd64. Preparing to unpack .../186-libparams-classify-perl_0.015-2+b3_amd64.deb ... Unpacking libparams-classify-perl:amd64 (0.015-2+b3) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../187-libmodule-runtime-perl_0.016-2_all.deb ... Unpacking libmodule-runtime-perl (0.016-2) ... Selecting previously unselected package libimport-into-perl. Preparing to unpack .../188-libimport-into-perl_1.002005-2_all.deb ... Unpacking libimport-into-perl (1.002005-2) ... Selecting previously unselected package librole-tiny-perl. Preparing to unpack .../189-librole-tiny-perl_2.002004-1_all.deb ... Unpacking librole-tiny-perl (2.002004-1) ... Selecting previously unselected package libsub-quote-perl. Preparing to unpack .../190-libsub-quote-perl_2.006008-1_all.deb ... Unpacking libsub-quote-perl (2.006008-1) ... Selecting previously unselected package libmoo-perl. Preparing to unpack .../191-libmoo-perl_2.005005-1_all.deb ... Unpacking libmoo-perl (2.005005-1) ... Selecting previously unselected package libencode-locale-perl. Preparing to unpack .../192-libencode-locale-perl_1.05-3_all.deb ... Unpacking libencode-locale-perl (1.05-3) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../193-libtimedate-perl_2.3300-2_all.deb ... Unpacking libtimedate-perl (2.3300-2) ... Selecting previously unselected package libhttp-date-perl. Preparing to unpack .../194-libhttp-date-perl_6.06-1_all.deb ... Unpacking libhttp-date-perl (6.06-1) ... Selecting previously unselected package libfile-listing-perl. Preparing to unpack .../195-libfile-listing-perl_6.16-1_all.deb ... Unpacking libfile-listing-perl (6.16-1) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../196-libhtml-tagset-perl_3.24-1_all.deb ... Unpacking libhtml-tagset-perl (3.24-1) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../197-liburi-perl_5.29-1_all.deb ... Unpacking liburi-perl (5.29-1) ... Selecting previously unselected package libhtml-parser-perl:amd64. Preparing to unpack .../198-libhtml-parser-perl_3.83-1_amd64.deb ... Unpacking libhtml-parser-perl:amd64 (3.83-1) ... Selecting previously unselected package libhtml-tree-perl. Preparing to unpack .../199-libhtml-tree-perl_5.07-3_all.deb ... Unpacking libhtml-tree-perl (5.07-3) ... Selecting previously unselected package libclone-perl:amd64. Preparing to unpack .../200-libclone-perl_0.47-1_amd64.deb ... Unpacking libclone-perl:amd64 (0.47-1) ... Selecting previously unselected package libio-html-perl. Preparing to unpack .../201-libio-html-perl_1.004-3_all.deb ... Unpacking libio-html-perl (1.004-3) ... Selecting previously unselected package liblwp-mediatypes-perl. Preparing to unpack .../202-liblwp-mediatypes-perl_6.04-2_all.deb ... Unpacking liblwp-mediatypes-perl (6.04-2) ... Selecting previously unselected package libhttp-message-perl. Preparing to unpack .../203-libhttp-message-perl_6.46-1_all.deb ... Unpacking libhttp-message-perl (6.46-1) ... Selecting previously unselected package libhttp-cookies-perl. Preparing to unpack .../204-libhttp-cookies-perl_6.11-1_all.deb ... Unpacking libhttp-cookies-perl (6.11-1) ... Selecting previously unselected package libhttp-negotiate-perl. Preparing to unpack .../205-libhttp-negotiate-perl_6.01-2_all.deb ... Unpacking libhttp-negotiate-perl (6.01-2) ... Selecting previously unselected package perl-openssl-defaults:amd64. Preparing to unpack .../206-perl-openssl-defaults_7+b2_amd64.deb ... Unpacking perl-openssl-defaults:amd64 (7+b2) ... Selecting previously unselected package libnet-ssleay-perl:amd64. Preparing to unpack .../207-libnet-ssleay-perl_1.94-1+b1_amd64.deb ... Unpacking libnet-ssleay-perl:amd64 (1.94-1+b1) ... Selecting previously unselected package libio-socket-ssl-perl. Preparing to unpack .../208-libio-socket-ssl-perl_2.089-1_all.deb ... Unpacking libio-socket-ssl-perl (2.089-1) ... Selecting previously unselected package libnet-http-perl. Preparing to unpack .../209-libnet-http-perl_6.23-1_all.deb ... Unpacking libnet-http-perl (6.23-1) ... Selecting previously unselected package liblwp-protocol-https-perl. Preparing to unpack .../210-liblwp-protocol-https-perl_6.14-1_all.deb ... Unpacking liblwp-protocol-https-perl (6.14-1) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../211-libtry-tiny-perl_0.32-1_all.deb ... Unpacking libtry-tiny-perl (0.32-1) ... Selecting previously unselected package libwww-robotrules-perl. Preparing to unpack .../212-libwww-robotrules-perl_6.02-1_all.deb ... Unpacking libwww-robotrules-perl (6.02-1) ... Selecting previously unselected package libwww-perl. Preparing to unpack .../213-libwww-perl_6.77-1_all.deb ... Unpacking libwww-perl (6.77-1) ... Selecting previously unselected package patchutils. Preparing to unpack .../214-patchutils_0.4.2-1_amd64.deb ... Unpacking patchutils (0.4.2-1) ... Selecting previously unselected package wdiff. Preparing to unpack .../215-wdiff_1.2.2-6_amd64.deb ... Unpacking wdiff (1.2.2-6) ... Selecting previously unselected package devscripts. Preparing to unpack .../216-devscripts_2.24.1_all.deb ... Unpacking devscripts (2.24.1) ... Selecting previously unselected package fastjar. Preparing to unpack .../217-fastjar_2%3a0.98-7_amd64.deb ... Unpacking fastjar (2:0.98-7) ... Selecting previously unselected package jarwrapper. Preparing to unpack .../218-jarwrapper_0.80_all.deb ... Unpacking jarwrapper (0.80) ... Selecting previously unselected package unzip. Preparing to unpack .../219-unzip_6.0-28_amd64.deb ... Unpacking unzip (6.0-28) ... Selecting previously unselected package java-wrappers. Preparing to unpack .../220-java-wrappers_0.5_all.deb ... Unpacking java-wrappers (0.5) ... Selecting previously unselected package javahelper. Preparing to unpack .../221-javahelper_0.80_all.deb ... Unpacking javahelper (0.80) ... Selecting previously unselected package libhamcrest-java. Preparing to unpack .../222-libhamcrest-java_2.2-2_all.deb ... Unpacking libhamcrest-java (2.2-2) ... Selecting previously unselected package junit4. Preparing to unpack .../223-junit4_4.13.2-4_all.deb ... Unpacking junit4 (4.13.2-4) ... Selecting previously unselected package libapiguardian-java. Preparing to unpack .../224-libapiguardian-java_1.1.2-1_all.deb ... Unpacking libapiguardian-java (1.1.2-1) ... Selecting previously unselected package libopentest4j-java. Preparing to unpack .../225-libopentest4j-java_1.2.0-4_all.deb ... Unpacking libopentest4j-java (1.2.0-4) ... Selecting previously unselected package libopentest4j-reporting-java. Preparing to unpack .../226-libopentest4j-reporting-java_0.1.0-M1-2_all.deb ... Unpacking libopentest4j-reporting-java (0.1.0-M1-2) ... Selecting previously unselected package libpicocli-java. Preparing to unpack .../227-libpicocli-java_4.6.2-2_all.deb ... Unpacking libpicocli-java (4.6.2-2) ... Selecting previously unselected package libunivocity-parsers-java. Preparing to unpack .../228-libunivocity-parsers-java_2.9.1-1_all.deb ... Unpacking libunivocity-parsers-java (2.9.1-1) ... Selecting previously unselected package junit5. Preparing to unpack .../229-junit5_5.10.3-1_all.deb ... Unpacking junit5 (5.10.3-1) ... Selecting previously unselected package libactivation-java. Preparing to unpack .../230-libactivation-java_1.2.0-2_all.deb ... Unpacking libactivation-java (1.2.0-2) ... Selecting previously unselected package libaopalliance-java. Preparing to unpack .../231-libaopalliance-java_20070526-7_all.deb ... Unpacking libaopalliance-java (20070526-7) ... Selecting previously unselected package libapache-pom-java. Preparing to unpack .../232-libapache-pom-java_29-2_all.deb ... Unpacking libapache-pom-java (29-2) ... Selecting previously unselected package libasm-java. Preparing to unpack .../233-libasm-java_9.7-2_all.deb ... Unpacking libasm-java (9.7-2) ... Selecting previously unselected package libatinject-jsr330-api-java. Preparing to unpack .../234-libatinject-jsr330-api-java_1.0+ds1-5_all.deb ... Unpacking libatinject-jsr330-api-java (1.0+ds1-5) ... Selecting previously unselected package libcommons-parent-java. Preparing to unpack .../235-libcommons-parent-java_56-1_all.deb ... Unpacking libcommons-parent-java (56-1) ... Selecting previously unselected package libcommons-lang3-java. Preparing to unpack .../236-libcommons-lang3-java_3.14.0-1_all.deb ... Unpacking libcommons-lang3-java (3.14.0-1) ... Selecting previously unselected package libfreemarker-java. Preparing to unpack .../237-libfreemarker-java_2.3.32-2_all.deb ... Unpacking libfreemarker-java (2.3.32-2) ... Selecting previously unselected package libgoogle-gson-java. Preparing to unpack .../238-libgoogle-gson-java_2.10.1-1_all.deb ... Unpacking libgoogle-gson-java (2.10.1-1) ... Selecting previously unselected package libjoptsimple-java. Preparing to unpack .../239-libjoptsimple-java_5.0.4-4_all.deb ... Unpacking libjoptsimple-java (5.0.4-4) ... Selecting previously unselected package libcommons-codec-java. Preparing to unpack .../240-libcommons-codec-java_1.16.0-1_all.deb ... Unpacking libcommons-codec-java (1.16.0-1) ... Selecting previously unselected package libcommons-logging-java. Preparing to unpack .../241-libcommons-logging-java_1.3.0-1_all.deb ... Unpacking libcommons-logging-java (1.3.0-1) ... Selecting previously unselected package libhttpcore-java. Preparing to unpack .../242-libhttpcore-java_4.4.16-1_all.deb ... Unpacking libhttpcore-java (4.4.16-1) ... Selecting previously unselected package libhttpclient-java. Preparing to unpack .../243-libhttpclient-java_4.5.14-1_all.deb ... Unpacking libhttpclient-java (4.5.14-1) ... Selecting previously unselected package liblightcouch-java. Preparing to unpack .../244-liblightcouch-java_0.2.0-1_all.deb ... Unpacking liblightcouch-java (0.2.0-1) ... Selecting previously unselected package libmongodb-java. Preparing to unpack .../245-libmongodb-java_3.6.3-2_all.deb ... Unpacking libmongodb-java (3.6.3-2) ... Selecting previously unselected package libslf4j-java. Preparing to unpack .../246-libslf4j-java_1.7.32-1_all.deb ... Unpacking libslf4j-java (1.7.32-1) ... Selecting previously unselected package liblog4j2-java. Preparing to unpack .../247-liblog4j2-java_2.19.0-2_all.deb ... Unpacking liblog4j2-java (2.19.0-2) ... Selecting previously unselected package libbarclay-java. Preparing to unpack .../248-libbarclay-java_5.0.0+dfsg-1_all.deb ... Unpacking libbarclay-java (5.0.0+dfsg-1) ... Selecting previously unselected package libjaxp1.3-java. Preparing to unpack .../249-libjaxp1.3-java_1.3.05-6_all.deb ... Unpacking libjaxp1.3-java (1.3.05-6) ... Selecting previously unselected package libxml-commons-external-java. Preparing to unpack .../250-libxml-commons-external-java_1.4.01-6_all.deb ... Unpacking libxml-commons-external-java (1.4.01-6) ... Selecting previously unselected package libcommons-io-java. Preparing to unpack .../251-libcommons-io-java_2.16.1-1_all.deb ... Unpacking libcommons-io-java (2.16.1-1) ... Selecting previously unselected package libxmlgraphics-commons-java. Preparing to unpack .../252-libxmlgraphics-commons-java_2.8-2_all.deb ... Unpacking libxmlgraphics-commons-java (2.8-2) ... Selecting previously unselected package libbatik-java. Preparing to unpack .../253-libbatik-java_1.17+dfsg-1_all.deb ... Unpacking libbatik-java (1.17+dfsg-1) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../254-libblas3_3.12.0-3_amd64.deb ... Unpacking libblas3:amd64 (3.12.0-3) ... Selecting previously unselected package libbsh-java. Preparing to unpack .../255-libbsh-java_2.0b4-20_all.deb ... Unpacking libbsh-java (2.0b4-20) ... Selecting previously unselected package libmaven-shared-utils-java. Preparing to unpack .../256-libmaven-shared-utils-java_3.3.4-1_all.deb ... Unpacking libmaven-shared-utils-java (3.3.4-1) ... Selecting previously unselected package libcommons-cli-java. Preparing to unpack .../257-libcommons-cli-java_1.6.0-1_all.deb ... Unpacking libcommons-cli-java (1.6.0-1) ... Selecting previously unselected package libgeronimo-annotation-1.3-spec-java. Preparing to unpack .../258-libgeronimo-annotation-1.3-spec-java_1.3-1_all.deb ... Unpacking libgeronimo-annotation-1.3-spec-java (1.3-1) ... Selecting previously unselected package liberror-prone-java. Preparing to unpack .../259-liberror-prone-java_2.18.0-1_all.deb ... Unpacking liberror-prone-java (2.18.0-1) ... Selecting previously unselected package libjsr305-java. Preparing to unpack .../260-libjsr305-java_0.1~+svn49-11_all.deb ... Unpacking libjsr305-java (0.1~+svn49-11) ... Selecting previously unselected package libguava-java. Preparing to unpack .../261-libguava-java_32.0.1-1_all.deb ... Unpacking libguava-java (32.0.1-1) ... Selecting previously unselected package libguice-java. Preparing to unpack .../262-libguice-java_4.2.3-2_all.deb ... Unpacking libguice-java (4.2.3-2) ... Selecting previously unselected package libmaven-parent-java. Preparing to unpack .../263-libmaven-parent-java_35-1_all.deb ... Unpacking libmaven-parent-java (35-1) ... Selecting previously unselected package libplexus-utils2-java. Preparing to unpack .../264-libplexus-utils2-java_3.4.2-1_all.deb ... Unpacking libplexus-utils2-java (3.4.2-1) ... Selecting previously unselected package libwagon-provider-api-java. Preparing to unpack .../265-libwagon-provider-api-java_3.5.3-1_all.deb ... Unpacking libwagon-provider-api-java (3.5.3-1) ... Selecting previously unselected package libmaven-resolver-java. Preparing to unpack .../266-libmaven-resolver-java_1.6.3-1_all.deb ... Unpacking libmaven-resolver-java (1.6.3-1) ... Selecting previously unselected package libplexus-cipher-java. Preparing to unpack .../267-libplexus-cipher-java_2.0-1_all.deb ... Unpacking libplexus-cipher-java (2.0-1) ... Selecting previously unselected package libplexus-classworlds-java. Preparing to unpack .../268-libplexus-classworlds-java_2.7.0-1_all.deb ... Unpacking libplexus-classworlds-java (2.7.0-1) ... Selecting previously unselected package libplexus-component-annotations-java. Preparing to unpack .../269-libplexus-component-annotations-java_2.1.1-1_all.deb ... Unpacking libplexus-component-annotations-java (2.1.1-1) ... Selecting previously unselected package libplexus-interpolation-java. Preparing to unpack .../270-libplexus-interpolation-java_1.26-1_all.deb ... Unpacking libplexus-interpolation-java (1.26-1) ... Selecting previously unselected package libplexus-sec-dispatcher-java. Preparing to unpack .../271-libplexus-sec-dispatcher-java_2.0-3_all.deb ... Unpacking libplexus-sec-dispatcher-java (2.0-3) ... Selecting previously unselected package libgeronimo-interceptor-3.0-spec-java. Preparing to unpack .../272-libgeronimo-interceptor-3.0-spec-java_1.0.1-4_all.deb ... Unpacking libgeronimo-interceptor-3.0-spec-java (1.0.1-4) ... Selecting previously unselected package libcdi-api-java. Preparing to unpack .../273-libcdi-api-java_1.2-3_all.deb ... Unpacking libcdi-api-java (1.2-3) ... Selecting previously unselected package libsisu-inject-java. Preparing to unpack .../274-libsisu-inject-java_0.3.4-2_all.deb ... Unpacking libsisu-inject-java (0.3.4-2) ... Selecting previously unselected package libsisu-plexus-java. Preparing to unpack .../275-libsisu-plexus-java_0.3.4-3_all.deb ... Unpacking libsisu-plexus-java (0.3.4-3) ... Selecting previously unselected package libmaven3-core-java. Preparing to unpack .../276-libmaven3-core-java_3.8.8-1_all.deb ... Unpacking libmaven3-core-java (3.8.8-1) ... Selecting previously unselected package libmaven-shared-io-java. Preparing to unpack .../277-libmaven-shared-io-java_3.0.0-4_all.deb ... Unpacking libmaven-shared-io-java (3.0.0-4) ... Selecting previously unselected package libmaven-file-management-java. Preparing to unpack .../278-libmaven-file-management-java_3.0.0-1_all.deb ... Unpacking libmaven-file-management-java (3.0.0-1) ... Selecting previously unselected package libbuild-helper-maven-plugin-java. Preparing to unpack .../279-libbuild-helper-maven-plugin-java_3.3.0-1_all.deb ... Unpacking libbuild-helper-maven-plugin-java (3.3.0-1) ... Selecting previously unselected package libbyte-buddy-java. Preparing to unpack .../280-libbyte-buddy-java_1.14.19-1_all.deb ... Unpacking libbyte-buddy-java (1.14.19-1) ... Selecting previously unselected package libcolt-free-java. Preparing to unpack .../281-libcolt-free-java_1.2.0+dfsg-8_all.deb ... Unpacking libcolt-free-java (1.2.0+dfsg-8) ... Selecting previously unselected package libcommons-collections3-java. Preparing to unpack .../282-libcommons-collections3-java_3.2.2-3_all.deb ... Unpacking libcommons-collections3-java (3.2.2-3) ... Selecting previously unselected package libcommons-beanutils-java. Preparing to unpack .../283-libcommons-beanutils-java_1.9.4-2_all.deb ... Unpacking libcommons-beanutils-java (1.9.4-2) ... Selecting previously unselected package libcommons-collections4-java. Preparing to unpack .../284-libcommons-collections4-java_4.4-2_all.deb ... Unpacking libcommons-collections4-java (4.4-2) ... Selecting previously unselected package libcommons-compress-java. Preparing to unpack .../285-libcommons-compress-java_1.25.0-1_all.deb ... Unpacking libcommons-compress-java (1.25.0-1) ... Selecting previously unselected package libcommons-lang-java. Preparing to unpack .../286-libcommons-lang-java_2.6-10_all.deb ... Unpacking libcommons-lang-java (2.6-10) ... Selecting previously unselected package libcommons-configuration-java. Preparing to unpack .../287-libcommons-configuration-java_1.10-6_all.deb ... Unpacking libcommons-configuration-java (1.10-6) ... Selecting previously unselected package libcommons-digester-java. Preparing to unpack .../288-libcommons-digester-java_1.8.1-6_all.deb ... Unpacking libcommons-digester-java (1.8.1-6) ... Selecting previously unselected package libcommons-exec-java. Preparing to unpack .../289-libcommons-exec-java_1.3-2_all.deb ... Unpacking libcommons-exec-java (1.3-2) ... Selecting previously unselected package libcommons-jexl2-java. Preparing to unpack .../290-libcommons-jexl2-java_2.1.1-6_all.deb ... Unpacking libcommons-jexl2-java (2.1.1-6) ... Selecting previously unselected package libcommons-math-java. Preparing to unpack .../291-libcommons-math-java_2.2-8_all.deb ... Unpacking libcommons-math-java (2.2-8) ... Selecting previously unselected package libcommons-math3-java. Preparing to unpack .../292-libcommons-math3-java_3.6.1-3_all.deb ... Unpacking libcommons-math3-java (3.6.1-3) ... Selecting previously unselected package libplexus-io-java. Preparing to unpack .../293-libplexus-io-java_3.3.1-2_all.deb ... Unpacking libplexus-io-java (3.3.1-2) ... Selecting previously unselected package libsnappy1v5:amd64. Preparing to unpack .../294-libsnappy1v5_1.2.1-1_amd64.deb ... Unpacking libsnappy1v5:amd64 (1.2.1-1) ... Selecting previously unselected package libsnappy-jni. Preparing to unpack .../295-libsnappy-jni_1.1.10.5-2_amd64.deb ... Unpacking libsnappy-jni (1.1.10.5-2) ... Selecting previously unselected package libsnappy-java. Preparing to unpack .../296-libsnappy-java_1.1.10.5-2_all.deb ... Unpacking libsnappy-java (1.1.10.5-2) ... Selecting previously unselected package libxz-java. Preparing to unpack .../297-libxz-java_1.9-1_all.deb ... Unpacking libxz-java (1.9-1) ... Selecting previously unselected package libplexus-archiver-java. Preparing to unpack .../298-libplexus-archiver-java_4.6.1-1_all.deb ... Unpacking libplexus-archiver-java (4.6.1-1) ... Selecting previously unselected package libmaven-archiver-java. Preparing to unpack .../299-libmaven-archiver-java_3.6.0-1_all.deb ... Unpacking libmaven-archiver-java (3.6.0-1) ... Selecting previously unselected package libmaven-jar-plugin-java. Preparing to unpack .../300-libmaven-jar-plugin-java_3.3.0-2_all.deb ... Unpacking libmaven-jar-plugin-java (3.3.0-2) ... Selecting previously unselected package libcommons-text-java. Preparing to unpack .../301-libcommons-text-java_1.11.0-1_all.deb ... Unpacking libcommons-text-java (1.11.0-1) ... Selecting previously unselected package libcommons-validator-java. Preparing to unpack .../302-libcommons-validator-java_1%3a1.7-1_all.deb ... Unpacking libcommons-validator-java (1:1.7-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../303-libnghttp2-14_1.63.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.63.0-1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../304-libpsl5t64_0.21.2-1.1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../305-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../306-libssh2-1t64_1.11.0-7_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.0-7) ... Selecting previously unselected package libcurl4t64:amd64. Preparing to unpack .../307-libcurl4t64_8.10.1-1_amd64.deb ... Unpacking libcurl4t64:amd64 (8.10.1-1) ... Selecting previously unselected package libdistlib-java. Preparing to unpack .../308-libdistlib-java_1.0-5_all.deb ... Unpacking libdistlib-java (1.0-5) ... Selecting previously unselected package libjaxen-java. Preparing to unpack .../309-libjaxen-java_1.1.6-4_all.deb ... Unpacking libjaxen-java (1.1.6-4) ... Selecting previously unselected package libdom4j-java. Preparing to unpack .../310-libdom4j-java_2.1.4-1_all.deb ... Unpacking libdom4j-java (2.1.4-1) ... Selecting previously unselected package libdoxia-core-java. Preparing to unpack .../311-libdoxia-core-java_1.12.0-1_all.deb ... Unpacking libdoxia-core-java (1.12.0-1) ... Selecting previously unselected package libfontbox2-java. Preparing to unpack .../312-libfontbox2-java_2.0.29-1_all.deb ... Unpacking libfontbox2-java (2.0.29-1) ... Selecting previously unselected package libqdox-java. Preparing to unpack .../313-libqdox-java_1.12.1-3_all.deb ... Unpacking libqdox-java (1.12.1-3) ... Selecting previously unselected package libfop-java. Preparing to unpack .../314-libfop-java_1%3a2.8-3_all.deb ... Unpacking libfop-java (1:2.8-3) ... Selecting previously unselected package libitext1-java. Preparing to unpack .../315-libitext1-java_1.4-7_all.deb ... Unpacking libitext1-java (1.4-7) ... Selecting previously unselected package libxbean-reflect-java. Preparing to unpack .../316-libxbean-reflect-java_4.5-8_all.deb ... Unpacking libxbean-reflect-java (4.5-8) ... Selecting previously unselected package libplexus-container-default-java. Preparing to unpack .../317-libplexus-container-default-java_2.1.1-1_all.deb ... Unpacking libplexus-container-default-java (2.1.1-1) ... Selecting previously unselected package libdoxia-java. Preparing to unpack .../318-libdoxia-java_1.12.0-1_all.deb ... Unpacking libdoxia-java (1.12.0-1) ... Selecting previously unselected package libmaven-reporting-api-java. Preparing to unpack .../319-libmaven-reporting-api-java_3.1.1-1_all.deb ... Unpacking libmaven-reporting-api-java (3.1.1-1) ... Selecting previously unselected package libplexus-i18n-java. Preparing to unpack .../320-libplexus-i18n-java_1.0-beta-10-6_all.deb ... Unpacking libplexus-i18n-java (1.0-beta-10-6) ... Selecting previously unselected package velocity. Preparing to unpack .../321-velocity_1.7-7_all.deb ... Unpacking velocity (1.7-7) ... Selecting previously unselected package libplexus-velocity-java. Preparing to unpack .../322-libplexus-velocity-java_1.2-3.1_all.deb ... Unpacking libplexus-velocity-java (1.2-3.1) ... Selecting previously unselected package liboro-java. Preparing to unpack .../323-liboro-java_2.0.8a-14_all.deb ... Unpacking liboro-java (2.0.8a-14) ... Selecting previously unselected package libvelocity-tools-java. Preparing to unpack .../324-libvelocity-tools-java_2.0-9_all.deb ... Unpacking libvelocity-tools-java (2.0-9) ... Selecting previously unselected package libxml-commons-resolver1.1-java. Preparing to unpack .../325-libxml-commons-resolver1.1-java_1.2-11_all.deb ... Unpacking libxml-commons-resolver1.1-java (1.2-11) ... Selecting previously unselected package libxerces2-java. Preparing to unpack .../326-libxerces2-java_2.12.2-1_all.deb ... Unpacking libxerces2-java (2.12.2-1) ... Selecting previously unselected package libxalan2-java. Preparing to unpack .../327-libxalan2-java_2.7.2-4_all.deb ... Unpacking libxalan2-java (2.7.2-4) ... Selecting previously unselected package libdoxia-sitetools-java. Preparing to unpack .../328-libdoxia-sitetools-java_1.11.1-1_all.deb ... Unpacking libdoxia-sitetools-java (1.11.1-1) ... Selecting previously unselected package libfastutil-java. Preparing to unpack .../329-libfastutil-java_8.5.14+dfsg-1_all.deb ... Unpacking libfastutil-java (8.5.14+dfsg-1) ... Selecting previously unselected package libxpp3-java. Preparing to unpack .../330-libxpp3-java_1.1.4c-3_all.deb ... Unpacking libxpp3-java (1.1.4c-3) ... Selecting previously unselected package libxstream-java. Preparing to unpack .../331-libxstream-java_1.4.20-1_all.deb ... Unpacking libxstream-java (1.4.20-1) ... Selecting previously unselected package libjsap-java. Preparing to unpack .../332-libjsap-java_2.1-5_all.deb ... Unpacking libjsap-java (2.1-5) ... Selecting previously unselected package liblogback-java. Preparing to unpack .../333-liblogback-java_1%3a1.2.11-5_all.deb ... Unpacking liblogback-java (1:1.2.11-5) ... Selecting previously unselected package libdsiutils-java. Preparing to unpack .../334-libdsiutils-java_2.7.3+dfsg-1_all.deb ... Unpacking libdsiutils-java (2.7.3+dfsg-1) ... Selecting previously unselected package libobjenesis-java. Preparing to unpack .../335-libobjenesis-java_3.3-3_all.deb ... Unpacking libobjenesis-java (3.3-3) ... Selecting previously unselected package libeasymock-java. Preparing to unpack .../336-libeasymock-java_5.2.0-1_all.deb ... Unpacking libeasymock-java (5.2.0-1) ... Selecting previously unselected package libel-api-java. Preparing to unpack .../337-libel-api-java_3.0.0-3_all.deb ... Unpacking libel-api-java (3.0.0-3) ... Selecting previously unselected package libexec-maven-plugin-java. Preparing to unpack .../338-libexec-maven-plugin-java_3.1.0-2_all.deb ... Unpacking libexec-maven-plugin-java (3.1.0-2) ... Selecting previously unselected package libgatk-native-bindings-java. Preparing to unpack .../339-libgatk-native-bindings-java_1.0.0+dfsg-2_all.deb ... Unpacking libgatk-native-bindings-java (1.0.0+dfsg-2) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../340-libgfortran5_14.2.0-3_amd64.deb ... Unpacking libgfortran5:amd64 (14.2.0-3) ... Selecting previously unselected package libmjson-java. Preparing to unpack .../341-libmjson-java_1.4.0-3_all.deb ... Unpacking libmjson-java (1.4.0-3) ... Selecting previously unselected package libmbedcrypto7t64:amd64. Preparing to unpack .../342-libmbedcrypto7t64_2.28.8-1_amd64.deb ... Unpacking libmbedcrypto7t64:amd64 (2.28.8-1) ... Selecting previously unselected package libmbedx509-1t64:amd64. Preparing to unpack .../343-libmbedx509-1t64_2.28.8-1_amd64.deb ... Unpacking libmbedx509-1t64:amd64 (2.28.8-1) ... Selecting previously unselected package libmbedtls14t64:amd64. Preparing to unpack .../344-libmbedtls14t64_2.28.8-1_amd64.deb ... Unpacking libmbedtls14t64:amd64 (2.28.8-1) ... Selecting previously unselected package ncbi-vdb-data. Preparing to unpack .../345-ncbi-vdb-data_3.0.2+dfsg-2_all.deb ... Unpacking ncbi-vdb-data (3.0.2+dfsg-2) ... Selecting previously unselected package libncbi-vdb3:amd64. Preparing to unpack .../346-libncbi-vdb3_3.0.2+dfsg-2+b1_amd64.deb ... Unpacking libncbi-vdb3:amd64 (3.0.2+dfsg-2+b1) ... Selecting previously unselected package libncbi-ngs3:amd64. Preparing to unpack .../347-libncbi-ngs3_3.0.3+dfsg-9_amd64.deb ... Unpacking libncbi-ngs3:amd64 (3.0.3+dfsg-9) ... Selecting previously unselected package libngs-jni:amd64. Preparing to unpack .../348-libngs-jni_3.0.3+dfsg-9_amd64.deb ... Unpacking libngs-jni:amd64 (3.0.3+dfsg-9) ... Selecting previously unselected package libngs-java:amd64. Preparing to unpack .../349-libngs-java_3.0.3+dfsg-9_amd64.deb ... Unpacking libngs-java:amd64 (3.0.3+dfsg-9) ... Selecting previously unselected package librhino-java. Preparing to unpack .../350-librhino-java_1.7.14-2.1_all.deb ... Unpacking librhino-java (1.7.14-2.1) ... Selecting previously unselected package libhtsjdk-java. Preparing to unpack .../351-libhtsjdk-java_4.1.0+dfsg-2_all.deb ... Unpacking libhtsjdk-java (4.1.0+dfsg-2) ... Selecting previously unselected package libgkl-java. Preparing to unpack .../352-libgkl-java_0.8.11+dfsg-2_all.deb ... Unpacking libgkl-java (0.8.11+dfsg-2) ... Selecting previously unselected package libicu4j-java. Preparing to unpack .../353-libicu4j-java_73.2-1_all.deb ... Unpacking libicu4j-java (73.2-1) ... Selecting previously unselected package liblog4j1.2-java. Preparing to unpack .../354-liblog4j1.2-java_1.2.17-11_all.deb ... Unpacking liblog4j1.2-java (1.2.17-11) ... Selecting previously unselected package libicb-utils-java. Preparing to unpack .../355-libicb-utils-java_2.0.1+git20161002.afee1d9-5_all.deb ... Unpacking libicb-utils-java (2.0.1+git20161002.afee1d9-5) ... Selecting previously unselected package libice6:amd64. Preparing to unpack .../356-libice6_2%3a1.0.10-1+b1_amd64.deb ... Unpacking libice6:amd64 (2:1.0.10-1+b1) ... Selecting previously unselected package libjansi-java. Preparing to unpack .../357-libjansi-java_2.4.1-2_all.deb ... Unpacking libjansi-java (2.4.1-2) ... Selecting previously unselected package libjavassist-java. Preparing to unpack .../358-libjavassist-java_1%3a3.27.0-1_all.deb ... Unpacking libjavassist-java (1:3.27.0-1) ... Selecting previously unselected package libjaxb-api-java. Preparing to unpack .../359-libjaxb-api-java_2.3.1-1_all.deb ... Unpacking libjaxb-api-java (2.3.1-1) ... Selecting previously unselected package libjboss-logging-java. Preparing to unpack .../360-libjboss-logging-java_3.5.3-1_all.deb ... Unpacking libjboss-logging-java (3.5.3-1) ... Selecting previously unselected package libjboss-vfs-java. Preparing to unpack .../361-libjboss-vfs-java_3.2.15.Final-3_all.deb ... Unpacking libjboss-vfs-java (3.2.15.Final-3) ... Selecting previously unselected package libjbzip2-java. Preparing to unpack .../362-libjbzip2-java_0.9.1-8_all.deb ... Unpacking libjbzip2-java (0.9.1-8) ... Selecting previously unselected package libjcommander-java. Preparing to unpack .../363-libjcommander-java_1.71-4_all.deb ... Unpacking libjcommander-java (1.71-4) ... Selecting previously unselected package libjsp-api-java. Preparing to unpack .../364-libjsp-api-java_2.3.4-3_all.deb ... Unpacking libjsp-api-java (2.3.4-3) ... Selecting previously unselected package libservlet-api-java. Preparing to unpack .../365-libservlet-api-java_4.0.1-2_all.deb ... Unpacking libservlet-api-java (4.0.1-2) ... Selecting previously unselected package libwebsocket-api-java. Preparing to unpack .../366-libwebsocket-api-java_1.1-2_all.deb ... Unpacking libwebsocket-api-java (1.1-2) ... Selecting previously unselected package libjetty9-java. Preparing to unpack .../367-libjetty9-java_9.4.55-1_all.deb ... Unpacking libjetty9-java (9.4.55-1) ... Selecting previously unselected package libjsoup-java. Preparing to unpack .../368-libjsoup-java_1.15.3-1_all.deb ... Unpacking libjsoup-java (1.15.3-1) ... Selecting previously unselected package libjtidy-java. Preparing to unpack .../369-libjtidy-java_7+svn20110807-5_all.deb ... Unpacking libjtidy-java (7+svn20110807-5) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../370-liblapack3_3.12.0-3_amd64.deb ... Unpacking liblapack3:amd64 (3.12.0-3) ... Selecting previously unselected package libmaven-antrun-plugin-java. Preparing to unpack .../371-libmaven-antrun-plugin-java_3.1.0-1_all.deb ... Unpacking libmaven-antrun-plugin-java (3.1.0-1) ... Selecting previously unselected package libmaven-common-artifact-filters-java. Preparing to unpack .../372-libmaven-common-artifact-filters-java_3.3.2-1_all.deb ... Unpacking libmaven-common-artifact-filters-java (3.3.2-1) ... Selecting previously unselected package libmaven-artifact-transfer-java. Preparing to unpack .../373-libmaven-artifact-transfer-java_0.13.1-2_all.deb ... Unpacking libmaven-artifact-transfer-java (0.13.1-2) ... Selecting previously unselected package libplexus-build-api-java. Preparing to unpack .../374-libplexus-build-api-java_0.0.7-4_all.deb ... Unpacking libplexus-build-api-java (0.0.7-4) ... Selecting previously unselected package libmaven-filtering-java. Preparing to unpack .../375-libmaven-filtering-java_3.3.0-1_all.deb ... Unpacking libmaven-filtering-java (3.3.0-1) ... Selecting previously unselected package libmaven-assembly-plugin-java. Preparing to unpack .../376-libmaven-assembly-plugin-java_3.4.2-1_all.deb ... Unpacking libmaven-assembly-plugin-java (3.4.2-1) ... Selecting previously unselected package libmaven-clean-plugin-java. Preparing to unpack .../377-libmaven-clean-plugin-java_3.2.0-2_all.deb ... Unpacking libmaven-clean-plugin-java (3.2.0-2) ... Selecting previously unselected package libmaven-shared-incremental-java. Preparing to unpack .../378-libmaven-shared-incremental-java_1.1-4_all.deb ... Unpacking libmaven-shared-incremental-java (1.1-4) ... Selecting previously unselected package libplexus-compiler-java. Preparing to unpack .../379-libplexus-compiler-java_2.12.1-3_all.deb ... Unpacking libplexus-compiler-java (2.12.1-3) ... Selecting previously unselected package libqdox2-java. Preparing to unpack .../380-libqdox2-java_2.0.3-1_all.deb ... Unpacking libqdox2-java (2.0.3-1) ... Selecting previously unselected package libplexus-languages-java. Preparing to unpack .../381-libplexus-languages-java_1.1.1-2_all.deb ... Unpacking libplexus-languages-java (1.1.1-2) ... Selecting previously unselected package libmaven-compiler-plugin-java. Preparing to unpack .../382-libmaven-compiler-plugin-java_3.10.1-2_all.deb ... Unpacking libmaven-compiler-plugin-java (3.10.1-2) ... Selecting previously unselected package libmaven-dependency-analyzer-java. Preparing to unpack .../383-libmaven-dependency-analyzer-java_1.14.1-1_all.deb ... Unpacking libmaven-dependency-analyzer-java (1.14.1-1) ... Selecting previously unselected package libmaven-dependency-tree-java. Preparing to unpack .../384-libmaven-dependency-tree-java_3.2.1-1_all.deb ... Unpacking libmaven-dependency-tree-java (3.2.1-1) ... Selecting previously unselected package libmaven-reporting-impl-java. Preparing to unpack .../385-libmaven-reporting-impl-java_3.2.0-2_all.deb ... Unpacking libmaven-reporting-impl-java (3.2.0-2) ... Selecting previously unselected package libmaven-dependency-plugin-java. Preparing to unpack .../386-libmaven-dependency-plugin-java_3.5.0-1_all.deb ... Unpacking libmaven-dependency-plugin-java (3.5.0-1) ... Selecting previously unselected package libmaven-invoker-java. Preparing to unpack .../387-libmaven-invoker-java_3.2.0-1_all.deb ... Unpacking libmaven-invoker-java (3.2.0-1) ... Selecting previously unselected package libplexus-interactivity-api-java. Preparing to unpack .../388-libplexus-interactivity-api-java_1.1-2_all.deb ... Unpacking libplexus-interactivity-api-java (1.1-2) ... Selecting previously unselected package libmaven-javadoc-plugin-java. Preparing to unpack .../389-libmaven-javadoc-plugin-java_3.4.1-3_all.deb ... Unpacking libmaven-javadoc-plugin-java (3.4.1-3) ... Selecting previously unselected package libplexus-container-default1.5-java. Preparing to unpack .../390-libplexus-container-default1.5-java_2.1.1-1_all.deb ... Unpacking libplexus-container-default1.5-java (2.1.1-1) ... Selecting previously unselected package libplexus-ant-factory-java. Preparing to unpack .../391-libplexus-ant-factory-java_1.0~alpha2.1-4_all.deb ... Unpacking libplexus-ant-factory-java (1.0~alpha2.1-4) ... Selecting previously unselected package libplexus-bsh-factory-java. Preparing to unpack .../392-libplexus-bsh-factory-java_1.0~alpha7-5_all.deb ... Unpacking libplexus-bsh-factory-java (1.0~alpha7-5) ... Selecting previously unselected package libmaven-plugin-tools-java. Preparing to unpack .../393-libmaven-plugin-tools-java_3.7.1-1_all.deb ... Unpacking libmaven-plugin-tools-java (3.7.1-1) ... Selecting previously unselected package libmaven-reporting-exec-java. Preparing to unpack .../394-libmaven-reporting-exec-java_1.6.0-1_all.deb ... Unpacking libmaven-reporting-exec-java (1.6.0-1) ... Selecting previously unselected package libmaven-resources-plugin-java. Preparing to unpack .../395-libmaven-resources-plugin-java_3.3.1-1_all.deb ... Unpacking libmaven-resources-plugin-java (3.3.1-1) ... Selecting previously unselected package libmaven-site-plugin-java. Preparing to unpack .../396-libmaven-site-plugin-java_3.12.1-2_all.deb ... Unpacking libmaven-site-plugin-java (3.12.1-2) ... Selecting previously unselected package libmaven-source-plugin-java. Preparing to unpack .../397-libmaven-source-plugin-java_3.2.1-2_all.deb ... Unpacking libmaven-source-plugin-java (3.2.1-2) ... Selecting previously unselected package libpaper1:amd64. Preparing to unpack .../398-libpaper1_1.1.29+b1_amd64.deb ... Unpacking libpaper1:amd64 (1.1.29+b1) ... Selecting previously unselected package libpaper-utils. Preparing to unpack .../399-libpaper-utils_1.1.29+b1_amd64.deb ... Unpacking libpaper-utils (1.1.29+b1) ... Selecting previously unselected package libpicard-java. Preparing to unpack .../400-libpicard-java_3.1.1+dfsg-1_all.deb ... Unpacking libpicard-java (3.1.1+dfsg-1) ... Selecting previously unselected package libpj-java. Preparing to unpack .../401-libpj-java_0.0~20150107+dfsg-5_all.deb ... Unpacking libpj-java (0.0~20150107+dfsg-5) ... Selecting previously unselected package libpkgconf3:amd64. Preparing to unpack .../402-libpkgconf3_1.8.1-3_amd64.deb ... Unpacking libpkgconf3:amd64 (1.8.1-3) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../403-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Selecting previously unselected package libprotobuf32t64:amd64. Preparing to unpack .../404-libprotobuf32t64_3.21.12-9_amd64.deb ... Unpacking libprotobuf32t64:amd64 (3.21.12-9) ... Selecting previously unselected package libprotobuf-lite32t64:amd64. Preparing to unpack .../405-libprotobuf-lite32t64_3.21.12-9_amd64.deb ... Unpacking libprotobuf-lite32t64:amd64 (3.21.12-9) ... Selecting previously unselected package libprotobuf-dev:amd64. Preparing to unpack .../406-libprotobuf-dev_3.21.12-9_amd64.deb ... Unpacking libprotobuf-dev:amd64 (3.21.12-9) ... Selecting previously unselected package libprotobuf-java. Preparing to unpack .../407-libprotobuf-java_3.21.12-9_all.deb ... Unpacking libprotobuf-java (3.21.12-9) ... Selecting previously unselected package libprotoc32t64:amd64. Preparing to unpack .../408-libprotoc32t64_3.21.12-9_amd64.deb ... Unpacking libprotoc32t64:amd64 (3.21.12-9) ... Selecting previously unselected package libreflections-java. Preparing to unpack .../409-libreflections-java_0.10.2+dfsg-2_all.deb ... Unpacking libreflections-java (0.10.2+dfsg-2) ... Selecting previously unselected package libsm6:amd64. Preparing to unpack .../410-libsm6_2%3a1.2.3-1+b1_amd64.deb ... Unpacking libsm6:amd64 (2:1.2.3-1+b1) ... Selecting previously unselected package libsurefire-java. Preparing to unpack .../411-libsurefire-java_2.22.3-2_all.deb ... Unpacking libsurefire-java (2.22.3-2) ... Selecting previously unselected package libtcl8.6:amd64. Preparing to unpack .../412-libtcl8.6_8.6.15+dfsg-2_amd64.deb ... Unpacking libtcl8.6:amd64 (8.6.15+dfsg-2) ... Selecting previously unselected package libxft2:amd64. Preparing to unpack .../413-libxft2_2.3.6-1+b1_amd64.deb ... Unpacking libxft2:amd64 (2.3.6-1+b1) ... Selecting previously unselected package libxss1:amd64. Preparing to unpack .../414-libxss1_1%3a1.2.3-1+b1_amd64.deb ... Unpacking libxss1:amd64 (1:1.2.3-1+b1) ... Selecting previously unselected package libtk8.6:amd64. Preparing to unpack .../415-libtk8.6_8.6.15-1_amd64.deb ... Unpacking libtk8.6:amd64 (8.6.15-1) ... Selecting previously unselected package libwagon-file-java. Preparing to unpack .../416-libwagon-file-java_3.5.3-1_all.deb ... Unpacking libwagon-file-java (3.5.3-1) ... Selecting previously unselected package libwagon-http-shaded-java. Preparing to unpack .../417-libwagon-http-shaded-java_3.5.3-1_all.deb ... Unpacking libwagon-http-shaded-java (3.5.3-1) ... Selecting previously unselected package libxml2-utils. Preparing to unpack .../418-libxml2-utils_2.12.7+dfsg+really2.9.14-0.1_amd64.deb ... Unpacking libxml2-utils (2.12.7+dfsg+really2.9.14-0.1) ... Selecting previously unselected package libxt6t64:amd64. Preparing to unpack .../419-libxt6t64_1%3a1.2.1-1.2_amd64.deb ... Unpacking libxt6t64:amd64 (1:1.2.1-1.2) ... Selecting previously unselected package maven. Preparing to unpack .../420-maven_3.8.8-1_all.deb ... Unpacking maven (3.8.8-1) ... Selecting previously unselected package maven-repo-helper. Preparing to unpack .../421-maven-repo-helper_1.11_all.deb ... Unpacking maven-repo-helper (1.11) ... Selecting previously unselected package maven-debian-helper. Preparing to unpack .../422-maven-debian-helper_2.6.4_all.deb ... Unpacking maven-debian-helper (2.6.4) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../423-pkgconf-bin_1.8.1-3_amd64.deb ... Unpacking pkgconf-bin (1.8.1-3) ... Selecting previously unselected package pkgconf:amd64. Preparing to unpack .../424-pkgconf_1.8.1-3_amd64.deb ... Unpacking pkgconf:amd64 (1.8.1-3) ... Selecting previously unselected package protobuf-compiler. Preparing to unpack .../425-protobuf-compiler_3.21.12-9_amd64.deb ... Unpacking protobuf-compiler (3.21.12-9) ... Selecting previously unselected package zip. Preparing to unpack .../426-zip_3.0-14_amd64.deb ... Unpacking zip (3.0-14) ... Selecting previously unselected package xdg-utils. Preparing to unpack .../427-xdg-utils_1.1.3-4.1_all.deb ... Unpacking xdg-utils (1.1.3-4.1) ... Selecting previously unselected package r-base-core. Preparing to unpack .../428-r-base-core_4.4.1-3_amd64.deb ... Unpacking r-base-core (4.4.1-3) ... Selecting previously unselected package r-cran-rjava. Preparing to unpack .../429-r-cran-rjava_1.0-11-1_amd64.deb ... Unpacking r-cran-rjava (1.0-11-1) ... Selecting previously unselected package testng. Preparing to unpack .../430-testng_6.9.12-4_all.deb ... Unpacking testng (6.9.12-4) ... Setting up libprotobuf-lite32t64:amd64 (3.21.12-9) ... Setting up libksba8:amd64 (1.6.7-2) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up fastjar (2:0.98-7) ... Setting up libgraphite2-3:amd64 (1.3.14-2) ... Setting up liblcms2-2:amd64 (2.14-2+b1) ... Setting up libpixman-1-0:amd64 (0.42.2-1+b1) ... Setting up libjcommander-java (1.71-4) ... Setting up libfastutil-java (8.5.14+dfsg-1) ... Setting up wdiff (1.2.2-6) ... Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... Setting up libwayland-server0:amd64 (1.23.0-1) ... Setting up libpciaccess0:amd64 (0.17-3+b1) ... Setting up libslf4j-java (1.7.32-1) ... Setting up libprotobuf32t64:amd64 (3.21.12-9) ... Setting up libfile-which-perl (1.27-2) ... Setting up systemd-sysv (256.6-1) ... Setting up libxau6:amd64 (1:1.0.9-1+b1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up libplexus-utils2-java (3.4.2-1) ... Setting up libnpth0t64:amd64 (1.6-3.1) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libplexus-classworlds-java (2.7.0-1) ... Setting up libxcb1:amd64 (1.17.0-2) ... Setting up libqdox-java (1.12.1-3) ... Setting up libopentest4j-reporting-java (0.1.0-M1-2) ... Setting up libicu72:amd64 (72.1-5) ... Setting up libplexus-build-api-java (0.0.7-4) ... Setting up libxcb-xfixes0:amd64 (1.17.0-2) ... Setting up liblerc4:amd64 (4.0.0+ds-4+b1) ... Setting up libjsr305-java (0.1~+svn49-11) ... Setting up bsdextrautils (2.40.2-9) ... Setting up hicolor-icon-theme (0.18-1) ... Setting up libgatk-native-bindings-java (1.0.0+dfsg-2) ... Setting up libmbedcrypto7t64:amd64 (2.28.8-1) ... Setting up libicu4j-java (73.2-1) ... Setting up java-common (0.76) ... Setting up libdynaloader-functions-perl (0.004-1) ... Setting up libdatrie1:amd64 (0.2.13-3) ... Setting up libobjenesis-java (3.3-3) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up libqdox2-java (2.0.3-1) ... Setting up libaopalliance-java (20070526-7) ... Setting up libcommons-cli-java (1.6.0-1) ... Setting up libio-pty-perl (1:1.20-1+b1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libcommons-exec-java (1.3-2) ... Setting up libxcb-render0:amd64 (1.17.0-2) ... Setting up liblogback-java (1:1.2.11-5) ... Setting up libclone-perl:amd64 (0.47-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglvnd0:amd64 (1.7.0-1+b1) ... Setting up libgoogle-gson-java (2.10.1-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libmjson-java (1.4.0-3) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libxcb-glx0:amd64 (1.17.0-2) ... Setting up unzip (6.0-28) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:amd64 (1.1.0-2+b4) ... Setting up libedit2:amd64 (3.1-20240808-1) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libpicocli-java (4.6.2-2) ... Setting up libasm-java (9.7-2) ... Setting up x11-common (1:7.7+23.1) ... Running in chroot, ignoring request. Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libtry-tiny-perl (0.32-1) ... Setting up libsensors-config (1:3.6.0-10) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.63.0-1) ... Setting up libdeflate0:amd64 (1.22-1) ... Setting up perl-openssl-defaults:amd64 (7+b2) ... Setting up liblog4j1.2-java (1.2.17-11) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libel-api-java (3.0.0-3) ... Setting up xkb-data (2.42-1) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libplexus-component-annotations-java (2.1.1-1) ... Setting up libxcb-shm0:amd64 (1.17.0-2) ... Setting up libcom-err2:amd64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libjboss-logging-java (3.5.3-1) ... Setting up libunivocity-parsers-java (2.9.1-1) ... Setting up libjbig0:amd64 (2.1-6.1+b1) ... Setting up libelf1t64:amd64 (0.191-2) ... Setting up liboro-java (2.0.8a-14) ... Setting up libsnappy1v5:amd64 (1.2.1-1) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libexec-maven-plugin-java (3.1.0-2) ... Setting up libfontbox2-java (2.0.29-1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Nov 14 05:39:16 UTC 2025. Universal Time is now: Fri Nov 14 05:39:16 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:amd64 (1.17.0-2) ... Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... Setting up libgeronimo-interceptor-3.0-spec-java (1.0.1-4) ... Setting up libcommons-collections3-java (3.2.2-3) ... Setting up libasound2-data (1.2.12-1) ... Setting up libjavassist-java (1:3.27.0-1) ... Setting up zip (3.0-14) ... Setting up librhino-java (1.7.14-2.1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.8.12-3.1+b2) ... Setting up libglib2.0-0t64:amd64 (2.82.1-1) ... Setting up libblas3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libpkgconf3:amd64 (1.8.1-3) ... Setting up libasound2t64:amd64 (1.2.12-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3) ... Setting up libjaxen-java (1.1.6-4) ... Setting up libapiguardian-java (1.1.2-1) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libepoxy0:amd64 (1.5.10-2) ... Setting up libnspr4:amd64 (2:4.35-1.1+b1) ... Setting up gnupg-l10n (2.2.43-8) ... Setting up libxcb-sync1:amd64 (1.17.0-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libjtidy-java (7+svn20110807-5) ... Setting up libjansi-java (2.4.1-2) ... Setting up libapache-pom-java (29-2) ... Setting up libavahi-common-data:amd64 (0.8-13+b2) ... Setting up libxpp3-java (1.1.4c-3) ... Setting up libatinject-jsr330-api-java (1.0+ds1-5) ... Setting up libdbus-1-3:amd64 (1.14.10-4+b1) ... Setting up libwebsocket-api-java (1.1-2) ... Setting up libfribidi0:amd64 (1.0.15-1) ... Setting up libproc2-0:amd64 (2:4.0.4-6) ... Setting up libplexus-interpolation-java (1.26-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.44-2) ... Setting up libxml-commons-resolver1.1-java (1.2-11) ... Setting up libxz-java (1.9-1) ... Setting up libitext1-java (1.4-7) ... Setting up libio-html-perl (1.004-3) ... Setting up libtcl8.6:amd64 (8.6.15+dfsg-2) ... Setting up autopoint (0.22.5-2) ... Setting up binfmt-support (2.2.2-7) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Created symlink '/etc/systemd/system/multi-user.target.wants/binfmt-support.service' -> '/usr/lib/systemd/system/binfmt-support.service'. Setting up libb-hooks-op-check-perl:amd64 (0.22-3+b1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libjbzip2-java (0.9.1-8) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up libpcsclite1:amd64 (2.3.0-1) ... Setting up pkgconf-bin (1.8.1-3) ... Setting up libsensors5:amd64 (1:3.6.0-10) ... Setting up libmongodb-java (3.6.3-2) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libactivation-java (1.2.0-2) ... Setting up libhamcrest-java (2.2-2) ... Setting up libglapi-mesa:amd64 (24.2.4-1) ... Setting up libbsh-java (2.0b4-20) ... Setting up libjsp-api-java (2.3.4-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:amd64 (14.2.0-3) ... Setting up libvulkan1:amd64 (1.3.290.0-1) ... Setting up autoconf (2.72-3) ... Setting up libwebp7:amd64 (1.4.0-0.1) ... Setting up libcolt-free-java (1.2.0+dfsg-8) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libxcb-dri2-0:amd64 (1.17.0-2) ... Setting up libgif7:amd64 (5.2.2-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up libfreemarker-java (2.3.32-2) ... Setting up sensible-utils (0.0.24) ... Setting up libxshmfence1:amd64 (1.3-1+b1) ... Setting up libjsoup-java (1.15.3-1) ... Setting up at-spi2-common (2.54.0-1) ... Setting up libcommons-math-java (2.2-8) ... Setting up libtiff6:amd64 (4.5.1+git230720-5) ... Setting up libxcb-randr0:amd64 (1.17.0-2) ... Setting up dbus-session-bus-common (1.14.10-4) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libassuan9:amd64 (3.0.1-2) ... Setting up libxml-commons-external-java (1.4.01-6) ... Setting up procps (2:4.0.4-6) ... Setting up libxbean-reflect-java (4.5-8) ... Setting up libservlet-api-java (4.0.1-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libopentest4j-java (1.2.0-4) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up ncbi-vdb-data (3.0.2+dfsg-2) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up libcommons-math3-java (3.6.1-3) ... Setting up sgml-base (1.31) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b3) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libwagon-http-shaded-java (3.5.3-1) ... Setting up libwayland-egl1:amd64 (1.23.0-1) ... Setting up libssh2-1t64:amd64 (1.11.0-7) ... Setting up libhttpcore-java (4.4.16-1) ... Setting up libjoptsimple-java (5.0.4-4) ... Setting up libprotoc32t64:amd64 (3.21.12-9) ... Setting up libxerces2-java (2.12.2-1) ... Setting up libfile-dirlist-perl (0.05-3) ... Setting up dbus-system-bus-common (1.14.10-4) ... useradd: Warning: missing or non-executable shell '/usr/sbin/nologin' Setting up libjaxp1.3-java (1.3.05-6) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up libpj-java (0.0~20150107+dfsg-5) ... Setting up openssl (3.3.2-1) ... Setting up libdrm-common (2.4.123-1) ... Setting up libcdi-api-java (1.2-3) ... Setting up libsnappy-jni (1.1.10.5-2) ... Setting up libxcomposite1:amd64 (1:0.4.5-1+b1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up liburi-perl (5.29-1) ... Setting up dbus-bin (1.14.10-4+b1) ... Setting up libfile-touch-perl (0.12-2) ... Setting up dctrl-tools (2.24-3+b1) ... Setting up libxkbcommon0:amd64 (1.6.0-1+b1) ... Setting up libwayland-client0:amd64 (1.23.0-1) ... Setting up libnet-ssleay-perl:amd64 (1.94-1+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up pinentry-curses (1.2.1-4+b1) ... Setting up libdom4j-java (2.1.4-1) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libxcb-dri3-0:amd64 (1.17.0-2) ... Setting up libwagon-provider-api-java (3.5.3-1) ... Setting up libllvm19:amd64 (1:19.1.1-1) ... Setting up libx11-xcb1:amd64 (2:1.8.7-1+b1) ... Setting up libice6:amd64 (2:1.0.10-1+b1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up libxstream-java (1.4.20-1) ... Setting up liblapack3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libmbedx509-1t64:amd64 (2.28.8-1) ... Setting up libjetty9-java (9.4.55-1) ... Setting up libxdamage1:amd64 (1:1.1.6-1+b1) ... Setting up java-wrappers (0.5) ... Setting up libatk1.0-0t64:amd64 (2.54.0-1) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libplexus-languages-java (1.1.1-2) ... Setting up protobuf-compiler (3.21.12-9) ... Setting up libjboss-vfs-java (3.2.15.Final-3) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up jarwrapper (0.80) ... Setting up libtool (2.4.7-7) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libmaven-parent-java (35-1) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-13+b2) ... Setting up libcloudproviders0:amd64 (0.3.6-1) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libnet-http-perl (6.23-1) ... Setting up libsisu-inject-java (0.3.4-2) ... Setting up libnss3:amd64 (2:3.105-2) ... Setting up dbus-daemon (1.14.10-4+b1) ... Setting up libdevel-callchecker-perl:amd64 (0.009-1) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3) ... Setting up libcolord2:amd64 (1.4.7-1+b1) ... Setting up libmaven-dependency-analyzer-java (1.14.1-1) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up pkgconf:amd64 (1.8.1-3) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libprotobuf-dev:amd64 (3.21.12-9) ... Setting up libdconf1:amd64 (0.40.0-4+b2) ... Setting up dh-autoreconf (20) ... Setting up patchutils (0.4.2-1) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up libthai0:amd64 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.4-3) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libxfixes3:amd64 (1:6.0.0-2+b1) ... Setting up libxalan2-java (2.7.2-4) ... Setting up testng (6.9.12-4) ... Setting up dbus (1.14.10-4+b1) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up shared-mime-info (2.4-5+b1) ... Setting up libxinerama1:amd64 (2:1.1.4-3+b1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libxrandr2:amd64 (2:1.5.4-1) ... Setting up libcommons-collections4-java (4.4-2) ... Setting up ucf (3.0043+nmu1) ... Setting up libcommons-lang3-java (3.14.0-1) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libdrm2:amd64 (2.4.123-1) ... Setting up libmaven-common-artifact-filters-java (3.3.2-1) ... Setting up libmbedtls14t64:amd64 (2.28.8-1) ... Setting up groff-base (1.23.0-5) ... Setting up libwayland-cursor0:amd64 (1.23.0-1) ... Setting up libhtml-parser-perl:amd64 (3.83-1) ... Setting up gpgconf (2.2.43-8+b1) ... Setting up libpam-systemd:amd64 (256.6-1) ... Setting up libcommons-beanutils-java (1.9.4-2) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libharfbuzz0b:amd64 (9.0.0-1) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-1) ... Setting up libsnappy-java (1.1.10.5-2) ... Setting up libxss1:amd64 (1:1.2.3-1+b1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libcommons-configuration-java (1.10-6) ... Setting up libwagon-file-java (3.5.3-1) ... Setting up libxml2-utils (2.12.7+dfsg+really2.9.14-0.1) ... Setting up libcommons-codec-java (1.16.0-1) ... Setting up libsm6:amd64 (2:1.2.3-1+b1) ... Setting up libreflections-java (0.10.2+dfsg-2) ... Setting up libavahi-client3:amd64 (0.8-13+b2) ... Setting up libio-socket-ssl-perl (2.089-1) ... Setting up gpg (2.2.43-8+b1) ... Setting up libhttp-message-perl (6.46-1) ... Setting up libdrm-amdgpu1:amd64 (2.4.123-1) ... Setting up libpaper1:amd64 (1.1.29+b1) ... Creating config file /etc/papersize with new version Setting up gtk-update-icon-cache (4.16.3+ds-1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up velocity (1.7-7) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b1) ... Setting up gpg-agent (2.2.43-8+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 openjdk-21-jre-headless:amd64 (21.0.5~8ea-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 libcommons-compress-java (1.25.0-1) ... Setting up libcurl4t64:amd64 (8.10.1-1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up libcommons-io-java (2.16.1-1) ... Setting up libdrm-radeon1:amd64 (2.4.123-1) ... Setting up libcommons-digester-java (1.8.1-6) ... Setting up libxtst6:amd64 (2:1.2.3-1.1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libtk8.6:amd64 (8.6.15-1) ... Setting up libdistlib-java (1.0-5) ... Setting up libxcursor1:amd64 (1:1.2.2-1) ... Setting up libparams-classify-perl:amd64 (0.015-2+b3) ... Setting up gpgsm (2.2.43-8+b1) ... Setting up libpango-1.0-0:amd64 (1.54.0+ds-2) ... Setting up libdrm-intel1:amd64 (2.4.123-1) ... Setting up libncbi-vdb3:amd64 (3.0.2+dfsg-2+b1) ... Setting up libxmlgraphics-commons-java (2.8-2) ... Setting up libpaper-utils (1.1.29+b1) ... 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 dirmngr (2.2.43-8+b1) ... Created symlink '/etc/systemd/user/sockets.target.wants/dirmngr.socket' -> '/usr/lib/systemd/user/dirmngr.socket'. Setting up libmaven-filtering-java (3.3.0-1) ... Setting up dbus-user-session (1.14.10-4+b1) ... Setting up libmaven-resolver-java (1.6.3-1) ... Setting up adwaita-icon-theme (47.0-1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up libmodule-runtime-perl (0.016-2) ... Setting up libatspi2.0-0t64:amd64 (2.54.0-1) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up libmaven-dependency-tree-java (3.2.1-1) ... Setting up libnsl2:amd64 (1.3.0-3+b2) ... Setting up gnupg (2.2.43-8) ... Setting up liblightcouch-java (0.2.0-1) ... Setting up libcairo-gobject2:amd64 (1.18.2-2) ... Setting up libmaven-shared-utils-java (3.3.4-1) ... Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-2) ... Setting up libmaven-resources-plugin-java (3.3.1-1) ... Setting up libcups2t64:amd64 (2.4.10-2) ... Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-2) ... Setting up libncbi-ngs3:amd64 (3.0.3+dfsg-9) ... Setting up libatk-bridge2.0-0t64:amd64 (2.54.0-1) ... Setting up mesa-libgallium:amd64 (24.2.4-1) ... Setting up libngs-jni:amd64 (3.0.3+dfsg-9) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up libpython3.12-stdlib:amd64 (3.12.6-1) ... Setting up libcommons-validator-java (1:1.7-1) ... Setting up libgbm1:amd64 (24.2.4-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libbatik-java (1.17+dfsg-1) ... Setting up libmoo-perl (2.005005-1) ... Setting up liblog4j2-java (2.19.0-2) ... Setting up python3.12 (3.12.6-1) ... Setting up libgl1-mesa-dri:amd64 (24.2.4-1) ... Setting up libmaven-invoker-java (3.2.0-1) ... Setting up debhelper (13.20) ... Setting up dconf-service (0.40.0-4+b2) ... Setting up r-base-core (4.4.1-3) ... Creating config file /etc/R/Renviron with new version Setting up libmaven-clean-plugin-java (3.2.0-2) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libngs-java:amd64 (3.0.3+dfsg-9) ... Setting up libhtsjdk-java (4.1.0+dfsg-2) ... Setting up libbarclay-java (5.0.0+dfsg-1) ... Setting up libpython3-stdlib:amd64 (3.12.6-1) ... Setting up libglx-mesa0:amd64 (24.2.4-1) ... Setting up libfop-java (1:2.8-3) ... Setting up libglx0:amd64 (1.7.0-1+b1) ... Setting up dconf-gsettings-backend:amd64 (0.40.0-4+b2) ... Setting up libgkl-java (0.8.11+dfsg-2) ... Setting up libmaven-archiver-java (3.6.0-1) ... Setting up python3 (3.12.6-1) ... Setting up libpicard-java (3.1.1+dfsg-1) ... Setting up libgl1:amd64 (1.7.0-1+b1) ... Setting up libgtk-3-common (3.24.43-4) ... Setting up libgtk-3-0t64:amd64 (3.24.43-4) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libwww-perl (6.77-1) ... Setting up devscripts (2.24.1) ... Setting up libguava-java (32.0.1-1) ... Setting up javahelper (0.80) ... Setting up libprotobuf-java (3.21.12-9) ... Setting up libplexus-container-default-java (2.1.1-1) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libguice-java (4.2.3-2) ... Setting up libplexus-i18n-java (1.0-beta-10-6) ... Setting up libplexus-container-default1.5-java (2.1.1-1) ... Setting up libplexus-interactivity-api-java (1.1-2) ... Setting up libplexus-velocity-java (1.2-3.1) ... Setting up libmaven3-core-java (3.8.8-1) ... Setting up libmaven-shared-incremental-java (1.1-4) ... Setting up libmaven-shared-io-java (3.0.0-4) ... Setting up libplexus-bsh-factory-java (1.0~alpha7-5) ... Setting up libplexus-compiler-java (2.12.1-3) ... Setting up libmaven-compiler-plugin-java (3.10.1-2) ... Setting up libmaven-artifact-transfer-java (0.13.1-2) ... Setting up libmaven-file-management-java (3.0.0-1) ... Setting up libmaven-source-plugin-java (3.2.1-2) ... Setting up libbyte-buddy-java (1.14.19-1) ... Setting up libbuild-helper-maven-plugin-java (3.3.0-1) ... Setting up libeasymock-java (5.2.0-1) ... Setting up libmaven-jar-plugin-java (3.3.0-2) ... Setting up libmaven-assembly-plugin-java (3.4.2-1) ... Setting up libcommons-text-java (1.11.0-1) ... Setting up libdoxia-core-java (1.12.0-1) ... Setting up libdoxia-java (1.12.0-1) ... Setting up libmaven-reporting-api-java (3.1.1-1) ... Setting up libmaven-reporting-exec-java (1.6.0-1) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for systemd (256.6-1) ... 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:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up maven (3.8.8-1) ... update-alternatives: using /usr/share/maven/bin/mvn to provide /usr/bin/mvn (mvn) in auto mode Setting up openjdk-21-jre:amd64 (21.0.5~8ea-1) ... Setting up ant (1.10.15-1) ... Setting up junit4 (4.13.2-4) ... Setting up openjdk-21-jdk-headless:amd64 (21.0.5~8ea-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 ant-contrib (1.0~b3+svn177-12) ... 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 openjdk-21-jdk:amd64 (21.0.5~8ea-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 libjsap-java (2.1-5) ... Setting up r-cran-rjava (1.0-11-1) ... Setting up libdsiutils-java (2.7.3+dfsg-1) ... Setting up junit5 (5.10.3-1) ... Setting up default-jdk (2:1.21-76) ... Setting up libicb-utils-java (2.0.1+git20161002.afee1d9-5) ... Processing triggers for sgml-base (1.31) ... Setting up libvelocity-tools-java (2.0-9) ... Setting up libdoxia-sitetools-java (1.11.1-1) ... Setting up libmaven-site-plugin-java (3.12.1-2) ... Setting up libmaven-javadoc-plugin-java (3.4.1-3) ... Setting up libmaven-reporting-impl-java (3.2.0-2) ... Setting up libmaven-dependency-plugin-java (3.5.0-1) ... Setting up libmaven-plugin-tools-java (3.7.1-1) ... Setting up libsurefire-java (2.22.3-2) ... Setting up maven-debian-helper (2.6.4) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/1730115/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/1730115/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/libgoby-java-3.3.1+dfsg2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libgoby-java_3.3.1+dfsg2-11_source.changes dpkg-buildpackage: info: source package libgoby-java dpkg-buildpackage: info: source version 3.3.1+dfsg2-11 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Pierre Gruet dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean 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 -plibgoby-io-java jh_clean debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2' dh_clean rm -rf goby-distribution/test-data goby-distribution/test-results rm -rf test-results/ make[1]: Leaving directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2' debian/rules binary dh binary --with javahelper dh_update_autotools_config dh_autoreconf dh_auto_configure mh_patchpoms -plibgoby-io-java --debian-build --keep-pom-version --maven-repo=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian/maven-repo jh_linkjars 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/libgoby-java-3.3.1\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian -Dmaven.repo.local=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian/maven-repo --batch-mode package -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.campagnelab.goby:goby-distribution:jar:3.3.1 [WARNING] 'dependencies.dependency.systemPath' for org.rosuda.REngine:REngine:jar should use a variable instead of a hard-coded path /usr/lib/R/site-library/rJava/jri/JRI.jar @ line 227, column 16 [WARNING] 'dependencies.dependency.systemPath' for com.github.broadinstitute:picard:jar should use a variable instead of a hard-coded path /usr/share/java/picard.jar @ line 293, column 16 [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: it.unimi.dsi:dsiutils:jar -> duplicate declaration of version debian @ line 295, column 15 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-io:jar:3.3.1 [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: com.google.protobuf:protobuf-java:jar -> duplicate declaration of version debian @ line 350, column 15 [WARNING] 'dependencies.dependency.systemPath' for org.itadaki:bzip2:jar should use a variable instead of a hard-coded path /usr/share/java/jbzip2-0.9.1.jar @ line 391, column 16 [WARNING] 'build.plugins.plugin.(groupId:artifactId)' must be unique but found duplicate declaration of plugin org.apache.maven.plugins:maven-antrun-plugin @ line 291, column 12 [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] Goby Framework [pom] [INFO] Goby I/O [jar] [INFO] Goby Full Distribution [jar] [INFO] [INFO] ----------------< org.campagnelab.goby:goby-framework >----------------- [INFO] Building Goby Framework 3.3.1 [1/3] [INFO] from pom.xml [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --------------------< org.campagnelab.goby:goby-io >-------------------- [INFO] Building Goby I/O 3.3.1 [2/3] [INFO] from goby-io/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The artifact org.apache.maven.plugins:maven-resources-plugin:jar:2.6 has been relocated to org.apache.maven.plugins:maven-resources-plugin:jar:3.3.1 [WARNING] The artifact org.apache.maven.plugins:maven-surefire-plugin:jar:2.12.4 has been relocated to org.apache.maven.plugins:maven-surefire-plugin:jar:2.22.3 [WARNING] The artifact org.apache.maven.plugins:maven-jar-plugin:jar:2.4 has been relocated to org.apache.maven.plugins:maven-jar-plugin:jar:3.3.0 [INFO] [INFO] --- build-helper-maven-plugin:3.3.0:add-source (add-classes) @ goby-io --- [INFO] Source directory: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/generated-sources added. [INFO] [INFO] --- maven-antrun-plugin:3.1.0:run (exec-java-protoc) @ goby-io --- [INFO] Executing tasks [INFO] [mkdir] Created dir: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/generated-sources [INFO] Executed tasks [INFO] [INFO] --- maven-antrun-plugin:3.1.0:run (exec-python-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] --- maven-antrun-plugin:3.1.0:run (exec-python-cpp-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ goby-io --- [INFO] Copying 2 resources [INFO] Copying 1 resource [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ goby-io --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 260 source files to /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/classes [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java uses or overrides a deprecated API that is marked for removal. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java: Recompile with -Xlint:removal for details. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-antrun-plugin:3.1.0:run (default) @ goby-io --- [WARNING] Parameter tasks is deprecated, use target instead [INFO] Executing tasks [INFO] [copy] Copying 1 file to /build/reproducible-path/libgoby-java-3.3.1+dfsg2 [INFO] [copy] Copying 1 file to /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/classes [INFO] Executed tasks [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ goby-io --- [INFO] skip non existing resourceDirectory /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ goby-io --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ goby-io --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ goby-io --- [INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/goby-io-3.3.1.jar [INFO] [INFO] >>> maven-source-plugin:3.2.1:jar (attach-sources) > generate-sources @ goby-io >>> [INFO] [INFO] --- build-helper-maven-plugin:3.3.0:add-source (add-classes) @ goby-io --- [INFO] Source directory: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/generated-sources added. [INFO] [INFO] --- maven-antrun-plugin:3.1.0:run (exec-java-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] --- maven-antrun-plugin:3.1.0:run (exec-python-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] --- maven-antrun-plugin:3.1.0:run (exec-python-cpp-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] <<< maven-source-plugin:3.2.1:jar (attach-sources) < generate-sources @ goby-io <<< [INFO] [INFO] [INFO] --- maven-source-plugin:3.2.1:jar (attach-sources) @ goby-io --- [INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/goby-io-3.3.1-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (attach-javadocs) @ goby-io --- [INFO] Adding the --ignore-source-errors option [INFO] No previous run data found, generating javadoc. [WARNING] Javadoc Warnings [WARNING] Loading source files for package samples... [WARNING] Loading source files for package org.campagnelab.goby.util... [WARNING] Loading source files for package org.campagnelab.goby.util.commits... [WARNING] Loading source files for package org.campagnelab.goby.util.dynoptions... [WARNING] Loading source files for package org.campagnelab.goby.util.barcode... [WARNING] Loading source files for package org.campagnelab.goby.util.motifs... [WARNING] Loading source files for package org.campagnelab.goby.util.pool... [WARNING] Loading source files for package org.campagnelab.goby.stats... [WARNING] Loading source files for package org.campagnelab.goby.exception... [WARNING] Loading source files for package org.campagnelab.goby.modes... [WARNING] Loading source files for package org.campagnelab.goby.modes.formats... [WARNING] Loading source files for package org.campagnelab.goby.modes.dsv... [WARNING] Loading source files for package org.campagnelab.goby.modes.core... [WARNING] Loading source files for package org.campagnelab.goby.compression... [WARNING] Loading source files for package org.campagnelab.goby.xml... [WARNING] Loading source files for package org.campagnelab.goby.cli... [WARNING] Loading source files for package org.campagnelab.goby.alignments... [WARNING] Loading source files for package org.campagnelab.goby.alignments.processors... [WARNING] Loading source files for package org.campagnelab.goby.alignments.filters... [WARNING] Loading source files for package org.campagnelab.goby.alignments.htsjdk... [WARNING] Loading source files for package org.campagnelab.goby.alignments.perms... [WARNING] Loading source files for package org.campagnelab.goby.baseinfo... [WARNING] Loading source files for package org.campagnelab.goby... [WARNING] Loading source files for package org.campagnelab.goby.readers.vcf... [WARNING] Loading source files for package org.campagnelab.goby.readers.sam... [WARNING] Loading source files for package org.campagnelab.goby.readers... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.compression... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.algorithm... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.algorithm.dmr... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.dsv... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.indels... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data.xml... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data.ranges... [WARNING] Loading source files for package org.campagnelab.goby.counts... [WARNING] Loading source files for package org.campagnelab.goby.counts.compound... [WARNING] Loading source files for package org.campagnelab.goby.predictions... [WARNING] Loading source files for package org.campagnelab.goby.config... [WARNING] Loading source files for package org.campagnelab.goby.methylation... [WARNING] Loading source files for package org.campagnelab.goby.parsers... [WARNING] Loading source files for package org.campagnelab.goby.R... [WARNING] Loading source files for package org.campagnelab.goby.reads... [WARNING] Loading source files for package org.campagnelab.dl.varanalysis.protobuf... [WARNING] Constructing Javadoc information... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactRCalculator.java:26: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactRCalculator.java:68: error: cannot find symbol [WARNING] Rengine rEngine; [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class FisherExactRCalculator [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactTestCalculator.java:21: error: package DistLib does not exist [WARNING] import DistLib.hypergeometric; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/EstimatedDistribution.java:22: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/AnnotationAveragingWriter.java:39: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:32: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.ParallelTeam; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:43: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBContext; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:44: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBException; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:45: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.Unmarshaller; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:76: error: cannot find symbol [WARNING] private ParallelTeam team; [WARNING] ^ [WARNING] symbol: class ParallelTeam [WARNING] location: class StatsMode [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:34: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBContext; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:35: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBException; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:36: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.Marshaller; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/xml/MethylStats.java:21: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlRootElement; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/xml/MethylStats.java:31: error: cannot find symbol [WARNING] @XmlRootElement [WARNING] ^ [WARNING] symbol: class XmlRootElement [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:696: error: cannot find symbol [WARNING] private void writeXml(PrintWriter output, String[] samples, MethylStats[] methylStats) throws JAXBException { [WARNING] ^ [WARNING] symbol: class JAXBException [WARNING] location: class MethylStatsMode [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/SimulateBisulfiteReads.java:23: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:30: error: package org.apache.commons.exec does not exist [WARNING] import org.apache.commons.exec.CommandLine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:31: error: package org.apache.commons.exec does not exist [WARNING] import org.apache.commons.exec.DefaultExecutor; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:32: error: package org.apache.commons.exec does not exist [WARNING] import org.apache.commons.exec.PumpStreamHandler; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/TestRConnectionMode.java:25: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/PercentMismatchesQualityFilter.java:23: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:39: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.IntegerForLoop; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:40: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.ParallelRegion; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:41: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.ParallelTeam; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:53: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBContext; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:54: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBException; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:55: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.Marshaller; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:106: error: cannot find symbol [WARNING] private ParallelTeam team; [WARNING] ^ [WARNING] symbol: class ParallelTeam [WARNING] location: class CompactAlignmentToAnnotationCountsMode [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:325: error: cannot find symbol [WARNING] protected synchronized ParallelTeam getParallelTeam() { [WARNING] ^ [WARNING] symbol: class ParallelTeam [WARNING] location: class CompactAlignmentToAnnotationCountsMode [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:22: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlElement; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:23: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlElementWrapper; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:24: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlRootElement; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:32: error: cannot find symbol [WARNING] @XmlRootElement(name = "info-output") [WARNING] ^ [WARNING] symbol: class XmlRootElement [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:441: error: cannot find symbol [WARNING] private void writeInfoOutput() throws JAXBException, IOException { [WARNING] ^ [WARNING] symbol: class JAXBException [WARNING] location: class CompactAlignmentToAnnotationCountsMode [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:21: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlAccessType; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:22: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlAccessorType; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:29: error: cannot find symbol [WARNING] @XmlAccessorType(XmlAccessType.FIELD) [WARNING] ^ [WARNING] symbol: class XmlAccessorType [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:21: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlAccessType; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:22: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlAccessorType; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:29: error: cannot find symbol [WARNING] @XmlAccessorType(XmlAccessType.FIELD) [WARNING] ^ [WARNING] symbol: class XmlAccessorType [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:283: error: cannot find symbol [WARNING] class BasenameParallelRegion extends ParallelRegion { [WARNING] ^ [WARNING] symbol: class ParallelRegion [WARNING] location: class CompactAlignmentToAnnotationCountsMode [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/FastaToCompactMode.java:23: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.PJProperties; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/BetweenGroupSequenceVariationOutputFormat.java:40: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/CompareGroupsVCFOutputFormat.java:42: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/MethylationRateVCFOutputFormat.java:45: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/FoldChangeForExonPairs.java:22: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/PlantIndels.java:22: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:23: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.IntegerForLoop; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:24: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.ParallelRegion; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:31: error: cannot find symbol [WARNING] class BasenameParallelRegion extends ParallelRegion { [WARNING] ^ [WARNING] symbol: class ParallelRegion [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/DoInParallel.java:21: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.ParallelTeam; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/DoInParallel.java:33: error: cannot find symbol [WARNING] private ParallelTeam team; [WARNING] ^ [WARNING] symbol: class ParallelTeam [WARNING] location: class DoInParallel [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/DoInParallel.java:47: error: cannot find symbol [WARNING] protected synchronized ParallelTeam getParallelTeam() { [WARNING] ^ [WARNING] symbol: class ParallelTeam [WARNING] location: class DoInParallel [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/FisherExactTestAdaptor.java:23: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/methylation/MethylSimilarityScan.java:23: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:23: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.RMainLoopCallbacks; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:24: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:29: error: cannot find symbol [WARNING] class RLoggerMainLoopCallback implements RMainLoopCallbacks { [WARNING] ^ [WARNING] symbol: class RMainLoopCallbacks [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:42: error: cannot find symbol [WARNING] public void rWriteConsole(final Rengine rengine, final String text, final int type) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:57: error: cannot find symbol [WARNING] public void rBusy(final Rengine rengine, final int which) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:77: error: cannot find symbol [WARNING] public String rReadConsole(final Rengine rengine, final String prompt, final int addToHistory) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:88: error: cannot find symbol [WARNING] public void rShowMessage(final Rengine rengine, final String message) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:99: error: cannot find symbol [WARNING] public String rChooseFile(final Rengine rengine, final int newFile) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:108: error: cannot find symbol [WARNING] public void rFlushConsole(final Rengine rengine) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:118: error: cannot find symbol [WARNING] public void rSaveHistory(final Rengine rengine, final String filename) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:127: error: cannot find symbol [WARNING] public void rLoadHistory(final Rengine re, final String filename) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:24: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:56: error: cannot find symbol [WARNING] private Rengine rengine; [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class GobyRengine [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:127: error: cannot find symbol [WARNING] public Rengine getRengine() { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class GobyRengine [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:27: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.REXP; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:28: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.RVector; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:29: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:208: error: cannot find symbol [WARNING] private static Result evaluateFisherExpression(final Rengine rengine, [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class FisherExact [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:21: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.RMainLoopCallbacks; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:22: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:27: error: cannot find symbol [WARNING] class RConsoleMainLoopCallback implements RMainLoopCallbacks { [WARNING] ^ [WARNING] symbol: class RMainLoopCallbacks [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:35: error: cannot find symbol [WARNING] public void rWriteConsole(final Rengine rengine, final String text, final int type) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:50: error: cannot find symbol [WARNING] public void rBusy(final Rengine rengine, final int which) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:70: error: cannot find symbol [WARNING] public String rReadConsole(final Rengine rengine, final String prompt, final int addToHistory) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:81: error: cannot find symbol [WARNING] public void rShowMessage(final Rengine rengine, final String message) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:92: error: cannot find symbol [WARNING] public String rChooseFile(final Rengine rengine, final int newFile) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:101: error: cannot find symbol [WARNING] public void rFlushConsole(final Rengine rengine) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:111: error: cannot find symbol [WARNING] public void rSaveHistory(final Rengine rengine, final String filename) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:120: error: cannot find symbol [WARNING] public void rLoadHistory(final Rengine re, final String filename) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:29: error: cannot find symbol [WARNING] @XmlAccessorType(XmlAccessType.FIELD) [WARNING] ^ [WARNING] symbol: variable XmlAccessType [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:35: error: cannot find symbol [WARNING] @XmlElement(name = "al") [WARNING] ^ [WARNING] symbol: class XmlElement [WARNING] location: class InfoOutput [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:36: error: cannot find symbol [WARNING] @XmlElementWrapper(name = "annotation-lengths") [WARNING] ^ [WARNING] symbol: class XmlElementWrapper [WARNING] location: class InfoOutput [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:29: error: cannot find symbol [WARNING] @XmlAccessorType(XmlAccessType.FIELD) [WARNING] ^ [WARNING] symbol: variable XmlAccessType [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:39: error: cannot find symbol [WARNING] @XmlElement(name = "tc") [WARNING] ^ [WARNING] symbol: class XmlElement [WARNING] location: class InfoOutput [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:40: error: cannot find symbol [WARNING] @XmlElementWrapper(name = "total-counts") [WARNING] ^ [WARNING] symbol: class XmlElementWrapper [WARNING] location: class InfoOutput [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 21.0.5-ea+8-Debian-1 [WARNING] Building tree for all the packages and classes... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/AbstractAlignmentEntryFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AbstractAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AbstractAlignmentToCompactMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AbstractAlignmentToCompactMode.TransferIds.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AbstractCommandLineMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AbstractConcatAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AbstractGobyMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/AbstractMethylationAdapter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/AbstractOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/AddTrueGenotypeHelperI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/AddTrueGenotypeHelperI.WillKeepI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AggregatePeaksByPeakDistanceMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AggregatePeaksByRPKMDifferenceMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/AlignedCountNormalization.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignedSequence.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentCollectionHandler.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentCollectionHandler.CombinedLists.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/AlignmentHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentPositionComparator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/AlignmentProcessorFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/AlignmentProcessorInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/AlignmentQualityFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentReader.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderFactoryBase.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderImpl.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentCollection.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentCollection.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentCollectionOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentEntry.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentEntry.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentEntryOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentHeader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentHeader.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentHeaderOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentIndex.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentIndex.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentIndexOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentTooManyHits.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentTooManyHits.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentTooManyHitsOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AmbiguousLocation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AmbiguousLocation.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AmbiguousLocationOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierInfo.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierInfoOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierMapping.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierMapping.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierMappingOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.ReadOriginInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.ReadOriginInfo.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.ReadOriginInfoOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.RelatedAlignmentEntry.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.RelatedAlignmentEntry.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.RelatedAlignmentEntryOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.SequenceVariation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.SequenceVariation.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.SequenceVariationOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentSliceHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentStats.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentTooManyHitsReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentTooManyHitsWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AlignmentToPileupMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AlignmentToPileupMode.OutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AlignmentToTextMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentToTextWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentWriterImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/AlleleFrequencyOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/Annotation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/AnnotationAveragingWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCountInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCountIterateAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AnnotationPenaltyMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/AnnotationRPKM.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AnnotationsToCountsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationWeightCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/AnyTransitionCountsIterator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ATGCCorrectionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/AtLeastAQuarterFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ATProportionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/AverageCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/AverageFisherRCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/BarcodeDecoderMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/BarcodeMatcher.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/BarcodeMatcherResult.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformation.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformationCollection.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformationCollection.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformationCollectionOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformationOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.CountInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.CountInfo.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.CountInfoOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.NumberWithFrequency.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.NumberWithFrequency.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.NumberWithFrequencyOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SampleInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SampleInfo.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SampleInfoOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SomaticOutput.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SomaticOutput.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SomaticOutputOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/BasenameUtils.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/BaseProportionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/BaseStatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/BaseToStringHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/BenjaminiHochbergAdjustment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/BestScoreAmbiguityAlignmentFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/BestScoreOnlyAlignmentFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/BetweenGroupSequenceVariationOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/BisulfiteConversionMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/BonferroniAdjustment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/BufferedSortingAlignmentWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/BufferedSortingSamBamWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/BuggyDeltaStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/BuildSequenceCacheMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/By5BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/BZip2ChunkCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CachingCountsArchiveReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/ChiSquareTestAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/ChiSquareTestCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/ChromosomeMapper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/ChunkCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/ChunkCodecHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/CodecHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/ColorSpaceConverter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnField.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnFields.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnMetaInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/Columns.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnType.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/CommitPropertiesStatAccumulator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/commits/CommitPropertyHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/CommonIndelArtifactFilter.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/dsv/CommonIndelArtifactFilter.java:17: warning: invalid input: '<' [WARNING] * larger than expected (P<0.05, with Poisson cumulative distribution) from prior observations (most of them are assumed to be errors). [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToCountsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToReadSetMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToTranscriptCountsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactFileStatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactToFastaMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactToFastaMode.OutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactToSAMMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CompareAlignmentToGenomeMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/CompareGroupsVCFOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDataInput.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDataOutput.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDirectoryEntry.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileTool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileTool.PROGRAM_MODE.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/CompressedRead.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeCountInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeStartCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeWeightCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/ConcatAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/ConcatenateAlignmentMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/ConcatenateCompactReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/ConcatenatePermutations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/ConcatSortedAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/ConstantAccumulator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/ConversionConfig.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/ConvertSamBAMReadToGobyAlignment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CountAdaptiveBinningAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CountArchiveToPeakAnnotationsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CountBinningAdapterI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CountBinningAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/CountCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/CountFixer.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/CountFixerInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/CountFixerNoThresholdingEffect.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CountIndexBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/CountRawSampleIdsCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsAggregatorI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsArchiveReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CountsArchiveToBedGraphMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CountsArchiveToUnionPeaksAnnotationMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CountsArchiveToWiggleMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsArchiveWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsReaderI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsWriterHelperI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsWriterI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CountWriterHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CountWriterHelper2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/CovariateInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/CovariateStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/CoverageAnalysis.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CoverageMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/CumulativeArrayKeeperFast.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/DataProvider.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/DefaultAlignmentProcessorFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/DefaultAlignmentReaderFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/DeltaStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/DeNovoDMRfinder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/DiffAlignmentMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionAnalysis.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionCalculator.ElementType.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionResults.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/DifferentiallyMethylatedRegion.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/DifferentiallyMethylatedRegion.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/DiploidFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/DiscoverSequenceVariantsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/DiscoverVariantIterateSortedAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/DiscoverVariantIterateSortedAlignments.PositionBaseInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/dsv/DiscoverVariantPositionData.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/DisplaySequenceVariationsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/DistinctIntValueCounterBitSet.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/DistinctIntValueCounterInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/cli/DoInParallel.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/DualRandomAccessSequenceCache.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/DummyFormatConfigurator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/DummyGenomeAlignmentTargetMapper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/DummyObservationWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/DummyProcessor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/DummyProcessorUnsorted.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/DummyTrueGenotypeHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/cli/DumpTargetInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/dynoptions/DynamicOptionClient.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/ElementIndexComparator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/EmpiricalPMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/EmpiricalPValueEstimator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/EntropicIndelArtifactFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/EntryFlagHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/indels/EquivalentIndelRegion.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/EquivalentIndelRegionCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/EstimatedDistribution.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/EstimatedTestDistributions.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/EvidenceCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/ExportableAlignmentEntryData.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ExportSplicingEvents.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/ExtractSplicingEventsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/FalseDiscoveryRateMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/parsers/FastaParser.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/FastArithmeticCoder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/FastArithmeticCoderI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/FastArithmeticCoderOrder1.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/FastArithmeticCoderPlus.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/FastArithmeticDecoder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/FastArithmeticDecoderI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/FastArithmeticDecoderOrder1.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/FastArithmeticDecoderPlus.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/FastaToCompactMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/FastBufferedMessageChunksReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/FastSmallAndLog10BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/FastXEntry.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/FastXReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/FDRAdjustment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FenwickTree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FenwickTree.answer.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/FileExtensionHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/FileExtensionHelper.CompactFileType.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/FileSlice.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/FilesToAttributesMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/R/FisherExact.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/R/FisherExact.AlternativeHypothesis.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/R/FisherExact.Result.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/FisherExactRCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/FisherExactTestAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/FisherExactTestCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/FoldChangeCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/cli/FoldChangeForExonPairs.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/FoldChangeMagnitudeCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/FormatConfigurator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/FormatFieldCounter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/FormatIndelVCF.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/FormatIndelVCF2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/FormatIndelVCF3.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FormulaWeightAnnotationCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FormulaWeightAnnotationCount.FormulaChoice.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FormulaWeightCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FrequencyTable.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/FromToFreq.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/GCProportionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/GenericToolsDriver.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/GeneTranscriptRelationships.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/GenomeAlignmentTargetMapper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/GenomeDebugHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/GenomicRange.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/GenotypeFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/GenotypePredictor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/GenotypesOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/GobyAlignmentReaderFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/config/GobyConfiguration.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/GobyDriver.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/exception/GobyException.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/GobyQuickSeqvar.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/R/GobyRengine.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/exception/GobyRuntimeException.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/GobySamRecord.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/GobySamSegment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/GobyVersion.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/GrepReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/GroupAssociations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/GroupComparison.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/GZipChunkCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/GzipOutputStreamWithCustomLevel.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/HeaderUtil.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/HeptamerInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/HeptamerWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/HeptamerWeightsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/HiCMerge.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/HTSJdkReaderFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/htsjdk/HTSJDKReaderImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/HybridChunkCodec1.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/HybridChunkCodec2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/IndelCountOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/InferSexFromAlignmentsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/InfoForTarget.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/InformativeColumns.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/InformativeDouble.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/InformativeNonZeroNonNaN.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/Interval.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/InvalidChecksumException.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/IOUtil.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/IsDone.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/IterateAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/IterateAlignmentsCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/IterateSortedAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/IterateSortedAlignmentsListImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/IterateSortedAlignmentsListImpl2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/IterateSortedAlignmentsListImpl2.PositionBaseInfo2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/IterateSortedAlignmentsToPileup.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/KnownIndelSet.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/LastParser.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/LastToCompactMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/LeftOverFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/LinearBinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/LocalSortProcessor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Log10BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Log2BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/Log2FoldChangeCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/LogGCCorrectionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/LoggingOutputStream.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/LogIsConfigured.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/LongNamedCounter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/cli/MakeBisulfiteFastaExample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/MaxCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/MedianCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Merge.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/MergeCompactAlignmentsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/MergeIndelFrom.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/MergeIndelFrom.SplitIndel.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/MessageChunksReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/MessageChunksWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/MethylationData.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/MethylationFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/MethylationRateDifferenceStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/MethylationRateVCFOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/MethylationRegion.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/MethylationRegionsOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/MethylationSimilarityMatch.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/MethylationSite.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/MethylationSiteIterator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/MethylCountInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/MethylCountProvider.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/MethylCountProviderFromRegionsOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/MethylCountProviderTestSupport.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/MethylRateInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/MethylSimilarityScan.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/xml/MethylStats.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/MethylStatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/MinCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/ModifyAlignmentsCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/motifs/MotifMatcher.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/MoveToFrontCoder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/MultiReads.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/NamedCounters.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/NonAmbiguousAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/NonAmbiguousAlignmentReaderFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/NoOpPermutation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/NoOpPermutationReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/NormalizationMethod.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/NotCompressedChunkCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/NoUpgradeAlignmentReaderFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/NullChunkCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/pool/NullResettableObjectPool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/ObservationWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/ObservationWriter.TypeOfPair.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/ObservedIndel.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/OffsetCountsReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/OneBinStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/OutputInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/OutputInfoFromWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/OverlapResult.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/ParseAlignmentEntriesCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/ParseAlignmentEntriesWithIndexCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/ParseReadsCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/PassThroughStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/Peak.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/PeakAggregator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/PercentMismatchesQualityFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/PermutationReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/PermutationReaderInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/PermutationWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/PicardFastaIndexedSequence.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/cli/PlantIndels.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/PositionAdapter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/PositionBaseInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/PositionFacadeAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/PositionToBasesMap.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/PostBarcodeMatcher.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/PreBarcodeMatcher.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/Predictor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/cli/PrintWeights.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/ProtobuffCollectionHandler.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/ProtoHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestMciProviderStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/PVAlueProvider.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/QFast.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/QualityEncoding.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/QualityScoreFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/QueryIndexPermutation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/QueryIndexPermutationInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/pool/QueueResettableObjectPool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/RandomAccessAnnotations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/RandomAccessSequenceCache.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/RandomAccessSequenceInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/RandomAccessSequenceTestSupport.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/Range.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/Ranges.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/Read.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/Read.ReadSortByEnd.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/Read.ReadSortByStart.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadCodec2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadCodecImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/parsers/ReaderFastaParser.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/ReadGroupHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/ReadIndexStats.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/ReadNameToIndex.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/ReadOriginInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadProtobuffCollectionHandler.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/ReadQualityStatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.MetaData.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.MetaData.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.MetaDataOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.ReadCollection.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.ReadCollection.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.ReadCollectionOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.ReadEntry.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.ReadEntry.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.ReadEntryOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadSet.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/ReadSetToTextMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadsLoader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadsReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/cli/ReadsToText.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadsToTextWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/ReadsToWeightsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadsWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadsWriterImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/ReadWithIndex.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/RealignmentProcessor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/ReferenceLocation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/ReformatCompactReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/RegionAveragingWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/RegionWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/dynoptions/RegisterThis.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/Release1_9_7_2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/RemoveBasesMatchingIndelsGenotypeFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/RemoveIndelArtifactsFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/cli/RenameWeights.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/RepositionableInputStream.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/pool/Resettable.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/pool/ResettableObjectPoolInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/RpkmLikeNormalizationMethod.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/RunParallelMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/SamComparison.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/SamComparisonInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/SAMComparisonMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/SamExtractReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/SamHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/SamPerPositionComparison.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/SampleCountCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/dsv/SampleCountInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/SamplePair.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/SamplePairEnumerator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/SampleQualityScoresMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/SampleStats.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/SamRecordGenomicPositionComparator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/SAMRecordIterable.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/SamRecordParser.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/SamSequenceVariation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/SAMToCompactMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/SAMToCompactOldMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/SAMToCompactSamHelperMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/ScanReferenceSequence.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/Segment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.Base.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.Base.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.BaseOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.ReferencePosition.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.ReferencePosition.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.ReferencePositionOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.Sample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.Sample.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.SampleOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.SegmentInformation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.SegmentInformation.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.SegmentInformationCollection.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.SegmentInformationCollection.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.SegmentInformationCollectionOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.SegmentInformationOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/SequenceBaseInfoCollectionHandler.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/SequenceBaseInformationOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/SequenceBaseInformationReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/SequenceBaseInformationWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/SequenceDigests.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/SequenceEncoder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/SequenceSegmentInfoCollectionHandler.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/SequenceSegmentInformationReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/SequenceSegmentInformationWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/SequenceVariationOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SequenceVariationPool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SequenceVariationPool.ReadIndexInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SequenceVariationPool.Variation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/SequenceVariationStats2Mode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/SequenceVariationStatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/cli/SimulateBisulfiteReads.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/SimulateReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/SitesInFixedWindow.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/SkipToListIterator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/SkipToSortedReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/SlidingCountArray.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/SmallAndLog10BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/SomaticPredictor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/SomaticVariationOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/Sort1Mode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SortedAnnotations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/SortIterateAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/SortMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/SplicedSamHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/SplicedSamHelper.Limits.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/SplitCompactReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/SplitFastaMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/SplitTranscriptsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat3StatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat4StatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat5MciProviderStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat5StatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorBaseQuality.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorDistancesToReadVariations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorDistanceToEndOfRead.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorDistanceToStartOfRead.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorInsertSizes.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorNumVariationsInRead.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorPairFlags.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorQueryAlignedLength.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorQueryPosition.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorReadMappingQuality.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorTargetAlignedLength.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/StatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/StatisticCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/StatisticComparator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/StatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/StrandBiasFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/StreamSignal.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/motifs/SubSequenceMotifMatcher.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/SuggestPositionSlicesMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SummedCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/TabToColumnInfoMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/TallyBasesMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/TallyReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/TestRConnectionMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/cli/TestSkipTo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/Timer.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/TranscriptBestScoreAlignmentFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/TranscriptsAlignmentFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/TrimMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/TSVWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/TTestCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/UnboundedFifoPool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/UnionAlgorithmSkeleton.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/UnionDumpIterator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/UpgradeMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/core/UpgradeModeCore.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/UpgradeTo1_9_6.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/Variant.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/Variant.FromTo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/Variant.GobyIndelFromVCF.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/VariantMapCreator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/VariantMapHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/VCFCompareMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/VCFCompareMode.VCFPosition.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/VCFParser.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/VCFParser.SyntaxException.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/VCFSubsetMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/VCFToGenotypeMapMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/VCFToKnownIndelsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/VcfToTabMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/VCFWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/VersionMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/WarningCounter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/WeightCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/WeightParameters.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/WeightsInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/WiggleWindow.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/WithinGroupVariabilityMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/compression/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/compression/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/dsv/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/dsv/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/indels/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/indels/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/htsjdk/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/htsjdk/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/cli/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/cli/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/config/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/config/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/exception/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/exception/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/core/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/core/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/parsers/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/parsers/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/R/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/R/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/commits/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/commits/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/dynoptions/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/dynoptions/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/motifs/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/motifs/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/pool/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/pool/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/xml/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/xml/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/serialized-form.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/class-use/ModifyAlignmentsCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/class-use/ParseReadsCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/class-use/ParseAlignmentEntriesCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/class-use/IterateAlignmentsCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/class-use/ParseAlignmentEntriesWithIndexCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/StreamSignal.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/LoggingOutputStream.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/UnboundedFifoPool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/FileExtensionHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/FileExtensionHelper.CompactFileType.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/GenomeDebugHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/VariantMapHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/SamHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/SamSequenceVariation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/KnownIndelSet.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/CodecHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/LongNamedCounter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/AlignmentHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/FromToFreq.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/VariantMapCreator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/HeaderUtil.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/IOUtil.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/LogIsConfigured.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/GrepReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/Variant.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/Variant.GobyIndelFromVCF.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/Variant.FromTo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/NamedCounters.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/WarningCounter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/OutputInfoFromWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/OutputInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/BaseToStringHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/Timer.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/IsDone.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/commits/class-use/CommitPropertyHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/dynoptions/class-use/DynamicOptionRegistry.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/dynoptions/class-use/RegisterThis.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/dynoptions/class-use/DynamicOptionClient.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/class-use/PostBarcodeMatcher.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/class-use/PreBarcodeMatcher.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/class-use/OverlapResult.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/class-use/BarcodeMatcherResult.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/class-use/BarcodeMatcher.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/motifs/class-use/MotifMatcher.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/motifs/class-use/SubSequenceMotifMatcher.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/pool/class-use/Resettable.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/pool/class-use/QueueResettableObjectPool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/pool/class-use/NullResettableObjectPool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/pool/class-use/ResettableObjectPoolInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/RpkmLikeNormalizationMethod.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/CountRawSampleIdsCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/ElementIndexComparator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/FisherExactRCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/Log2FoldChangeCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/AverageFisherRCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/TSVWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/DataProvider.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/MinCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/AverageCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/MethylCountProvider.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/InformativeColumns.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/MethylCountProviderFromRegionsOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/BonferroniAdjustment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/RegionWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/BullardUpperQuartileNormalization.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/FisherExactTestCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/SampleCountCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/FoldChangeCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/FDRAdjustment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/CountCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/FoldChangeMagnitudeCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionResults.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionAnalysis.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/AbstractOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/AlignedCountNormalization.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/NormalizationMethod.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/EstimatedTestDistributions.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/VCFWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/InformativeDouble.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/EmpiricalPValueEstimator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/FormatFieldCounter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/InformativeNonZeroNonNaN.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/StatisticCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/SampleStats.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/TTestCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/DummyObservationWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionCalculator.ElementType.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/StatisticComparator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/SamplePair.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/MethylCountProviderTestSupport.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/ChiSquareTestCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/AnnotationAveragingWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/BenjaminiHochbergAdjustment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/exception/class-use/GobyRuntimeException.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/exception/class-use/GobyException.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractCommandLineMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SplitTranscriptsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/VCFSubsetMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SplicedSamHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SplicedSamHelper.Limits.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/VCFCompareMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/VCFCompareMode.VCFPosition.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/TallyBasesMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AnnotationsToCountsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/StatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AlignmentToTextMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SAMToCompactSamHelperMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactFileStatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SampleQualityScoresMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AggregatePeaksByRPKMDifferenceMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/MethylStatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SimulateReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToUnionPeaksAnnotationMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/BarcodeDecoderMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SAMComparisonMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompareAlignmentToGenomeMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SortMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/DummyFormatConfigurator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/WeightParameters.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/FormatConfigurator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/EmpiricalPMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/BuildSequenceCacheMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/LastToCompactMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/BaseStatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/RunParallelMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/MethylationFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/FilesToAttributesMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/WithinGroupVariabilityMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToBedGraphMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/BisulfiteConversionMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AlignmentToPileupMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AlignmentToPileupMode.OutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/VcfToTabMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/InferSexFromAlignmentsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToReadSetMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ConcatenateCompactReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SequenceVariationStatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractAlignmentToCompactMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractAlignmentToCompactMode.TransferIds.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/TrimMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/TestRConnectionMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SequenceVariationStats2Mode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/Sort1Mode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SplitCompactReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/FalseDiscoveryRateMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/HeptamerWeightsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/UpgradeMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactToFastaMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactToFastaMode.OutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CoverageMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/DiscoverSequenceVariantsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ColorSpaceConverter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SuggestPositionSlicesMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/PercentMismatchesQualityFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/TabToColumnInfoMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/GenericToolsDriver.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/VCFToKnownIndelsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AnnotationPenaltyMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToWiggleMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractGobyMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToCountsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ReadQualityStatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ReformatCompactReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/GobyDriver.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CountArchiveToPeakAnnotationsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AggregatePeaksByPeakDistanceMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ConcatenateAlignmentMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/MergeCompactAlignmentsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToTranscriptCountsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SamExtractReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/DiffAlignmentMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/TallyReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/IterateSortedAlignmentsToPileup.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ExtractSplicingEventsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToAnnotationCountsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ReadsToWeightsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SplitFastaMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/VCFToGenotypeMapMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/VersionMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SAMToCompactOldMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/DisplaySequenceVariationsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ReadSetToTextMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/FastaToCompactMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SAMToCompactMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactToSAMMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SequenceVariationOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/IndelCountOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SequenceBaseInformationOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/BetweenGroupSequenceVariationOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/AlleleFrequencyOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SomaticVariationOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/MethylationRegionsOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/CompareGroupsVCFOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/GenotypesOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/MethylationRateVCFOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixerNoThresholdingEffect.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/StrandBiasFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/GenotypeFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/QualityScoreFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/IterateSortedAlignmentsListImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixerInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiscoverVariantIterateSortedAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiscoverVariantIterateSortedAlignments.PositionBaseInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixer.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/LeftOverFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CommonIndelArtifactFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/RemoveIndelArtifactsFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/AtLeastAQuarterFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/RemoveBasesMatchingIndelsGenotypeFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiploidFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/EntropicIndelArtifactFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/core/class-use/UpgradeModeCore.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/core/class-use/TabToColumnInfoModeCore.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/SequenceBaseInfoCollectionHandler.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/GzipOutputStreamWithCustomLevel.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/MessageChunksReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/SequenceSegmentInfoCollectionHandler.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/HybridChunkCodec1.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/BZip2ChunkCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/NotCompressedChunkCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/ChunkCodecHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/InvalidChecksumException.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/ChunkCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastBufferedMessageChunksReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/NullChunkCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/MessageChunksWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/HybridChunkCodec2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/ProtobuffCollectionHandler.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/GZipChunkCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoderOrder1.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoderOrder1.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoderI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoderI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/MoveToFrontCoder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoderPlus.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoderPlus.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/xml/class-use/MethylStats.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/TestSkipTo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/SimulateBisulfiteReads.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/FoldChangeForExonPairs.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/DumpTargetInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/MakeBisulfiteFastaExample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/PlantIndels.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/PrintWeights.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/DoInParallel.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/RenameWeights.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/ReadsToText.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/FileSlice.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AbstractConcatAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/RepositionableInputStream.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentSliceHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionFacadeAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentTooManyHitsReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderFactoryBase.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignedSequence.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionToBasesMap.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadIndexStats.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/DefaultAlignmentReaderFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Merge.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadGroupHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionBaseInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/BufferedSortingSamBamWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/BufferedSortingAlignmentWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateSortedAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AbstractAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/LastParser.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/UpgradeTo1_9_6.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateSortedAlignmentsListImpl2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateSortedAlignmentsListImpl2.PositionBaseInfo2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ScanReferenceSequence.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadOriginInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentStats.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/SortIterateAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/SamRecordGenomicPositionComparator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/NonAmbiguousAlignmentReaderFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/NonAmbiguousAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentWriterImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ConcatAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ReferenceLocation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentCollectionHandler.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentCollectionHandler.CombinedLists.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/HTSJdkReaderFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ConcatSortedAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentPositionComparator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentTooManyHitsWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/EntryFlagHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentToTextWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/GobyAlignmentReaderFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/NoUpgradeAlignmentReaderFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ExportableAlignmentEntryData.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/GenomicRange.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentIndex.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentIndex.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentIndexOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AmbiguousLocation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AmbiguousLocation.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AmbiguousLocationOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentTooManyHits.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentTooManyHits.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentTooManyHitsOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.ReadOriginInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.ReadOriginInfo.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.ReadOriginInfoOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.IdentifierInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.IdentifierInfo.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.IdentifierInfoOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.IdentifierMapping.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.IdentifierMapping.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.IdentifierMappingOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentHeader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentHeader.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentHeaderOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.SequenceVariation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.SequenceVariation.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.SequenceVariationOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.RelatedAlignmentEntry.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.RelatedAlignmentEntry.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.RelatedAlignmentEntryOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentEntry.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentEntry.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentEntryOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentCollection.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentCollection.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentCollectionOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/RealignmentProcessor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/InfoForTarget.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/LocalSortProcessor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/SkipToSortedReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/AlignmentProcessorInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/SkipToListIterator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/ObservedIndel.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/GenomeAlignmentTargetMapper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DefaultAlignmentProcessorFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DummyProcessorUnsorted.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DummyProcessor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/AlignmentProcessorFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DummyGenomeAlignmentTargetMapper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/GeneTranscriptRelationships.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/AbstractAlignmentEntryFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/TranscriptsAlignmentFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/BestScoreAmbiguityAlignmentFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/TranscriptBestScoreAlignmentFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/BestScoreOnlyAlignmentFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/AlignmentQualityFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/htsjdk/class-use/HTSJDKReaderImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/ReadNameToIndex.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/QueryIndexPermutation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/NoOpPermutationReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/NoOpPermutation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/PermutationReaderInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/ConcatenatePermutations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/PermutationReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/QueryIndexPermutationInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/PermutationWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorDistanceToStartOfRead.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorInsertSizes.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorDistancesToReadVariations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorNumVariationsInRead.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceBaseInformationWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceSegmentInformationReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorBaseQuality.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/BasenameUtils.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorTargetAlignedLength.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorReadMappingQuality.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceSegmentInformationWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorPairFlags.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorDistanceToEndOfRead.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceBaseInformationReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/ConstantAccumulator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/CommitPropertiesStatAccumulator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorQueryPosition.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorQueryAlignedLength.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/class-use/GobyVersion.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/class-use/Release1_9_7_2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnFields.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/Columns.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnField.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/GroupAssociations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnType.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/VCFParser.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/VCFParser.SyntaxException.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnMetaInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobySamRecord.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ChromosomeMapper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobySamSegment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamRecordParser.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobyQuickSeqvar.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ConversionConfig.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ConvertSamBAMReadToGobyAlignment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamComparisonInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SAMRecordIterable.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamPerPositionComparison.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamComparison.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/class-use/FastXReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/class-use/FastXEntry.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightAnnotationCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightAnnotationCount.FormulaChoice.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/EquivalentIndelRegionCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/BaseProportionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeCountInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/MaxCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.ReadIndexInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.Variation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/LogGCCorrectionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/RandomAccessAnnotations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeStartCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/QFast.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ATGCCorrectionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationWeightCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FrequencyTable.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ExportSplicingEvents.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/CoverageAnalysis.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeWeightCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/HiCMerge.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/EvidenceCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SummedCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SortedAnnotations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/GCProportionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FenwickTree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FenwickTree.answer.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/MedianCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCountIterateAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/WeightCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCountInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ATProportionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/HeptamerWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/CumulativeArrayKeeperFast.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PTestStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/AbstractMethylationAdapter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/ObservationWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/ObservationWriter.TypeOfPair.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DeNovoDMRfinder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SlidingCountArray.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Log10BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/CovariateStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat5MciProviderStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/By5BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/ChiSquareTestAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PassThroughStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/OneBinStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat3StatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DeltaStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/StatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/MethylationRateDifferenceStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/BuggyDeltaStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat4StatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PVAlueProvider.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/LinearBinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SmallAndLog10BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat5StatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DifferentiallyMethylatedRegion.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/FastSmallAndLog10BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PTestMciProviderStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Log2BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/RegionAveragingWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/EstimatedDistribution.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/FisherExactTestAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SitesInFixedWindow.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/dsv/class-use/DiscoverVariantPositionData.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/dsv/class-use/SampleCountInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/indels/class-use/EquivalentIndelRegion.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Interval.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Read.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Read.ReadSortByEnd.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Read.ReadSortByStart.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/ReadWithIndex.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/SamplePairEnumerator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/MethylRateInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Annotation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/HeptamerInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/DistinctIntValueCounterBitSet.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/GroupComparison.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/WeightsInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/CovariateInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/AnnotationRPKM.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/DistinctIntValueCounterInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/MethylCountInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Segment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/class-use/InfoOutput.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/class-use/SampleTotalCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/class-use/AnnotationLength.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/class-use/Range.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/class-use/Ranges.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/PeakAggregator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsWriterI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountWriterHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsAggregatorI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/UnionDumpIterator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/Peak.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountIndexBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountBinningAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountBinningAdapterI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/PositionAdapter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsReaderI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsArchiveWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountAdaptiveBinningAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/UnionAlgorithmSkeleton.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CachingCountsArchiveReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/OffsetCountsReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/WiggleWindow.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsArchiveReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountWriterHelper2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/AnyTransitionCountsIterator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsWriterHelperI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundDataOutput.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundDirectoryEntry.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundDataInput.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileTool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileTool.PROGRAM_MODE.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/Predictor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/MergeIndelFrom.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/MergeIndelFrom.SplitIndel.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/ProtoHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/DummyTrueGenotypeHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF3.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/GenotypePredictor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/SomaticPredictor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/AddTrueGenotypeHelperI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/AddTrueGenotypeHelperI.WillKeepI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/config/class-use/GobyConfiguration.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationRegion.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSimilarityMatch.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/HitBoundedPriorityQueue.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylSimilarityScan.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationData.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSite.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/DifferentiallyMethylatedRegion.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSiteIterator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/parsers/class-use/FastaParser.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/parsers/class-use/ReaderFastaParser.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/R/class-use/GobyRengine.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.Result.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.AlternativeHypothesis.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsWriterImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsToTextWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodec2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/DualRandomAccessSequenceCache.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceCache.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceTestSupport.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/MultiReads.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadSet.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadProtobuffCollectionHandler.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodecImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/SequenceDigests.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/QualityEncoding.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/CompressedRead.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/SequenceEncoder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/PicardFastaIndexedSequence.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsLoader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.MetaData.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.MetaData.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.MetaDataOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.ReadEntry.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.ReadEntry.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.ReadEntryOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.ReadCollection.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.ReadCollection.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.ReadCollectionOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.ReferencePosition.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.ReferencePosition.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.ReferencePositionOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.Base.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.Base.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.BaseOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.Sample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.Sample.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SampleOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformation.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformationOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformationCollection.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformationCollection.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformationCollectionOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SomaticOutput.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SomaticOutput.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SomaticOutputOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.NumberWithFrequency.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.NumberWithFrequency.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.NumberWithFrequencyOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.CountInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.CountInfo.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.CountInfoOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SampleInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SampleInfo.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SampleInfoOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformation.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformationOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformationCollection.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformationCollection.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformationCollectionOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/compression/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/dsv/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/indels/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/htsjdk/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/cli/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/config/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/exception/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/core/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/parsers/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/R/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/commits/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/dynoptions/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/motifs/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/pool/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/xml/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/deprecated-list.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/allclasses-index.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/index-all.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/search.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/help-doc.html... [WARNING] 100 warnings [INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/goby-io-3.3.1-javadoc.jar [INFO] [INFO] ---------------< org.campagnelab.goby:goby-distribution >--------------- [INFO] Building Goby Full Distribution 3.3.1 [3/3] [INFO] from goby-distribution/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ goby-distribution --- [INFO] Copying 3 resources [INFO] Copying 72 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ goby-distribution --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 525 source files to /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/classes [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java uses or overrides a deprecated API that is marked for removal. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java: Recompile with -Xlint:removal for details. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/VariantMapHelper.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/VariantMapHelper.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ goby-distribution --- [INFO] skip non existing resourceDirectory /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ goby-distribution --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 120 source files to /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/test-classes [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/TestQFast.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/TestQFast.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/dmr/TestDeNovoDMRfinder.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/dmr/TestDeNovoDMRfinder.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ goby-distribution --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ goby-distribution --- [INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/goby-distribution-3.3.1.jar [INFO] [INFO] >>> maven-source-plugin:3.2.1:jar (attach-sources) > generate-sources @ goby-distribution >>> [INFO] [INFO] <<< maven-source-plugin:3.2.1:jar (attach-sources) < generate-sources @ goby-distribution <<< [INFO] [INFO] [INFO] --- maven-source-plugin:3.2.1:jar (attach-sources) @ goby-distribution --- [INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/goby-distribution-3.3.1-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (attach-javadocs) @ goby-distribution --- [INFO] Adding the --ignore-source-errors option [INFO] No previous run data found, generating javadoc. [WARNING] Javadoc Warnings [WARNING] Loading source files for package samples... [WARNING] Loading source files for package org.campagnelab.goby.util... [WARNING] Loading source files for package org.campagnelab.goby.util.commits... [WARNING] Loading source files for package org.campagnelab.goby.util.dynoptions... [WARNING] Loading source files for package org.campagnelab.goby.util.barcode... [WARNING] Loading source files for package org.campagnelab.goby.util.motifs... [WARNING] Loading source files for package org.campagnelab.goby.util.pool... [WARNING] Loading source files for package org.campagnelab.goby.stats... [WARNING] Loading source files for package org.campagnelab.goby.exception... [WARNING] Loading source files for package org.campagnelab.goby.modes... [WARNING] Loading source files for package org.campagnelab.goby.modes.formats... [WARNING] Loading source files for package org.campagnelab.goby.modes.dsv... [WARNING] Loading source files for package org.campagnelab.goby.modes.core... [WARNING] Loading source files for package org.campagnelab.goby.compression... [WARNING] Loading source files for package org.campagnelab.goby.xml... [WARNING] Loading source files for package org.campagnelab.goby.cli... [WARNING] Loading source files for package org.campagnelab.goby.alignments... [WARNING] Loading source files for package org.campagnelab.goby.alignments.processors... [WARNING] Loading source files for package org.campagnelab.goby.alignments.filters... [WARNING] Loading source files for package org.campagnelab.goby.alignments.htsjdk... [WARNING] Loading source files for package org.campagnelab.goby.alignments.perms... [WARNING] Loading source files for package org.campagnelab.goby.baseinfo... [WARNING] Loading source files for package org.campagnelab.goby... [WARNING] Loading source files for package org.campagnelab.goby.readers.vcf... [WARNING] Loading source files for package org.campagnelab.goby.readers.sam... [WARNING] Loading source files for package org.campagnelab.goby.readers... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.compression... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.algorithm... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.algorithm.dmr... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.dsv... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.indels... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data.xml... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data.ranges... [WARNING] Loading source files for package org.campagnelab.goby.counts... [WARNING] Loading source files for package org.campagnelab.goby.counts.compound... [WARNING] Loading source files for package org.campagnelab.goby.predictions... [WARNING] Loading source files for package org.campagnelab.goby.config... [WARNING] Loading source files for package org.campagnelab.goby.methylation... [WARNING] Loading source files for package org.campagnelab.goby.parsers... [WARNING] Loading source files for package org.campagnelab.goby.R... [WARNING] Loading source files for package org.campagnelab.goby.reads... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 21.0.5-ea+8-Debian-1 [WARNING] Building tree for all the packages and classes... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/AbstractAlignmentEntryFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AbstractAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AbstractAlignmentToCompactMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AbstractAlignmentToCompactMode.TransferIds.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AbstractCommandLineMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AbstractConcatAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AbstractGobyMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/AbstractMethylationAdapter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/AbstractOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/AddTrueGenotypeHelperI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/AddTrueGenotypeHelperI.WillKeepI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AggregatePeaksByPeakDistanceMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AggregatePeaksByRPKMDifferenceMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/AlignedCountNormalization.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignedSequence.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentCollectionHandler.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentCollectionHandler.CombinedLists.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/AlignmentHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentPositionComparator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/AlignmentProcessorFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/AlignmentProcessorInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/AlignmentQualityFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentReader.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderFactoryBase.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderImpl.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentSliceHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentStats.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentTooManyHitsReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentTooManyHitsWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AlignmentToPileupMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AlignmentToPileupMode.OutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AlignmentToTextMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentToTextWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentWriterImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/AlleleFrequencyOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Annotation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/AnnotationAveragingWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCountInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCountIterateAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AnnotationPenaltyMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/AnnotationRPKM.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AnnotationsToCountsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationWeightCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/AnyTransitionCountsIterator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ATGCCorrectionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/AtLeastAQuarterFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ATProportionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/AverageCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/AverageFisherRCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/BarcodeDecoderMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/BarcodeMatcher.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/BarcodeMatcherResult.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/BasenameUtils.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/BaseProportionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/BaseStatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/BaseToStringHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/BenjaminiHochbergAdjustment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/BestScoreAmbiguityAlignmentFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/BestScoreOnlyAlignmentFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/BetweenGroupSequenceVariationOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/BisulfiteConversionMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/BonferroniAdjustment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/BufferedSortingAlignmentWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/BufferedSortingSamBamWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/BuggyDeltaStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/BuildSequenceCacheMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/By5BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/BZip2ChunkCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CachingCountsArchiveReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/ChiSquareTestAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/ChiSquareTestCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/ChromosomeMapper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/ChunkCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/ChunkCodecHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/CodecHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ColorSpaceConverter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnField.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnFields.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnMetaInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/Columns.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnType.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/CommitPropertiesStatAccumulator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/commits/CommitPropertyHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/CommonIndelArtifactFilter.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/dsv/CommonIndelArtifactFilter.java:17: warning: invalid input: '<' [WARNING] * larger than expected (P<0.05, with Poisson cumulative distribution) from prior observations (most of them are assumed to be errors). [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToCountsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToReadSetMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToTranscriptCountsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactFileStatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactToFastaMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactToFastaMode.OutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactToSAMMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompareAlignmentToGenomeMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/CompareGroupsVCFOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDataInput.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDataOutput.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDirectoryEntry.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileTool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileTool.PROGRAM_MODE.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/CompressedRead.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeCountInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeStartCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeWeightCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ConcatAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ConcatenateAlignmentMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ConcatenateCompactReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/ConcatenatePermutations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ConcatSortedAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/ConstantAccumulator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/ConversionConfig.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/ConvertSamBAMReadToGobyAlignment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountAdaptiveBinningAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CountArchiveToPeakAnnotationsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountBinningAdapterI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountBinningAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/CountCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/CountFixer.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/CountFixerInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/CountFixerNoThresholdingEffect.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountIndexBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/CountRawSampleIdsCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsAggregatorI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsArchiveReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CountsArchiveToBedGraphMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CountsArchiveToUnionPeaksAnnotationMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CountsArchiveToWiggleMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsArchiveWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsReaderI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsWriterHelperI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsWriterI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountWriterHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountWriterHelper2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/CovariateInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/CovariateStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/CoverageAnalysis.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CoverageMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/CumulativeArrayKeeperFast.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/DataProvider.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/DefaultAlignmentProcessorFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/DefaultAlignmentReaderFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/DeltaStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/DeNovoDMRfinder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/DiffAlignmentMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionAnalysis.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionCalculator.ElementType.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionResults.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/DifferentiallyMethylatedRegion.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/DifferentiallyMethylatedRegion.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/DiploidFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/DiscoverSequenceVariantsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/DiscoverVariantIterateSortedAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/DiscoverVariantIterateSortedAlignments.PositionBaseInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/DiscoverVariantPositionData.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/DisplaySequenceVariationsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/DistinctIntValueCounterBitSet.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/DistinctIntValueCounterInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/DoInParallel.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/DualRandomAccessSequenceCache.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/DummyFormatConfigurator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/DummyGenomeAlignmentTargetMapper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/DummyObservationWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/DummyProcessor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/DummyProcessorUnsorted.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/DummyTrueGenotypeHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/DumpTargetInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/DynamicOptionClient.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/ElementIndexComparator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/EmpiricalPMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/EmpiricalPValueEstimator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/EntropicIndelArtifactFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/EntryFlagHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/indels/EquivalentIndelRegion.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/EquivalentIndelRegionCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/EstimatedDistribution.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/EstimatedTestDistributions.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/EvidenceCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ExportableAlignmentEntryData.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ExportSplicingEvents.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ExtractSplicingEventsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/FalseDiscoveryRateMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/FastaParser.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticCoder.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticCoder.java:56: warning: reference not found: it.unimi.dsi.mg4j.io.ArithmeticDecoder [WARNING] * @see it.unimi.dsi.mg4j.io.ArithmeticDecoder (MG4J). [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticCoderI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticCoderOrder1.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticCoderPlus.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticDecoder.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoder.java:33: warning: reference not found: it.unimi.dsi.mg4j.io.ArithmeticDecoder [WARNING] * @see it.unimi.dsi.mg4j.io.ArithmeticDecoder (MG4J) [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticDecoderI.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:51: warning: reference not found: #BITS [WARNING] * the call, exactly {@link #BITS} excess bits will be present in the [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:60: warning: @return tag cannot be used in method with void return type. [WARNING] void flush(InputBitStream ibs) throws IOException; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:65: warning: reference not found: #BITS [WARNING] * @return the current bit stream window in the lower {@link #BITS} bits. [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticDecoderOrder1.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:51: warning: reference not found: #BITS [WARNING] * the call, exactly {@link #BITS} excess bits will be present in the [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:65: warning: reference not found: #BITS [WARNING] * @return the current bit stream window in the lower {@link #BITS} bits. [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticDecoderPlus.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:51: warning: reference not found: #BITS [WARNING] * the call, exactly {@link #BITS} excess bits will be present in the [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:65: warning: reference not found: #BITS [WARNING] * @return the current bit stream window in the lower {@link #BITS} bits. [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/FastaToCompactMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastBufferedMessageChunksReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/FastSmallAndLog10BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/FastXEntry.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/FastXReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/FDRAdjustment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FenwickTree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FenwickTree.answer.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/FileExtensionHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/FileExtensionHelper.CompactFileType.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/FileSlice.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/FilesToAttributesMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/FisherExact.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:364: warning: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:388: warning: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:340: warning: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:340: warning: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:364: warning: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:388: warning: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/FisherExact.AlternativeHypothesis.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/FisherExact.Result.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/FisherExactRCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/FisherExactTestAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/FisherExactTestCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/FoldChangeCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/FoldChangeForExonPairs.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/FoldChangeMagnitudeCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/FormatConfigurator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/FormatFieldCounter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/FormatIndelVCF.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/FormatIndelVCF2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/FormatIndelVCF3.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FormulaWeightAnnotationCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FormulaWeightAnnotationCount.FormulaChoice.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FormulaWeightCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FrequencyTable.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/FromToFreq.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/GCProportionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/GenericToolsDriver.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/GeneTranscriptRelationships.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/GenomeAlignmentTargetMapper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/GenomeDebugHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/GenomicRange.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/GenotypeFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/GenotypePredictor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/GenotypesOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/GobyAlignmentReaderFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/config/GobyConfiguration.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:72: warning: reference not found: org.campagnelab.goby.aligners.LastagAligner [WARNING] * @see org.campagnelab.goby.aligners.LastagAligner [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:79: warning: reference not found: org.campagnelab.goby.aligners.LastAligner [WARNING] * @see org.campagnelab.goby.aligners.LastAligner [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:87: warning: reference not found: org.campagnelab.goby.aligners.BWAAligner [WARNING] * @see org.campagnelab.goby.aligners.BWAAligner [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:95: warning: reference not found: org.campagnelab.goby.aligners.GSnapAligner [WARNING] * @see org.campagnelab.goby.aligners.GSnapAligner [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/GobyDriver.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/exception/GobyException.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/GobyQuickSeqvar.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/GobyRengine.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/exception/GobyRuntimeException.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/GobySamRecord.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/GobySamSegment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/GobyVersion.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/GrepReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/GroupAssociations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/GroupComparison.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/GZipChunkCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/GzipOutputStreamWithCustomLevel.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/HeaderUtil.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/HeptamerInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/HeptamerWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/HeptamerWeightsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/HiCMerge.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:127: warning: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore [WARNING] * Dequeues a document from the queue, returning an instance of {@link [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:127: warning: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore [WARNING] * Dequeues a document from the queue, returning an instance of {@link [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:131: warning: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore [WARNING] * @return the next {@link edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore}. [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/HTSJdkReaderFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/htsjdk/HTSJDKReaderImpl.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/HybridChunkCodec1.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/HybridChunkCodec2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/IndelCountOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/InferSexFromAlignmentsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/InfoForTarget.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/InformativeColumns.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/InformativeDouble.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/InformativeNonZeroNonNaN.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Interval.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/InvalidChecksumException.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/IOUtil.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/IsDone.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/IterateAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/IterateAlignmentsCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/IterateSortedAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/IterateSortedAlignmentsListImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/IterateSortedAlignmentsListImpl2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/IterateSortedAlignmentsListImpl2.PositionBaseInfo2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/IterateSortedAlignmentsToPileup.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/KnownIndelSet.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/LastParser.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/LastToCompactMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/LeftOverFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/LinearBinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/LocalSortProcessor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Log10BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Log2BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/Log2FoldChangeCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/LogGCCorrectionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/LoggingOutputStream.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/LogIsConfigured.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/LongNamedCounter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/MakeBisulfiteFastaExample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/MaxCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/MedianCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/Merge.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/MergeCompactAlignmentsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/MergeIndelFrom.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/MergeIndelFrom.SplitIndel.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/MessageChunksReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/MessageChunksWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationData.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/MethylationFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/MethylationRateDifferenceStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/MethylationRateVCFOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationRegion.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/MethylationRegionsOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationSimilarityMatch.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationSite.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationSiteIterator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/MethylCountInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/MethylCountProvider.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/MethylCountProviderFromRegionsOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/MethylCountProviderTestSupport.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/MethylRateInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylSimilarityScan.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/xml/MethylStats.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/MethylStatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/MinCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/ModifyAlignmentsCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/MotifMatcher.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/MoveToFrontCoder.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/MoveToFrontCoder.java:42: warning: invalid input: '<' [WARNING] * @param symbol Symbol to encode with move to front (precondition: 0<= symbol ?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/QualityEncoding.java:41: warning: invalid input: '<' [WARNING] * !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/QualityScoreFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/QueryIndexPermutation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/QueryIndexPermutationInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/QueueResettableObjectPool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/RandomAccessAnnotations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/RandomAccessSequenceCache.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/RandomAccessSequenceInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/RandomAccessSequenceTestSupport.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/Range.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/Ranges.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Read.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Read.ReadSortByEnd.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Read.ReadSortByStart.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadCodec2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadCodecImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/ReaderFastaParser.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ReadGroupHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ReadIndexStats.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/ReadNameToIndex.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ReadOriginInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadProtobuffCollectionHandler.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ReadQualityStatsMode.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:193: warning: invalid input: '<' [WARNING] * Number of reads observed because of sampleFraction value < 1.0d. If sampleFraction == 1.0d [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:185: warning: invalid input: '<' [WARNING] * Number of reads skipped because of sampleFraction value < 1.0d. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:185: warning: invalid input: '<' [WARNING] * Number of reads skipped because of sampleFraction value < 1.0d. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:193: warning: invalid input: '<' [WARNING] * Number of reads observed because of sampleFraction value < 1.0d. If sampleFraction == 1.0d [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadSet.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ReadSetToTextMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsLoader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/ReadsToText.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsToTextWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ReadsToWeightsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsWriterImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ReadWithIndex.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/RealignmentProcessor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ReferenceLocation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ReformatCompactReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/RegionAveragingWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/RegionWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/RegisterThis.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/Release1_9_7_2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/RemoveBasesMatchingIndelsGenotypeFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/RemoveIndelArtifactsFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/RenameWeights.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/RepositionableInputStream.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/Resettable.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/ResettableObjectPoolInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/RpkmLikeNormalizationMethod.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/RunParallelMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SamComparison.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/readers/sam/SamComparison.java:233: warning: @return tag cannot be used in method with void return type. [WARNING] public void setCountComparisonFailures(final boolean countComparisonFailures) { [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/readers/sam/SamComparison.java:275: warning: @return tag cannot be used in method with void return type. [WARNING] public void setAllowSourceNs(boolean allowSourceNs) { [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SamComparisonInterface.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/readers/sam/SamComparisonInterface.java:130: warning: @return tag cannot be used in method with void return type. [WARNING] public void setAllowSourceNs(boolean allowSourceNs); [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SAMComparisonMode.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMComparisonMode.java:214: warning: @return tag cannot be used in method with void return type. [WARNING] public void setCheckMate(final boolean checkMate) { [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SamExtractReadsMode.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/SamExtractReadsMode.java:44: warning: invalid input: '<' [WARNING] * WARNING: If the file contains pairs, the source SAM/BAM file >>MUST<< be sorted by read name. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/SamExtractReadsMode.java:44: warning: invalid input: '<' [WARNING] * WARNING: If the file contains pairs, the source SAM/BAM file >>MUST<< be sorted by read name. [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/SamHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SamPerPositionComparison.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/SampleCountCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/SampleCountInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/SamplePair.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/SamplePairEnumerator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SampleQualityScoresMode.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/SampleQualityScoresMode.java:176: warning: invalid input: '<' [WARNING] * Set to <= 0 to process the entire file. [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/SampleStats.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/SamRecordGenomicPositionComparator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SAMRecordIterable.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SamRecordParser.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/SamSequenceVariation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SAMToCompactMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SAMToCompactOldMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SAMToCompactSamHelperMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ScanReferenceSequence.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Segment.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/Segment.java:137: warning: invalid input: '&' [WARNING] * Determine if the segment overlaps with position. This method evaluates to position>=start && position<=end; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/Segment.java:137: warning: invalid input: '&' [WARNING] * Determine if the segment overlaps with position. This method evaluates to position>=start && position<=end; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/Segment.java:137: warning: invalid input: '<' [WARNING] * Determine if the segment overlaps with position. This method evaluates to position>=start && position<=end; [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/SequenceBaseInfoCollectionHandler.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/SequenceBaseInformationOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/SequenceBaseInformationReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/SequenceBaseInformationWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/SequenceDigests.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/SequenceEncoder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/SequenceSegmentInfoCollectionHandler.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/SequenceSegmentInformationReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/SequenceSegmentInformationWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/SequenceVariationOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SequenceVariationPool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SequenceVariationPool.ReadIndexInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SequenceVariationPool.Variation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SequenceVariationStats2Mode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SequenceVariationStatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/SimulateBisulfiteReads.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SimulateReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/SitesInFixedWindow.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/SkipToListIterator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/SkipToSortedReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/SlidingCountArray.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/SmallAndLog10BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/SomaticPredictor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/SomaticVariationOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/Sort1Mode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SortedAnnotations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/SortIterateAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SortMode.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/SortMode.java:142: warning: invalid input: '<' [WARNING] * Set to < 0 for auto-detect number of cores. [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplicedSamHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplicedSamHelper.Limits.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplitCompactReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplitFastaMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplitTranscriptsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat3StatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat4StatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat5MciProviderStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat5StatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorBaseQuality.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorDistancesToReadVariations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorDistanceToEndOfRead.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorDistanceToStartOfRead.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorInsertSizes.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorNumVariationsInRead.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorPairFlags.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorQueryAlignedLength.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorQueryPosition.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorReadMappingQuality.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorTargetAlignedLength.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/StatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/StatisticCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/StatisticComparator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/StatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/StrandBiasFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/StreamSignal.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/SubSequenceMotifMatcher.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SuggestPositionSlicesMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SummedCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TabToColumnInfoMode.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:186: warning: invalid input: '<' [WARNING] * Get the number of input lines to read or set to <= 0 to read the entire file. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:194: warning: invalid input: '<' [WARNING] * Set the number of input lines to read or set to <= 0 to read the entire file. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:186: warning: invalid input: '<' [WARNING] * Get the number of input lines to read or set to <= 0 to read the entire file. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:194: warning: invalid input: '<' [WARNING] * Set the number of input lines to read or set to <= 0 to read the entire file. [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:216: warning: invalid input: '<' [WARNING] * Get the number of input lines to read or set to <= 0 to read the entire file. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:224: warning: invalid input: '<' [WARNING] * Set the number of input lines to read or set to <= 0 to read the entire file. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:216: warning: invalid input: '<' [WARNING] * Get the number of input lines to read or set to <= 0 to read the entire file. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:224: warning: invalid input: '<' [WARNING] * Set the number of input lines to read or set to <= 0 to read the entire file. [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TallyBasesMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TallyReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TestRConnectionMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/TestSkipTo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/Timer.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/TranscriptBestScoreAlignmentFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/TranscriptsAlignmentFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TrimMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/TSVWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/TTestCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/UnboundedFifoPool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/UnionAlgorithmSkeleton.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/UnionDumpIterator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/UpgradeMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/UpgradeModeCore.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/UpgradeTo1_9_6.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/Variant.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/Variant.FromTo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/Variant.GobyIndelFromVCF.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/VariantMapCreator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/VariantMapHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VCFCompareMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VCFCompareMode.VCFPosition.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/VCFParser.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/readers/vcf/VCFParser.java:179: warning: invalid input: '<' [WARNING] * Set to <= 0 to scan the entire file. This must be set before calling readHeader() for the value to be used. [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/VCFParser.SyntaxException.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VCFSubsetMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VCFToGenotypeMapMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VCFToKnownIndelsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VcfToTabMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/VCFWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VersionMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/WarningCounter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/WeightCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/WeightParameters.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/WeightsInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/WiggleWindow.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/WithinGroupVariabilityMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/compression/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/compression/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/indels/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/indels/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/htsjdk/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/htsjdk/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/config/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/config/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/exception/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/exception/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/commits/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/commits/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/xml/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/xml/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/serialized-form.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/class-use/ModifyAlignmentsCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/class-use/ParseReadsCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/class-use/ParseAlignmentEntriesCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/class-use/IterateAlignmentsCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/class-use/ParseAlignmentEntriesWithIndexCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/LongNamedCounter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/FromToFreq.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/HeaderUtil.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/GenomeDebugHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/OutputInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/CodecHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/WarningCounter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/LogIsConfigured.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/IsDone.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/KnownIndelSet.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/GrepReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/OutputInfoFromWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/VariantMapCreator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/UnboundedFifoPool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/StreamSignal.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/IOUtil.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/NamedCounters.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/BaseToStringHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/SamSequenceVariation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/FileExtensionHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/FileExtensionHelper.CompactFileType.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/Timer.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/Variant.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/Variant.GobyIndelFromVCF.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/Variant.FromTo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/LoggingOutputStream.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/SamHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/AlignmentHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/VariantMapHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/commits/class-use/CommitPropertyHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/class-use/RegisterThis.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/class-use/DynamicOptionRegistry.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/class-use/DynamicOptionClient.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/class-use/PreBarcodeMatcher.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/class-use/BarcodeMatcherResult.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/class-use/PostBarcodeMatcher.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/class-use/OverlapResult.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/class-use/BarcodeMatcher.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/class-use/MotifMatcher.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/class-use/SubSequenceMotifMatcher.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/class-use/NullResettableObjectPool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/class-use/ResettableObjectPoolInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/class-use/Resettable.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/class-use/QueueResettableObjectPool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/RpkmLikeNormalizationMethod.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/CountRawSampleIdsCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/ElementIndexComparator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/FisherExactRCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/Log2FoldChangeCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/AverageFisherRCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/TSVWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DataProvider.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/MinCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/AverageCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/MethylCountProvider.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/InformativeColumns.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/MethylCountProviderFromRegionsOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/BonferroniAdjustment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/RegionWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/BullardUpperQuartileNormalization.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/FisherExactTestCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/SampleCountCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/FoldChangeCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/FDRAdjustment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/CountCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/FoldChangeMagnitudeCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionResults.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionAnalysis.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/AbstractOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/AlignedCountNormalization.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/NormalizationMethod.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/EstimatedTestDistributions.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/VCFWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/InformativeDouble.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/EmpiricalPValueEstimator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/FormatFieldCounter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/InformativeNonZeroNonNaN.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/StatisticCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/SampleStats.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/TTestCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DummyObservationWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionCalculator.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionCalculator.ElementType.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/StatisticComparator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/SamplePair.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/MethylCountProviderTestSupport.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/ChiSquareTestCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/AnnotationAveragingWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/BenjaminiHochbergAdjustment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/exception/class-use/GobyException.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/exception/class-use/GobyRuntimeException.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractCommandLineMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SplitTranscriptsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VCFSubsetMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SplicedSamHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SplicedSamHelper.Limits.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VCFCompareMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VCFCompareMode.VCFPosition.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/TallyBasesMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AnnotationsToCountsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/StatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AlignmentToTextMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SAMToCompactSamHelperMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactFileStatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SampleQualityScoresMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AggregatePeaksByRPKMDifferenceMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/MethylStatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SimulateReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToUnionPeaksAnnotationMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/BarcodeDecoderMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SAMComparisonMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompareAlignmentToGenomeMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SortMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/DummyFormatConfigurator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/WeightParameters.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/FormatConfigurator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/EmpiricalPMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/BuildSequenceCacheMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/LastToCompactMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/BaseStatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/RunParallelMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/MethylationFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/FilesToAttributesMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/WithinGroupVariabilityMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToBedGraphMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/BisulfiteConversionMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AlignmentToPileupMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AlignmentToPileupMode.OutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VcfToTabMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/InferSexFromAlignmentsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToReadSetMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ConcatenateCompactReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SequenceVariationStatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractAlignmentToCompactMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractAlignmentToCompactMode.TransferIds.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/TrimMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/TestRConnectionMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SequenceVariationStats2Mode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/Sort1Mode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SplitCompactReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/FalseDiscoveryRateMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/HeptamerWeightsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/UpgradeMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactToFastaMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactToFastaMode.OutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CoverageMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/DiscoverSequenceVariantsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ColorSpaceConverter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SuggestPositionSlicesMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/PercentMismatchesQualityFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/TabToColumnInfoMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/GenericToolsDriver.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VCFToKnownIndelsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AnnotationPenaltyMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToWiggleMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractGobyMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToCountsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ReadQualityStatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ReformatCompactReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/GobyDriver.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CountArchiveToPeakAnnotationsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AggregatePeaksByPeakDistanceMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ConcatenateAlignmentMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/MergeCompactAlignmentsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToTranscriptCountsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SamExtractReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/DiffAlignmentMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/TallyReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/IterateSortedAlignmentsToPileup.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ExtractSplicingEventsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToAnnotationCountsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ReadsToWeightsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SplitFastaMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VCFToGenotypeMapMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VersionMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SAMToCompactOldMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/DisplaySequenceVariationsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ReadSetToTextMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/FastaToCompactMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SAMToCompactMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactToSAMMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SequenceVariationOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/IndelCountOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SequenceBaseInformationOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/BetweenGroupSequenceVariationOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/AlleleFrequencyOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SomaticVariationOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/MethylationRegionsOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/CompareGroupsVCFOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/GenotypesOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/MethylationRateVCFOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixerNoThresholdingEffect.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/StrandBiasFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/GenotypeFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/QualityScoreFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/IterateSortedAlignmentsListImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixerInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiscoverVariantIterateSortedAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiscoverVariantIterateSortedAlignments.PositionBaseInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixer.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/LeftOverFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CommonIndelArtifactFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/RemoveIndelArtifactsFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/AtLeastAQuarterFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/RemoveBasesMatchingIndelsGenotypeFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiploidFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/EntropicIndelArtifactFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/class-use/UpgradeModeCore.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/class-use/TabToColumnInfoModeCore.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoderI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/InvalidChecksumException.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/MessageChunksWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastBufferedMessageChunksReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/MessageChunksReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoderOrder1.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/BZip2ChunkCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoderOrder1.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoderPlus.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/ProtobuffCollectionHandler.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/HybridChunkCodec2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/ChunkCodecHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoderI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/ChunkCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/GZipChunkCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/SequenceBaseInfoCollectionHandler.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoderPlus.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/MoveToFrontCoder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/SequenceSegmentInfoCollectionHandler.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/NullChunkCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/HybridChunkCodec1.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/GzipOutputStreamWithCustomLevel.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/NotCompressedChunkCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/xml/class-use/MethylStats.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/TestSkipTo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/SimulateBisulfiteReads.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/FoldChangeForExonPairs.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/DumpTargetInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/MakeBisulfiteFastaExample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/PlantIndels.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/PrintWeights.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/DoInParallel.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/RenameWeights.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/ReadsToText.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/BufferedSortingAlignmentWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/GenomicRange.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/HTSJdkReaderFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentPositionComparator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/ExportableAlignmentEntryData.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/SamRecordGenomicPositionComparator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/ReferenceLocation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadGroupHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/LastParser.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentWriterImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderFactoryBase.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadIndexStats.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentSliceHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionBaseInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/NoUpgradeAlignmentReaderFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentTooManyHitsWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentTooManyHitsReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateSortedAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentToTextWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadOriginInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AbstractAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/UpgradeTo1_9_6.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/NonAmbiguousAlignmentReaderFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/ConcatAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/GobyAlignmentReaderFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentStats.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/BufferedSortingSamBamWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/NonAmbiguousAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignedSequence.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/ScanReferenceSequence.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/Merge.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/ConcatSortedAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/SortIterateAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentCollectionHandler.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentCollectionHandler.CombinedLists.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/EntryFlagHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AbstractConcatAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionFacadeAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/FileSlice.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateSortedAlignmentsListImpl2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateSortedAlignmentsListImpl2.PositionBaseInfo2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionToBasesMap.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/DefaultAlignmentReaderFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/RepositionableInputStream.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/ObservedIndel.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/InfoForTarget.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/AlignmentProcessorInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/AlignmentProcessorFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DefaultAlignmentProcessorFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/LocalSortProcessor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DummyGenomeAlignmentTargetMapper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/SkipToListIterator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DummyProcessorUnsorted.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/SkipToSortedReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DummyProcessor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/RealignmentProcessor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/GenomeAlignmentTargetMapper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/BestScoreAmbiguityAlignmentFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/AlignmentQualityFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/TranscriptBestScoreAlignmentFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/GeneTranscriptRelationships.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/AbstractAlignmentEntryFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/BestScoreOnlyAlignmentFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/TranscriptsAlignmentFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/htsjdk/class-use/HTSJDKReaderImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/ConcatenatePermutations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/ReadNameToIndex.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/PermutationReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/QueryIndexPermutation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/QueryIndexPermutationInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/NoOpPermutationReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/PermutationReaderInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/NoOpPermutation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/PermutationWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorQueryAlignedLength.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/ConstantAccumulator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceBaseInformationWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorReadMappingQuality.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorInsertSizes.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorQueryPosition.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceBaseInformationReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/CommitPropertiesStatAccumulator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorDistanceToEndOfRead.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorTargetAlignedLength.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorDistancesToReadVariations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/BasenameUtils.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceSegmentInformationWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorBaseQuality.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorDistanceToStartOfRead.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorPairFlags.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceSegmentInformationReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorNumVariationsInRead.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/class-use/GobyVersion.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/class-use/Release1_9_7_2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnFields.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/Columns.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnMetaInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/VCFParser.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/VCFParser.SyntaxException.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/GroupAssociations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnType.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnField.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamComparisonInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamRecordParser.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ChromosomeMapper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobyQuickSeqvar.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamComparison.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SAMRecordIterable.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobySamSegment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamPerPositionComparison.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ConversionConfig.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ConvertSamBAMReadToGobyAlignment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobySamRecord.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/class-use/FastXEntry.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/class-use/FastXReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/EquivalentIndelRegionCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightAnnotationCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightAnnotationCount.FormulaChoice.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/BaseProportionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeCountInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/MaxCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.ReadIndexInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.Variation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/LogGCCorrectionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/RandomAccessAnnotations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeStartCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/QFast.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ATGCCorrectionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationWeightCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FrequencyTable.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ExportSplicingEvents.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/CoverageAnalysis.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeWeightCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/HiCMerge.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/EvidenceCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SummedCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SortedAnnotations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/GCProportionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FenwickTree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FenwickTree.answer.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/MedianCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCountIterateAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/WeightCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCountInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ATProportionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/HeptamerWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/CumulativeArrayKeeperFast.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PTestStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/AbstractMethylationAdapter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/ObservationWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/ObservationWriter.TypeOfPair.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DeNovoDMRfinder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SlidingCountArray.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Log10BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/CovariateStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat5MciProviderStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/By5BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/ChiSquareTestAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PassThroughStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/OneBinStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat3StatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DeltaStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/StatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/MethylationRateDifferenceStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/BuggyDeltaStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat4StatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PVAlueProvider.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/LinearBinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SmallAndLog10BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat5StatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DifferentiallyMethylatedRegion.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/FastSmallAndLog10BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PTestMciProviderStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Log2BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/RegionAveragingWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/EstimatedDistribution.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/FisherExactTestAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SitesInFixedWindow.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/class-use/DiscoverVariantPositionData.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/class-use/SampleCountInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/indels/class-use/EquivalentIndelRegion.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Interval.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Read.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Read.ReadSortByEnd.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Read.ReadSortByStart.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/ReadWithIndex.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/SamplePairEnumerator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/MethylRateInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Annotation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/HeptamerInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/DistinctIntValueCounterBitSet.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/GroupComparison.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/WeightsInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/CovariateInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/AnnotationRPKM.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/DistinctIntValueCounterInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/MethylCountInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Segment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/class-use/InfoOutput.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/class-use/SampleTotalCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/class-use/AnnotationLength.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/class-use/Range.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/class-use/Ranges.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/AnyTransitionCountsIterator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsArchiveWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountWriterHelper2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/PeakAggregator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/UnionDumpIterator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/OffsetCountsReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountBinningAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsWriterI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountWriterHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsAggregatorI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/UnionAlgorithmSkeleton.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountIndexBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountBinningAdapterI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CachingCountsArchiveReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/WiggleWindow.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountAdaptiveBinningAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsArchiveReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsWriterHelperI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/Peak.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/PositionAdapter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsReaderI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileTool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileTool.PROGRAM_MODE.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundDataOutput.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundDirectoryEntry.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundDataInput.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/AddTrueGenotypeHelperI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/AddTrueGenotypeHelperI.WillKeepI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/GenotypePredictor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/MergeIndelFrom.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/MergeIndelFrom.SplitIndel.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/SomaticPredictor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/DummyTrueGenotypeHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF3.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/Predictor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/ProtoHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/config/class-use/GobyConfiguration.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationRegion.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSimilarityMatch.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:127: warning: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore [WARNING] * Dequeues a document from the queue, returning an instance of {@link [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/HitBoundedPriorityQueue.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylSimilarityScan.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationData.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSite.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/DifferentiallyMethylatedRegion.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSiteIterator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/class-use/ReaderFastaParser.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/class-use/FastaParser.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/class-use/GobyRengine.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.Result.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.AlternativeHypothesis.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadSet.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/PicardFastaIndexedSequence.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceCache.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsToTextWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/MultiReads.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodecImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodec2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadProtobuffCollectionHandler.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceTestSupport.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/SequenceEncoder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsLoader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/QualityEncoding.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/DualRandomAccessSequenceCache.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/CompressedRead.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsWriterImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/SequenceDigests.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/compression/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/indels/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/htsjdk/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/config/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/exception/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/commits/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/xml/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/deprecated-list.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/allclasses-index.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/index-all.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:127: warning: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore [WARNING] * Dequeues a document from the queue, returning an instance of {@link [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:216: warning: invalid input: '<' [WARNING] * Get the number of input lines to read or set to <= 0 to read the entire file. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:186: warning: invalid input: '<' [WARNING] * Get the number of input lines to read or set to <= 0 to read the entire file. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:193: warning: invalid input: '<' [WARNING] * Number of reads observed because of sampleFraction value < 1.0d. If sampleFraction == 1.0d [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:185: warning: invalid input: '<' [WARNING] * Number of reads skipped because of sampleFraction value < 1.0d. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:364: warning: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:388: warning: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:224: warning: invalid input: '<' [WARNING] * Set the number of input lines to read or set to <= 0 to read the entire file. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:194: warning: invalid input: '<' [WARNING] * Set the number of input lines to read or set to <= 0 to read the entire file. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:340: warning: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/search.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/help-doc.html... [WARNING] 91 warnings [INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/goby-distribution-3.3.1-javadoc.jar [INFO] [INFO] --- maven-assembly-plugin:3.4.2:single (make-assembly) @ goby-distribution --- [INFO] Reading assembly descriptor: assembly/assembly.xml [INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/goby-bin.jar [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Goby Framework 3.3.1: [INFO] [INFO] Goby Framework ..................................... SUCCESS [ 0.165 s] [INFO] Goby I/O ........................................... SUCCESS [ 17.252 s] [INFO] Goby Full Distribution ............................. SUCCESS [ 18.774 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 36.653 s [INFO] Finished at: 2025-11-14T19:40:31+14:00 [INFO] ------------------------------------------------------------------------ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2' # Create a symlink to the directory with test data for tests run from the # goby-distribution directory. ln -s ../test-data goby-distribution/test-data # The test-results directory should exist because test classes will write inside. if [ ! -e test-results ]; then mkdir test-results/; fi # Putting the JRI location in the path, as indicated in GobyRengine.java. # Also indicating R_HOME, as found in http://rforge.net/JRI/. export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/R/site-library/rJava/jri" && \ export R_HOME="/usr/lib/R" && \ dh_auto_test --no-parallel /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/libgoby-java-3.3.1\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian -Dmaven.repo.local=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/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.campagnelab.goby:goby-distribution:jar:3.3.1 [WARNING] 'dependencies.dependency.systemPath' for org.rosuda.REngine:REngine:jar should use a variable instead of a hard-coded path /usr/lib/R/site-library/rJava/jri/JRI.jar @ line 227, column 16 [WARNING] 'dependencies.dependency.systemPath' for com.github.broadinstitute:picard:jar should use a variable instead of a hard-coded path /usr/share/java/picard.jar @ line 293, column 16 [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: it.unimi.dsi:dsiutils:jar -> duplicate declaration of version debian @ line 295, column 15 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-io:jar:3.3.1 [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: com.google.protobuf:protobuf-java:jar -> duplicate declaration of version debian @ line 350, column 15 [WARNING] 'dependencies.dependency.systemPath' for org.itadaki:bzip2:jar should use a variable instead of a hard-coded path /usr/share/java/jbzip2-0.9.1.jar @ line 391, column 16 [WARNING] 'build.plugins.plugin.(groupId:artifactId)' must be unique but found duplicate declaration of plugin org.apache.maven.plugins:maven-antrun-plugin @ line 291, column 12 [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] Goby Framework [pom] [INFO] Goby I/O [jar] [INFO] Goby Full Distribution [jar] [INFO] [INFO] ----------------< org.campagnelab.goby:goby-framework >----------------- [INFO] Building Goby Framework 3.3.1 [1/3] [INFO] from pom.xml [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --------------------< org.campagnelab.goby:goby-io >-------------------- [INFO] Building Goby I/O 3.3.1 [2/3] [INFO] from goby-io/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The artifact org.apache.maven.plugins:maven-resources-plugin:jar:2.6 has been relocated to org.apache.maven.plugins:maven-resources-plugin:jar:3.3.1 [WARNING] The artifact org.apache.maven.plugins:maven-surefire-plugin:jar:2.12.4 has been relocated to org.apache.maven.plugins:maven-surefire-plugin:jar:2.22.3 [INFO] [INFO] --- build-helper-maven-plugin:3.3.0:add-source (add-classes) @ goby-io --- [INFO] Source directory: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/generated-sources added. [INFO] [INFO] --- maven-antrun-plugin:3.1.0:run (exec-java-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] --- maven-antrun-plugin:3.1.0:run (exec-python-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] --- maven-antrun-plugin:3.1.0:run (exec-python-cpp-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ goby-io --- [INFO] Copying 2 resources [INFO] Copying 1 resource [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ goby-io --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 260 source files to /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/classes [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java uses or overrides a deprecated API that is marked for removal. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java: Recompile with -Xlint:removal for details. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-antrun-plugin:3.1.0:run (default) @ goby-io --- [WARNING] Parameter tasks is deprecated, use target instead [INFO] Executing tasks [INFO] [copy] Copying 1 file to /build/reproducible-path/libgoby-java-3.3.1+dfsg2 [INFO] [copy] Copying 1 file to /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/classes [INFO] Executed tasks [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ goby-io --- [INFO] skip non existing resourceDirectory /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ goby-io --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ goby-io --- [INFO] No tests to run. [INFO] [INFO] ---------------< org.campagnelab.goby:goby-distribution >--------------- [INFO] Building Goby Full Distribution 3.3.1 [3/3] [INFO] from goby-distribution/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ goby-distribution --- [INFO] Copying 3 resources [INFO] Copying 72 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ goby-distribution --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 525 source files to /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/classes [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java uses or overrides a deprecated API that is marked for removal. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java: Recompile with -Xlint:removal for details. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/VariantMapHelper.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/VariantMapHelper.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ goby-distribution --- [INFO] skip non existing resourceDirectory /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ goby-distribution --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 120 source files to /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/test-classes [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/TestQFast.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/TestQFast.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/dmr/TestDeNovoDMRfinder.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/dmr/TestDeNovoDMRfinder.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ goby-distribution --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running TestSuite 19:40:43.184 INFO TestPostBarcodeMatcher - Num matches = 200, Num Ambiguous = 0, Num no matches = 0 19:40:43.189 INFO TestPostBarcodeMatcher - Time to parse 8 million reads 0 seconds SLF4J: Class path contains multiple SLF4J bindings. SLF4J: Found binding in [jar:file:/usr/share/java/slf4j-simple.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J: Found binding in [jar:file:/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven-repo/ch/qos/logback/logback-classic/debian/logback-classic-debian.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J: Found binding in [jar:file:/usr/share/java/logback-classic.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation. SLF4J: Actual binding is of type [org.slf4j.impl.SimpleLoggerFactory] Creating base test directory: test-results/stats [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. 19:40:43.346 INFO RLoggerMainLoopCallback - 19:40:43.347 INFO RLoggerMainLoopCallback - R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 19:40:43.347 INFO RLoggerMainLoopCallback - R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. 19:40:43.347 INFO RLoggerMainLoopCallback - R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. 19:40:43.347 INFO RLoggerMainLoopCallback - Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. ##fileformat=VCFv4.1 ##Goby=UNKNOWN ##FieldGroupAssociations=CHROM=genomic-coordinate,CHROM=cross-sample-field,POS=genomic-coordinate,POS=cross-sample-field,ID=external-identifiers,ID=cross-sample-field,REF=cross-sample-field,ALT=cross-sample-field,QUAL=cross-sample-field,FILTER=cross-sample-field,INFO=cross-sample-field,INFO/p-value1=cross-sample-field,INFO/p-value1=p-value,INFO/p-value2=cross-sample-field,INFO/p-value2=p-value,INFO/#Cm_Group[Group_1]=cross-sample-field,INFO/#Cm_Group[Group_1]=#Cm,FORMAT/Zygosity=zygozity,FORMAT/Zygosity=sample-data,FORMAT/Another=another,FORMAT/Another=sample-data, ##INFO= ##INFO= ##INFO= ##FORMAT= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SampleA SampleB 19:40:43.547 INFO BullardUpperQuartileNormalization - normalization denominator 50148.5 for sample B-7 19:40:43.547 INFO BullardUpperQuartileNormalization - normalization denominator 51306.8 for sample B-3 19:40:43.548 INFO BullardUpperQuartileNormalization - normalization denominator 102954 for sample A-3 19:40:43.548 INFO BullardUpperQuartileNormalization - normalization denominator 104044 for sample A-12 19:40:43.548 INFO BullardUpperQuartileNormalization - normalization denominator 53282.8 for sample B-15 19:40:43.548 INFO BullardUpperQuartileNormalization - normalization denominator 50693.6 for sample B-14 19:40:43.548 INFO BullardUpperQuartileNormalization - normalization denominator 49739.7 for sample B-11 19:40:43.549 INFO BullardUpperQuartileNormalization - normalization denominator 103568 for sample A-17 19:40:43.549 INFO BullardUpperQuartileNormalization - normalization denominator 51306.8 for sample B-2 19:40:43.549 INFO BullardUpperQuartileNormalization - normalization denominator 50966.1 for sample B-10 19:40:43.549 INFO BullardUpperQuartileNormalization - normalization denominator 102409 for sample A-16 19:40:43.549 INFO BullardUpperQuartileNormalization - normalization denominator 50421.0 for sample B-8 19:40:43.549 INFO BullardUpperQuartileNormalization - normalization denominator 50421.0 for sample B-4 19:40:43.550 INFO BullardUpperQuartileNormalization - normalization denominator 98661.7 for sample A-2 19:40:43.550 INFO BullardUpperQuartileNormalization - normalization denominator 101387 for sample A-0 19:40:43.550 INFO BullardUpperQuartileNormalization - normalization denominator 50898.0 for sample B-6 19:40:43.550 INFO BullardUpperQuartileNormalization - normalization denominator 101046 for sample A-9 19:40:43.550 INFO BullardUpperQuartileNormalization - normalization denominator 103840 for sample A-8 19:40:43.551 INFO BullardUpperQuartileNormalization - normalization denominator 100501 for sample A-5 19:40:43.551 INFO BullardUpperQuartileNormalization - normalization denominator 99615.6 for sample A-4 19:40:43.551 INFO BullardUpperQuartileNormalization - normalization denominator 103159 for sample A-6 19:40:43.551 INFO BullardUpperQuartileNormalization - normalization denominator 98661.7 for sample A-7 19:40:43.552 INFO BullardUpperQuartileNormalization - normalization denominator 51715.6 for sample B-5 19:40:43.552 INFO BullardUpperQuartileNormalization - normalization denominator 99683.8 for sample A-10 19:40:43.552 INFO BullardUpperQuartileNormalization - normalization denominator 102614 for sample A-14 19:40:43.552 INFO BullardUpperQuartileNormalization - normalization denominator 48785.8 for sample B-9 19:40:43.553 INFO BullardUpperQuartileNormalization - normalization denominator 101387 for sample A-1 19:40:43.553 INFO BullardUpperQuartileNormalization - normalization denominator 50352.9 for sample B-0 19:40:43.553 INFO BullardUpperQuartileNormalization - normalization denominator 50898.0 for sample B-12 19:40:43.553 INFO BullardUpperQuartileNormalization - normalization denominator 52737.7 for sample B-13 19:40:43.553 INFO BullardUpperQuartileNormalization - normalization denominator 103772 for sample A-19 19:40:43.553 INFO BullardUpperQuartileNormalization - normalization denominator 100297 for sample A-18 19:40:43.554 INFO BullardUpperQuartileNormalization - normalization denominator 102818 for sample A-15 19:40:43.554 INFO BullardUpperQuartileNormalization - normalization denominator 50352.9 for sample B-1 19:40:43.554 INFO BullardUpperQuartileNormalization - normalization denominator 102409 for sample A-13 19:40:43.554 INFO BullardUpperQuartileNormalization - normalization denominator 104930 for sample A-11 19:40:43.555 INFO BullardUpperQuartileNormalization - normalization denominator 51715.6 for sample B-16 19:40:43.555 INFO BullardUpperQuartileNormalization - normalization denominator 51988.2 for sample B-17 19:40:43.555 INFO BullardUpperQuartileNormalization - normalization denominator 50966.1 for sample B-19 19:40:43.555 INFO BullardUpperQuartileNormalization - normalization denominator 51034.3 for sample B-18 19:40:43.609 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value 19:40:43.645 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. 19:40:43.645 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value 19:40:43.657 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. 19:40:43.657 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value 19:40:43.765 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. 19:40:43.801 INFO FDRAdjustment - ... statistic t-test-P-value-Bonferroni-adjusted was found, FDR adjustment executed. 19:40:43.801 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value 19:40:43.894 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. 19:40:43.904 INFO FDRAdjustment - ... statistic another-p-value-Bonferroni-adjusted was found, FDR adjustment executed. list3:element-id p-value p-value-BH-FDR-q-value [ 0 [2.354054E-7, 1.177027E-5] ] [ 1 [2.10159E-5, 4.294736666666667E-4] ] [ 2 [2.576842E-5, 4.294736666666667E-4] ] [ 3 [9.814783E-5, 9.471342857142858E-4] ] [ 4 [1.05261E-4, 9.471342857142858E-4] ] [ 5 [1.241481E-4, 9.471342857142858E-4] ] [ 6 [1.325988E-4, 9.471342857142858E-4] ] [ 7 [1.568503E-4, 9.803143750000002E-4] ] [ 8 [2.254557E-4, 0.0012525316666666666] ] [ 9 [3.79538E-4, 0.00189769] ] [ 10 [6.114943E-4, 0.0027795195454545455] ] [ 11 [0.001613954, 0.006724808333333334] ] [ 12 [0.00330243, 0.012636935714285714] ] [ 13 [0.003538342, 0.012636935714285714] ] [ 14 [0.005236997, 0.017456656666666667] ] [ 15 [0.006831909, 0.020762429411764708] ] [ 16 [0.007059226, 0.020762429411764708] ] [ 17 [0.008805129, 0.024458691666666667] ] [ 18 [0.00940104, 0.02473957894736842] ] [ 19 [0.01129798, 0.028244949999999998] ] [ 20 [0.02115017, 0.050357547619047614] ] [ 21 [0.04922736, 0.11188036363636364] ] [ 22 [0.06053298, 0.1304633125] ] [ 23 [0.06262239, 0.1304633125] ] [ 24 [0.07395153, 0.14790306] ] [ 25 [0.08281103, 0.15925198076923075] ] [ 26 [0.08633331, 0.1598765] ] [ 27 [0.1190654, 0.21261678571428572] ] [ 28 [0.1890796, 0.32599931034482754] ] [ 29 [0.2058494, 0.3430823333333333] ] [ 30 [0.2209214, 0.3563248387096774] ] [ 31 [0.2856, 0.44625000000000004] ] [ 32 [0.3048895, 0.4619537878787878] ] [ 33 [0.4660682, 0.6835770833333333] ] [ 34 [0.4830809, 0.6835770833333333] ] [ 35 [0.4921755, 0.6835770833333333] ] [ 36 [0.5319453, 0.718845] ] [ 37 [0.575155, 0.7414352564102564] ] [ 38 [0.5783195, 0.7414352564102564] ] [ 39 [0.6185894, 0.7626062790697675] ] [ 40 [0.636362, 0.7626062790697675] ] [ 41 [0.6448587, 0.7626062790697675] ] [ 42 [0.6558414, 0.7626062790697675] ] [ 43 [0.6885884, 0.7824868181818182] ] [ 44 [0.7189864, 0.7988737777777778] ] [ 45 [0.8179539, 0.8802645744680851] ] [ 46 [0.8274487, 0.8802645744680851] ] [ 47 [0.89713, 0.9304775510204082] ] [ 48 [0.911868, 0.9304775510204082] ] [ 49 [0.943789, 0.943789] ] element-id average RPKM group A(AC) average RPKM group B(AC) average log2_RPKM group A(AC) average log2_RPKM group B(AC) average count group A average count group B [ id-1 [0.9949106468576894, 0.49973229823135434, -0.007361132169582257, -1.0007726308812397, 0.0, 0.0] ] truncated fdr=3.53108e-05 original=3.53108e-05 truncated fdr=0.00128842 original=0.00128842 truncated fdr=0.00128842 original=0.00128842 truncated fdr=0.00284140 original=0.00284140 truncated fdr=0.00284140 original=0.00284140 truncated fdr=0.00284140 original=0.00284140 truncated fdr=0.00284140 original=0.00284140 truncated fdr=0.00294094 original=0.00294094 truncated fdr=0.00375760 original=0.00375760 truncated fdr=0.00569307 original=0.00569307 truncated fdr=0.00833856 original=0.00833856 truncated fdr=0.0201744 original=0.0201744 truncated fdr=0.0379108 original=0.0379108 truncated fdr=0.0379108 original=0.0379108 truncated fdr=0.0523700 original=0.0523700 truncated fdr=0.0622873 original=0.0622873 truncated fdr=0.0622873 original=0.0622873 truncated fdr=0.0733761 original=0.0733761 truncated fdr=0.0742187 original=0.0742187 truncated fdr=0.0847349 original=0.0847349 truncated fdr=0.151073 original=0.151073 truncated fdr=0.335641 original=0.335641 truncated fdr=0.391390 original=0.391390 truncated fdr=0.391390 original=0.391390 truncated fdr=0.443709 original=0.443709 truncated fdr=0.477756 original=0.477756 truncated fdr=0.479630 original=0.479630 truncated fdr=0.637850 original=0.637850 truncated fdr=0.977998 original=0.977998 truncated fdr=1.00000 original=1.00000 truncated fdr=1.00000 original=1.00000 truncated fdr=1.00000 original=1.00000 truncated fdr=1.00000 original=1.00000 [main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 42 threads. [main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 42 threads. [main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 42 threads. [main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 42 threads. Creating base test directory: test-results/stats-writer allele: A ref: [CC] alt: [T]19:40:56.111 WARN MessageChunksWriter - Using chunk-size=10000 Associating basename: basen0 to group: A Associating basename: basen1 to group: A Associating basename: basen2 to group: A Associating basename: basen3 to group: A Associating basename: basen4 to group: A Associating basename: basen5 to group: B Associating basename: basen6 to group: B Associating basename: basen7 to group: B Associating basename: basen8 to group: B Associating basename: basen9 to group: B Comparing A/B sample: basen0 group A sample: basen2 group A sample: basen4 group A sample: basen3 group A sample: basen1 group A sample: basen9 group B sample: basen6 group B sample: basen5 group B sample: basen7 group B sample: basen8 group B Using processor NONE Filtering reads that have these criteria: q<30 #count(allele) < (2 *#filtered) 19:40:56.430 WARN GobyVersion - Version number UNKNOWN not recognized. Assuming this version is the most recent. [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences 19:40:56.500 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 19:40:56.503 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 19:40:56.505 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 19:40:56.507 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 19:40:56.509 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 19:40:56.511 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 19:40:56.513 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 19:40:56.514 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 19:40:56.517 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 19:40:56.518 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A Associating basename: basen1 to group: A Associating basename: basen2 to group: A Associating basename: basen3 to group: A Associating basename: basen4 to group: A Associating basename: basen5 to group: B Associating basename: basen6 to group: B Associating basename: basen7 to group: B Associating basename: basen8 to group: B Associating basename: basen9 to group: B Comparing A/B sample: basen0 group A sample: basen2 group A sample: basen4 group A sample: basen3 group A sample: basen1 group A sample: basen9 group B sample: basen6 group B sample: basen5 group B sample: basen7 group B sample: basen8 group B Using processor NONE Filtering reads that have these criteria: q<30 #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences 19:40:56.663 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 19:40:56.665 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 19:40:56.666 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 19:40:56.668 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 19:40:56.669 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 19:40:56.671 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 19:40:56.672 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 19:40:56.675 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 19:40:56.676 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 19:40:56.678 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A Associating basename: basen1 to group: A Associating basename: basen2 to group: A Associating basename: basen3 to group: A Associating basename: basen4 to group: A Associating basename: basen5 to group: B Associating basename: basen6 to group: B Associating basename: basen7 to group: B Associating basename: basen8 to group: B Associating basename: basen9 to group: B Comparing A/B sample: basen0 group A sample: basen2 group A sample: basen4 group A sample: basen3 group A sample: basen1 group A sample: basen9 group B sample: basen6 group B sample: basen5 group B sample: basen7 group B sample: basen8 group B Using processor NONE Filtering reads that have these criteria: q<30 #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences 19:40:56.749 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 19:40:56.750 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 19:40:56.751 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 19:40:56.753 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 19:40:56.755 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 19:40:56.756 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 19:40:56.758 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 19:40:56.759 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 19:40:56.760 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 19:40:56.762 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A Associating basename: basen1 to group: A Associating basename: basen2 to group: A Associating basename: basen3 to group: A Associating basename: basen4 to group: A Associating basename: basen5 to group: B Associating basename: basen6 to group: B Associating basename: basen7 to group: B Associating basename: basen8 to group: B Associating basename: basen9 to group: B Comparing A/B sample: basen0 group A sample: basen2 group A sample: basen4 group A sample: basen3 group A sample: basen1 group A sample: basen9 group B sample: basen6 group B sample: basen5 group B sample: basen7 group B sample: basen8 group B Using processor NONE Filtering reads that have these criteria: q<30 #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences 19:40:56.824 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 19:40:56.825 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 19:40:56.826 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 19:40:56.827 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 19:40:56.829 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 19:40:56.830 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 19:40:56.832 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 19:40:56.833 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 19:40:56.834 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 19:40:56.835 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A Associating basename: basen1 to group: A Associating basename: basen2 to group: A Associating basename: basen3 to group: A Associating basename: basen4 to group: A Associating basename: basen5 to group: B Associating basename: basen6 to group: B Associating basename: basen7 to group: B Associating basename: basen8 to group: B Associating basename: basen9 to group: B Comparing A/B sample: basen0 group A sample: basen2 group A sample: basen4 group A sample: basen3 group A sample: basen1 group A sample: basen9 group B sample: basen6 group B sample: basen5 group B sample: basen7 group B sample: basen8 group B Using processor NONE Filtering reads that have these criteria: q<30 #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences 19:40:56.930 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 19:40:56.931 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 19:40:56.933 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 19:40:56.934 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 19:40:56.935 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 19:40:56.936 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 19:40:56.938 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 19:40:56.939 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 19:40:56.940 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 19:40:56.942 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A Associating basename: basen1 to group: A Associating basename: basen2 to group: A Associating basename: basen3 to group: A Associating basename: basen4 to group: A Associating basename: basen5 to group: B Associating basename: basen6 to group: B Associating basename: basen7 to group: B Associating basename: basen8 to group: B Associating basename: basen9 to group: B Comparing A/B sample: basen0 group A sample: basen2 group A sample: basen4 group A sample: basen3 group A sample: basen1 group A sample: basen9 group B sample: basen6 group B sample: basen5 group B sample: basen7 group B sample: basen8 group B Using processor NONE Filtering reads that have these criteria: q<30 #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences 19:40:56.991 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 19:40:56.992 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 19:40:56.993 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 19:40:56.995 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 19:40:56.997 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 19:40:56.999 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 19:40:57.001 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 19:40:57.002 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 19:40:57.004 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 19:40:57.005 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A Associating basename: basen1 to group: A Associating basename: basen2 to group: A Associating basename: basen3 to group: A Associating basename: basen4 to group: A Associating basename: basen5 to group: B Associating basename: basen6 to group: B Associating basename: basen7 to group: B Associating basename: basen8 to group: B Associating basename: basen9 to group: B Comparing A/B sample: basen0 group A sample: basen2 group A sample: basen4 group A sample: basen3 group A sample: basen1 group A sample: basen9 group B sample: basen6 group B sample: basen5 group B sample: basen7 group B sample: basen8 group B Using processor NONE Filtering reads that have these criteria: q<30 #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences 19:40:57.062 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 19:40:57.063 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 19:40:57.064 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 19:40:57.065 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 19:40:57.066 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 19:40:57.067 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 19:40:57.068 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 19:40:57.070 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 19:40:57.071 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 19:40:57.072 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A Associating basename: basen1 to group: A Associating basename: basen2 to group: A Associating basename: basen3 to group: A Associating basename: basen4 to group: A Associating basename: basen5 to group: B Associating basename: basen6 to group: B Associating basename: basen7 to group: B Associating basename: basen8 to group: B Associating basename: basen9 to group: B Comparing A/B sample: basen0 group A sample: basen2 group A sample: basen4 group A sample: basen3 group A sample: basen1 group A sample: basen9 group B sample: basen6 group B sample: basen5 group B sample: basen7 group B sample: basen8 group B Using processor NONE Filtering reads that have these criteria: q<30 #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences 19:40:57.115 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 19:40:57.116 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 19:40:57.117 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 19:40:57.118 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 19:40:57.119 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 19:40:57.120 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 19:40:57.121 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 19:40:57.122 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 19:40:57.123 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 19:40:57.124 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A Associating basename: basen1 to group: A Associating basename: basen2 to group: A Associating basename: basen3 to group: A Associating basename: basen4 to group: A Associating basename: basen5 to group: B Associating basename: basen6 to group: B Associating basename: basen7 to group: B Associating basename: basen8 to group: B Associating basename: basen9 to group: B Comparing A/B sample: basen0 group A sample: basen2 group A sample: basen4 group A sample: basen3 group A sample: basen1 group A sample: basen9 group B sample: basen6 group B sample: basen5 group B sample: basen7 group B sample: basen8 group B Using processor NONE Filtering reads that have these criteria: q<30 #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences 19:40:57.164 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 19:40:57.165 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 19:40:57.166 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 19:40:57.167 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 19:40:57.168 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 19:40:57.169 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 19:40:57.170 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 19:40:57.171 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 19:40:57.172 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 19:40:57.173 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A Associating basename: basen1 to group: A Associating basename: basen2 to group: A Associating basename: basen3 to group: A Associating basename: basen4 to group: A Associating basename: basen5 to group: B Associating basename: basen6 to group: B Associating basename: basen7 to group: B Associating basename: basen8 to group: B Associating basename: basen9 to group: B Comparing A/B sample: basen0 group A sample: basen2 group A sample: basen4 group A sample: basen3 group A sample: basen1 group A sample: basen9 group B sample: basen6 group B sample: basen5 group B sample: basen7 group B sample: basen8 group B Using processor NONE Filtering reads that have these criteria: q<30 #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences 19:40:57.213 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 19:40:57.214 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 19:40:57.215 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 19:40:57.216 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 19:40:57.217 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 19:40:57.218 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 19:40:57.219 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 19:40:57.220 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 19:40:57.221 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 19:40:57.222 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A Associating basename: basen1 to group: A Associating basename: basen2 to group: A Associating basename: basen3 to group: A Associating basename: basen4 to group: A Associating basename: basen5 to group: B Associating basename: basen6 to group: B Associating basename: basen7 to group: B Associating basename: basen8 to group: B Associating basename: basen9 to group: B Comparing A/B sample: basen0 group A sample: basen2 group A sample: basen4 group A sample: basen3 group A sample: basen1 group A sample: basen9 group B sample: basen6 group B sample: basen5 group B sample: basen7 group B sample: basen8 group B Using processor NONE Filtering reads that have these criteria: q<30 #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences 19:40:57.270 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 19:40:57.272 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 19:40:57.273 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 19:40:57.273 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 19:40:57.274 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 19:40:57.275 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 19:40:57.276 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 19:40:57.277 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 19:40:57.278 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 19:40:57.279 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A Associating basename: basen1 to group: A Associating basename: basen2 to group: A Associating basename: basen3 to group: A Associating basename: basen4 to group: A Associating basename: basen5 to group: B Associating basename: basen6 to group: B Associating basename: basen7 to group: B Associating basename: basen8 to group: B Associating basename: basen9 to group: B sample: basen0 group A sample: basen2 group A sample: basen4 group A sample: basen3 group A sample: basen1 group A sample: basen9 group B sample: basen6 group B sample: basen5 group B sample: basen7 group B sample: basen8 group B Using processor NONE Methylation format ignores thresholdDistinctReadIndices. Additionally, the minimum coverage needed for a site to be reported can be changed with --minimum-variation-support. Filtering reads that have these criteria: [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest_mci [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences 19:40:57.327 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 19:40:57.328 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 19:40:57.329 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 19:40:57.330 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 19:40:57.331 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 19:40:57.332 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 19:40:57.333 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 19:40:57.334 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 19:40:57.334 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 19:40:57.335 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 info: + ref: A s=0 info: + ref: A s=0 info: + ref: A s=0 info: + ref: A s=0 info: + ref: A s=0 info: + /T q=40 s=0 info: - /T q=40 s=0 info: + /C q=10 s=0 info: + /C q=20 s=0 info: + /C q=30 s=0 info: + /C q=40 s=0 info: + /C q=40 s=0 info: + /C q=40 s=0 info: + /C q=40 s=0 info: + /C q=10 s=0 info: + /C q=20 s=0 info: + /N q=30 s=0 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + /T q=40 s=1 info: + /T q=10 s=1 info: + /T q=20 s=1 info: + /T q=30 s=1 info: + /N q=40 s=1 info: + /N q=40 s=1 list: pos=-1 #bases: 33 #indels: 0 filtered: {+ ref: A s=0, + ref: A s=0, + ref: A s=0, + ref: A s=0, + ref: A s=0, + /C q=10 s=0, + /C q=20 s=0, + /C q=30 s=0, + /C q=40 s=0, + /C q=40 s=0, + /C q=40 s=0, + /C q=40 s=0, + /C q=10 s=0, + /C q=20 s=0, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + /T q=40 s=1, + /T q=10 s=1, + /T q=20 s=1, + /T q=30 s=1, + /N q=40 s=1, + /N q=40 s=1} Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences 1/1 ..T Loading test-data/fdr-mode/file1.vcf Loading test-data/fdr-mode/file2.vcf Loading test-data/fdr-mode/file3.vcf adjusting column: PCHI2 Combining test-data/fdr-mode/file1.vcf Combining test-data/fdr-mode/file2.vcf Combining test-data/fdr-mode/file3.vcf Loading test-data/fdr-mode/file-B-1.vcf Loading test-data/fdr-mode/file-B-2.vcf adjusting column: PCHI2 Combining test-data/fdr-mode/file-B-1.vcf Combining test-data/fdr-mode/file-B-2.vcf Loading test-data/fdr-mode/file-B-1.vcf Loading test-data/fdr-mode/file-B-2.vcf adjusting column: PCHI2 Combining test-data/fdr-mode/file-B-1.vcf Combining test-data/fdr-mode/file-B-2.vcf Loading test-data/fdr-mode/file1.vcf Loading test-data/fdr-mode/file2.vcf Loading test-data/fdr-mode/file3.vcf Combining test-data/fdr-mode/file1.vcf Combining test-data/fdr-mode/file2.vcf Combining test-data/fdr-mode/file3.vcf Scanning target file.. Target file had 1 entries. Wrote 1 target ids to alignment header. Setting quality threshold to 0.05 Total logical entries written: 2 Total bytes written: 0 Average bytes/logical entry: 0.0 Min query index: 0 Max query index: 0 Number of queries: 3 Number of targets: 3 Removed by quality filter: 0 Not best score: 1 Number of alignments written: 2 query_index: 0 target_index: 0 position: 14977972 score: 780.0 matching_reverse_strand: false multiplicity: 1 number_of_mismatches: 1 number_of_indels: 0 query_length: 142 query_aligned_length: 134 target_aligned_length: 134 sequence_variations { to: "T" from: "A" position: 6 to_quality: "/" read_index: 14 } fragment_index: 0 query_index_occurrences: 2 ambiguity: 1 Processing test-data/sample-qual-scores/30reads.fa Processed 0 read entries. Min quality score: 2147483647 Max quality score: -2147483648 Avg quality score: 0 Probable quality encoding scheme: fasta Processing test-data/sample-qual-scores/30reads.fq Processed 30 read entries. Min quality score: 69 Max quality score: 98 Avg quality score: 94 Probable quality encoding scheme: Illumina/Solexa TTC[27]->CGT[27] / qual=1:2:3 A[15]->G[20] / qual=20 A[15]->G[20] / qual=20 Setting quality threshold to 0.02 19:40:58.337 WARN MessageChunksWriter - Using chunk-size=1 19:40:58.342 WARN MessageChunksWriter - Using chunk-size=1 19:40:58.345 WARN MessageChunksWriter - Using chunk-size=1 19:40:58.348 WARN MessageChunksWriter - Using chunk-size=1 [main] WARN org.campagnelab.goby.alignments.BufferedSortingAlignmentWriter - Local sorting strategy failed to restore sort order. The destination has been marked as unsorted. You must sort the output manually to improve compression. 19:40:58.372 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.380 WARN MessageChunksWriter - Using chunk-size=1000 entry: score=30.0000 readOriginIndex=0 entry: score=30.0000 readOriginIndex=0 entry: score=50.0000 readOriginIndex=3 entry: score=50.0000 readOriginIndex=3 entry: score=50.0000 readOriginIndex=3 Scanned 5 entries 19:40:58.387 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.388 WARN MessageChunksWriter - Using chunk-size=1000 entry: score=30.0000 readOriginIndex=0 entry: score=30.0000 readOriginIndex=0 Scanned 2 entries 19:40:58.391 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.393 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.397 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.398 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.402 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.403 WARN MessageChunksWriter - Using chunk-size=1000 0 2 19:40:58.407 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.408 WARN MessageChunksWriter - Using chunk-size=1000 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/alignments/concat/concat-align-101 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/alignments/concat/concat-align-101 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/alignments/concat/concat-align-102 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/alignments/concat/concat-align-102 19:40:58.413 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.414 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.418 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.419 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.423 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.424 WARN MessageChunksWriter - Using chunk-size=1000 entry: score=50.0000 readOriginIndex=3 entry: score=50.0000 readOriginIndex=3 entry: score=50.0000 readOriginIndex=3 entry: score=30.0000 readOriginIndex=0 entry: score=30.0000 readOriginIndex=0 Scanned 5 entries 19:40:58.432 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.474 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.475 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.504 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 19:40:58.533 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.534 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.542 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. 19:40:58.572 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. 19:40:58.573 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass 19:40:58.573 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [1 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 3ms; used/avail/free/total/max mem: 81.13M/21.01G/86.64M/167.77M/21.09G 19:40:58.579 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. found entry: query_index: 0 target_index: 1999 position: 19991 score: 20020.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 1 target_index: 1999 position: 19992 score: 20021.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 2 target_index: 1999 position: 19993 score: 20022.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 3 target_index: 1999 position: 19994 score: 20023.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 4 target_index: 1999 position: 19995 score: 20024.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 5 target_index: 1999 position: 19996 score: 20025.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 6 target_index: 1999 position: 19997 score: 20026.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 7 target_index: 1999 position: 19998 score: 20027.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 8 target_index: 1999 position: 19999 score: 20028.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 9 target_index: 1999 position: 20000 score: 20029.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 19:40:58.615 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. 19:40:58.618 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. 19:40:58.648 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. 19:40:58.649 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. 19:40:58.649 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. 19:40:58.649 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass 19:40:58.649 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. 19:40:58.649 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms; used/avail/free/total/max mem: 131.46M/20.96G/36.31M/167.77M/21.09G 19:40:58.652 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. 19:40:58.670 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. 19:40:58.698 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.723 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.724 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.749 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 19:40:58.773 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.774 WARN MessageChunksWriter - Using chunk-size=1000 [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item]; used/avail/free/total/max mem: 104.76M/20.98G/79.79M/184.55M/21.09G found entry: query_index: 2 target_index: 1999 position: 19993 score: 20022.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 3 target_index: 1999 position: 19994 score: 20023.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 4 target_index: 1999 position: 19995 score: 20024.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 5 target_index: 1999 position: 19996 score: 20025.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 6 target_index: 1999 position: 19997 score: 20026.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 7 target_index: 1999 position: 19998 score: 20027.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 8 target_index: 1999 position: 19999 score: 20028.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 9 target_index: 1999 position: 20000 score: 20029.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 2 target_index: 3999 position: 19993 score: 20022.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 3 target_index: 3999 position: 19994 score: 20023.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 4 target_index: 3999 position: 19995 score: 20024.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 5 target_index: 3999 position: 19996 score: 20025.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 6 target_index: 3999 position: 19997 score: 20026.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 7 target_index: 3999 position: 19998 score: 20027.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 8 target_index: 3999 position: 19999 score: 20028.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 9 target_index: 3999 position: 20000 score: 20029.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 19:40:58.850 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.873 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.874 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.899 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 19:40:58.922 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.923 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.925 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. 19:40:58.930 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. 19:40:58.930 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass 19:40:58.930 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [1 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 81.52M/21.01G/103.03M/184.55M/21.09G 19:40:58.931 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. notBestScoreCount=16.6667 % geneAmbiguityCount=33.3333 % found entry: query_index: 0 target_index: 1 position: 2 score: 31.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 0 target_index: 2 position: 3 score: 31.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 2 target_index: 4 position: 6 score: 30.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 19:40:58.937 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.959 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.960 WARN MessageChunksWriter - Using chunk-size=1000 19:40:58.982 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 19:40:59.004 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.005 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.007 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. 19:40:59.008 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. 19:40:59.009 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. 19:40:59.009 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. 19:40:59.010 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. 19:40:59.010 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass 19:40:59.010 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. 19:40:59.010 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 108.00M/20.98G/76.55M/184.55M/21.09G 19:40:59.011 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. 19:40:59.018 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. 19:40:59.021 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.043 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.044 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.066 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 19:40:59.088 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.089 WARN MessageChunksWriter - Using chunk-size=1000 Finding max number of reads... Found input file with 2 target(s) 19:40:59.091 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. Found input file with 2 target(s) 19:40:59.091 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. ... max number of reads was 10 First pass: determine which reads should be kept in the merged alignment. Scanning align-105 Scanning align-106 Found 40 logical alignment entries. Prepare merged too many hits information. 19:40:59.093 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. 19:40:59.093 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. 19:40:59.093 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. 19:40:59.093 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass 19:40:59.093 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. 19:40:59.094 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms [2 items, 2,000.00 items/s, 500.00 ?s/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 50.53M/21.04G/134.02M/184.55M/21.09G Second pass: writing the merged alignment. 19:40:59.095 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. 19:40:59.096 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. Wrote 20 skipped: 20 50.000000% too many hits 0.000000% notBestScore: 50.000000% Total logical entries written: 20 Total bytes written: 0 Average bytes/logical entry: 0.0 Min query index: 0 Max query index: 9 Number of queries: 10 Number of targets: 4 Percent aligned: 100.0 19:40:59.099 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.121 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.122 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.144 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 19:40:59.166 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.167 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.168 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. 19:40:59.169 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. 19:40:59.169 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass 19:40:59.170 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [1 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 75.08M/21.01G/109.47M/184.55M/21.09G 19:40:59.171 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. found entry: query_index: 0 target_index: 1 position: 11 score: 40.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 1 target_index: 1 position: 12 score: 41.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 2 target_index: 1 position: 13 score: 42.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 3 target_index: 1 position: 14 score: 43.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 4 target_index: 1 position: 15 score: 44.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 5 target_index: 1 position: 16 score: 45.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 6 target_index: 1 position: 17 score: 46.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 7 target_index: 1 position: 18 score: 47.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 8 target_index: 1 position: 19 score: 48.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 9 target_index: 1 position: 20 score: 49.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 19:40:59.175 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.197 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.198 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.220 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 19:40:59.243 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.244 WARN MessageChunksWriter - Using chunk-size=1000 [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms [2 items, 2,000.00 items/s, 500.00 ?s/item]; used/avail/free/total/max mem: 50.24M/21.04G/704.73M/754.97M/21.09G found entry: query_index: 2 target_index: 1999 position: 19993 score: 20022.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 3 target_index: 1999 position: 19994 score: 20023.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 4 target_index: 1999 position: 19995 score: 20024.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 5 target_index: 1999 position: 19996 score: 20025.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 6 target_index: 1999 position: 19997 score: 20026.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 7 target_index: 1999 position: 19998 score: 20027.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 8 target_index: 1999 position: 19999 score: 20028.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 9 target_index: 1999 position: 20000 score: 20029.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 2 target_index: 3999 position: 19993 score: 20022.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 3 target_index: 3999 position: 19994 score: 20023.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 4 target_index: 3999 position: 19995 score: 20024.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 5 target_index: 3999 position: 19996 score: 20025.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 6 target_index: 3999 position: 19997 score: 20026.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 7 target_index: 3999 position: 19998 score: 20027.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 8 target_index: 3999 position: 19999 score: 20028.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 9 target_index: 3999 position: 20000 score: 20029.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 19:40:59.332 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.354 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.355 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.379 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 19:40:59.403 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.403 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.407 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. 19:40:59.410 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. 19:40:59.439 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. 19:40:59.439 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. 19:40:59.439 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. 19:40:59.439 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass 19:40:59.439 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. 19:40:59.439 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 140.38M/20.95G/614.60M/754.97M/21.09G 19:40:59.442 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. 19:40:59.455 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. found entry: query_index: 0 target_index: 1999 position: 19991 score: 20020.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 1 target_index: 1999 position: 19992 score: 20021.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 2 target_index: 1999 position: 19993 score: 20022.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 3 target_index: 1999 position: 19994 score: 20023.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 4 target_index: 1999 position: 19995 score: 20024.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 5 target_index: 1999 position: 19996 score: 20025.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 6 target_index: 1999 position: 19997 score: 20026.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 7 target_index: 1999 position: 19998 score: 20027.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 8 target_index: 1999 position: 19999 score: 20028.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 9 target_index: 1999 position: 20000 score: 20029.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 0 target_index: 3999 position: 19991 score: 20020.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 1 target_index: 3999 position: 19992 score: 20021.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 2 target_index: 3999 position: 19993 score: 20022.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 3 target_index: 3999 position: 19994 score: 20023.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 4 target_index: 3999 position: 19995 score: 20024.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 5 target_index: 3999 position: 19996 score: 20025.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 6 target_index: 3999 position: 19997 score: 20026.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 7 target_index: 3999 position: 19998 score: 20027.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 8 target_index: 3999 position: 19999 score: 20028.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 9 target_index: 3999 position: 20000 score: 20029.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 19:40:59.489 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 Min query index: 0 Max query index: 0 Number of queries: 1 Number of targets: 3 19:40:59.492 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 Min query index: 0 Max query index: 0 Number of queries: 1 Number of targets: 3 19:40:59.495 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 Min query index: 0 Max query index: 0 Number of queries: 1 Number of targets: 3 19:40:59.497 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 Min query index: 0 Max query index: 0 Number of queries: 1 Number of targets: 3 19:40:59.499 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 Min query index: 0 Max query index: 0 Number of queries: 1 Number of targets: 3 19:40:59.501 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 Min query index: 0 Max query index: 0 Number of queries: 1 Number of targets: 3 19:40:59.504 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 Min query index: 0 Max query index: 0 Number of queries: 1 Number of targets: 3 Processing queryIndex=8 with description '8 perfect start of ref' Processing queryIndex=9 with description '9 perfect start of ref reverse strand' Processing queryIndex=18 with description '18 mismatch at end x1, starting at -1' Processing queryIndex=19 with description '19 mismatch at end x2, starting at -1' Processing queryIndex=20 with description '20 mismatch at end x5, starting at -1' Processing queryIndex=21 with description '21 mismatch at end x1, starting at -2' Processing queryIndex=22 with description '22 mismatch at end x2, starting at -2' Processing queryIndex=23 with description '23 mismatch at end x5, starting at -2' Processing queryIndex=12 with description '12 mismatch at beginning x1, starting at 1, with mutation at 20' Processing queryIndex=13 with description '13 mismatch at beginning x2, starting at 1, with mutation at 20' Processing queryIndex=15 with description '15 mismatch at beginning x1, starting at 2' Processing queryIndex=16 with description '16 mismatch at beginning x2, starting at 2' Processing queryIndex=14 with description '14 mismatch at beginning x5, starting at 1 (pos 4 actually does match), with mutation at 20' Processing queryIndex=17 with description '17 mismatch at beginning x5, starting at 2 (pos 4 actually does match)' Processing queryIndex=0 with description '0 perfect match' Processing queryIndex=1 with description '1 perfect match on reverse strand' Processing queryIndex=2 with description '2 mutation' Processing queryIndex=3 with description '3 mutation on reverse strand' Processing queryIndex=4 with description '4 insertion' Processing queryIndex=6 with description '6 deletion' Processing queryIndex=7 with description '7 deletion on reverse strand' Processing queryIndex=27 with description '27 padding left & right, deletion then mutation' Processing queryIndex=24 with description '24 padding left & right, mutation, deletion' Processing queryIndex=5 with description '5 insertion on reverse strand' Processing queryIndex=10 with description '10 perfect end of ref' Processing queryIndex=11 with description '11 perfect end of ref reverse strand' query_index: 0 target_index: 0 position: 0 query_position: 0 matching_reverse_strand: false query_length: 75 query_aligned_length: 75 target_aligned_length: 75 mapping_quality: 255 pair_flags: 0 fragment_index: 0 ambiguity: 1 query_index: 1 target_index: 0 position: 1 query_position: 0 matching_reverse_strand: false query_length: 75 query_aligned_length: 75 target_aligned_length: 75 mapping_quality: 255 pair_flags: 0 fragment_index: 0 ambiguity: 1 entry:query_index: 0 target_index: 0 position: 5 score: 5.0 matching_reverse_strand: false query_length: 20 query_aligned_length: 20 target_aligned_length: 20 sequence_variations { to: "CTAG" from: "----" position: 10 read_index: 10 } entry:query_index: 1 target_index: 0 position: 5 matching_reverse_strand: false query_length: 20 query_aligned_length: 20 target_aligned_length: 20 sequence_variations { to: "CTAG" from: "----" position: 10 to_quality: "((((" read_index: 10 } entry: query_index: 0 target_index: 0 position: 0 matching_reverse_strand: false query_length: 10 query_aligned_length: 10 sequence_variations { to: "AAA" from: "---" position: 3 read_index: 3 } processing entry on target 0 at position 0 processing entry on target 0 at position 5 processing entry on target 1 at position 0 processing entry on target 1 at position 5 processing entry on target 4 at position 0 processing entry on target 4 at position 5 entry:query_index: 0 target_index: 0 position: 10 matching_reverse_strand: false query_length: 50 query_aligned_length: 50 sequence_variations { to: "AAA" from: "---" position: 20 read_index: 20 } entry:query_index: 1 target_index: 0 position: 1 matching_reverse_strand: false query_length: 50 query_aligned_length: 50 sequence_variations { to: "T" from: "A" position: 20 read_index: 20 } 19:40:59.617 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.621 WARN MessageChunksWriter - Using chunk-size=1000 Total logical entries written: 20000 Total bytes written: 77210 Average bytes/logical entry: 3.8605 Min query index: 0 Max query index: 1999 Number of queries: 2000 Number of targets: 10 19:40:59.701 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.703 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.709 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.711 WARN MessageChunksWriter - Using chunk-size=1000 0 23 19:40:59.722 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.724 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.725 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.731 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.732 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.733 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.739 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.739 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.740 WARN MessageChunksWriter - Using chunk-size=1000 entry.position(): 1 entry.position(): 2 entry.position(): 3 entry.position(): 5 entry.position(): 6 entry.position(): 7 entry.position(): 8 entry.position(): 9 entry.position(): 10 entry.position(): 10 entry.position(): 12 entry.position(): 99 19:40:59.747 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.747 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.748 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.754 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.755 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.755 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.758 INFO AlignmentTooManyHitsReader - basename test-results/sort-concat/sort-concat-1.tmh has no 'too many hits' information (test-results/sort-concat/sort-concat-1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/sort-concat/sort-concat-1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/sort-concat/sort-concat-1 19:40:59.759 INFO AlignmentTooManyHitsReader - basename test-results/sort-concat/sort-concat-2.tmh has no 'too many hits' information (test-results/sort-concat/sort-concat-2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/sort-concat/sort-concat-2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/sort-concat/sort-concat-2 19:40:59.760 INFO AlignmentTooManyHitsReader - basename test-results/sort-concat/sort-concat-3.tmh has no 'too many hits' information (test-results/sort-concat/sort-concat-3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/sort-concat/sort-concat-3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/sort-concat/sort-concat-3 19:40:59.762 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.763 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.764 WARN MessageChunksWriter - Using chunk-size=1000 19:40:59.866 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 0 Total bytes written: 31 Average bytes/logical entry: Infinity Min query index: 2147483647 Max query index: -2147483648 Number of queries: 2 Number of targets: 0 97 19:40:59.873 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 6 Total bytes written: 162 Average bytes/logical entry: 27.0 Min query index: 0 Max query index: 0 Number of queries: 1 Number of targets: 3 19:40:59.878 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 6 Total bytes written: 162 Average bytes/logical entry: 27.0 Min query index: 0 Max query index: 0 Number of queries: 1 Number of targets: 3 19:40:59.881 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 6 Total bytes written: 162 Average bytes/logical entry: 27.0 Min query index: 0 Max query index: 0 Number of queries: 1 Number of targets: 3 19:40:59.883 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 6 Total bytes written: 162 Average bytes/logical entry: 27.0 Min query index: 0 Max query index: 0 Number of queries: 1 Number of targets: 3 read =CTCCAGAACTGTAAGATAATAAGTTGGTGTTGTTTT expected =TTCCAGAACTGTAAGATAATAAGTTTGTGTTGTTTT recons. ref=TTCCAGAACTGTAAGATAATAAGTTTGTGTTGTTTT read =TTTCCCACATTTCCCATCACCACTACTACGGATACAGAACGGGG expected =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG read =TTTCCCAAATTTCACATCACTACTACACGGATACAGAACGGGG expected =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG read =TAAAACCTAAAAAAAAAAAAAAACCCC expected =TAAAA--TAAAAAAAAAAAAAAACCCC recons. ref=TAAAA--TAAAAAAAAAAAAAAACCCC read =TTTTGATGAAGTCTCTGTGTCCTGGGGCATCAATGATGGTCACA expected =TTTTGACGAAGTCTCTATGTCCT-GGGCATCAATGATGGTCACA recons. ref=TTTTGACGAAGTCTCTATGTCCT-GGGCATCAATGATGGTCACA read =TTTCCCAAATTTCACATCACTACACTACGGATACAGAACGGGG expected =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG read =CCATGACCAACATAACTGTGGTGTCATGCATTTGGTATCTTTTT expected =CCATGACCAACATAACTGTGGTGTCATGCATTTGGTAT-TTTTAAT recons. ref=CCATGACCAACATAACTGTGGTGTCATGCATTTGGTAT-TTTTAAT Total logical entries written: 1 Total bytes written: 0 Average bytes/logical entry: 0.0 Min query index: 0 Max query index: 0 Number of queries: 1 Number of targets: 45 field CHROM value: 0 field POS value: 145497099 field ID value: . field REF value: A field ALT value: G field QUAL value: 17.1 field FILTER value: . field INFO[DP] value: 2 field INFO[DP4] value: 0,0,2,0 field INFO[MQ] value: 25 field INFO[FQ] value: -30.8 field INFO[AF1] value: 0.9999 field INFO[CI95] value: 0.5,1 field INFO[PV4] value: field INFO[INDEL] value: INDEL field INFO[PC2] value: 3,3 field INFO[PCHI2] value: 0.752 field INFO[QCHI2] value: 1 field INFO[RP] value: field FORMAT[GT] value: field FORMAT[GQ] value: field FORMAT[GL] value: field FORMAT[DP] value: field FORMAT[SP] value: field FORMAT[PL] value: field results/IPBKRNW/IPBKRNW-replicate.bam[GT] value: 1/1 field results/IPBKRNW/IPBKRNW-replicate.bam[GQ] value: 42 field results/IPBKRNW/IPBKRNW-replicate.bam[GL] value: field results/IPBKRNW/IPBKRNW-replicate.bam[DP] value: field results/IPBKRNW/IPBKRNW-replicate.bam[SP] value: field results/IPBKRNW/IPBKRNW-replicate.bam[PL] value: 25,3,0 field results/IPBKRNW/IPBKRNW-sorted.bam[GT] value: 1/1 field results/IPBKRNW/IPBKRNW-sorted.bam[GQ] value: 42 field results/IPBKRNW/IPBKRNW-sorted.bam[GL] value: field results/IPBKRNW/IPBKRNW-sorted.bam[DP] value: field results/IPBKRNW/IPBKRNW-sorted.bam[SP] value: field results/IPBKRNW/IPBKRNW-sorted.bam[PL] value: 25,3,0 field CHROM gfi:0 value: 0 field POS gfi:1 value: 145497099 field ID gfi:2 value: . field REF gfi:3 value: A field ALT gfi:4 value: G field QUAL gfi:5 value: 17.1 field FILTER gfi:6 value: . field FORMAT[GT] gfi:7 value: field FORMAT[GQ] gfi:8 value: field FORMAT[GL] gfi:9 value: field FORMAT[DP] gfi:10 value: field FORMAT[SP] gfi:11 value: field FORMAT[PL] gfi:12 value: field results/IPBKRNW/IPBKRNW-replicate.bam[GT] gfi:13 value: 1/1 field results/IPBKRNW/IPBKRNW-replicate.bam[GQ] gfi:14 value: 11 field results/IPBKRNW/IPBKRNW-replicate.bam[GL] gfi:15 value: field results/IPBKRNW/IPBKRNW-replicate.bam[DP] gfi:16 value: field results/IPBKRNW/IPBKRNW-replicate.bam[SP] gfi:17 value: field results/IPBKRNW/IPBKRNW-replicate.bam[PL] gfi:18 value: 015,4,0 field results/IPBKRNW/IPBKRNW-sorted.bam[GT] gfi:19 value: 1/1 field results/IPBKRNW/IPBKRNW-sorted.bam[GQ] gfi:20 value: 42 field results/IPBKRNW/IPBKRNW-sorted.bam[GL] gfi:21 value: field results/IPBKRNW/IPBKRNW-sorted.bam[DP] gfi:22 value: field results/IPBKRNW/IPBKRNW-sorted.bam[SP] gfi:23 value: field results/IPBKRNW/IPBKRNW-sorted.bam[PL] gfi:24 value: 25,3,0 [ {N:15} {///////////00//0010} {N:15} {00101111001101100101111101111111/0/} |Encoded in 80 bits [ {N:15} {11111111111001100101100011111001011110011011001011111011111111} {0} {1} {1} {1} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->29 {N:15} {00101111001101100101111101111111101110000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->74decoding: 0 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 1 decoding: 2 decoding: 3 decoding: 4 decoding: 3 decoding: 1 decoding: 2 decoding: 1 decoding: 2 decoding: 3 decoding: 1 decoding: 2 decoding: 1 decoding: 2 decoding: 1 [ {0} {0} {1} {1} {0} {0} {1} {1} {0} {0} {1} {1} {0} {0} {1} {0} {0} {0} {1} {1} {0} {0} {1} {0} {0} {1} {1} {1} {0} {0} {0} {1} {0} {1} {0} {0} {1} {0} {0} {0} {1} {1} {0} {1} {0} {1} {0} {1} {1} {0} {1} {0} {0} {1} {0} {1} {1} {0} {1} {0} {0} {1} {0} {0} {1} |Encoded in 72 bits [ {00110011001100100011001001110001010010001101010110100101101001} {0} {0}decoding: 0 {1} {0}decoding: 4 {0} {0}decoding: 4 {0} {0}decoding: 4 {0}decoding: 4 {0}decoding: 4 {0}decoding: 4 decoding: 4 {0}decoding: 4 {0}decoding: 4 decoding: 4 {0}decoding: 4 decoding: 4 {0}decoding: 4 decoding: 4 {0} {0} {0} {0} {0}decoding: 1 {0} {0} {0} {0}decoding: 2 {0} {0} {0} {0} {0}decoding: 3 decoding: 4 {0} {0} {0} {0}decoding: 3 {0} {0} {0}decoding: 1 {0} {0} {0} {0}decoding: 2 {0} {0} {0}decoding: 1 {0} {0} {0}decoding: 2 {0} {0} {0} {0}decoding: 3 {0} {0} {0}decoding: 1 {0} {0} {0}decoding: 2 {0} {0}decoding: 1 {0} {0} {0}decoding: 2 {0} {0}decoding: 1 [ {N:2} {0010} {N:5} {011111} {N:5} {/0/00///01} {N:3} {//0/0/} {N:15} {///////////00//0010} |Encoded in 80 bits [ {N:2} {00101111010111111111011010011101111011110101110001111111111111} {1} {1} {1} {0} {0} {1} {1} | ->10 {N:5} {01111111110110100111011110111101011100011111111111111110011001} {0} {1} {1} {0} {0} {0} {0} {0} {0} | ->22 {N:5} {10100111011110111101011100011111111111111110011001011000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->38 {N:3} {11010111000111111111111111100110010110000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->50 {N:15} {11111111111001100101100000000000000000000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->79decoding: 0 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 1 decoding: 2 decoding: 3 decoding: 4 decoding: 3 decoding: 1 decoding: 2 decoding: 1 decoding: 2 decoding: 3 decoding: 1 decoding: 2 decoding: 1 decoding: 2 decoding: 1 Total logical entries written: 4 Total bytes written: 0 Average bytes/logical entry: 0.0 Min query index: 1 Max query index: 1 Number of queries: 1 Number of targets: 2 Total logical entries written: 4 Total bytes written: 62 Average bytes/logical entry: 15.5 Min query index: 1 Max query index: 1 Number of queries: 1 Number of targets: 2 Annotations loaded Annotations loaded Annotations loaded Annotations loaded Annotations loaded count perbase{0=>0, 13=>0, 11=>2, 3=>2, 5=>3} count keys [0, 3, 5, 11, 13] -1 0.0 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 overlapping count 3, 4 0.0 overlapping count 15, 17 0.0 overlapping count 9, 18 2.0 overlapping count 3, 8 2.0 overlapping count 11, 12 0.0 overlapping count 9, 10 1.0 overlapping count 8, 9 0.0 overlapping count 8, 8 0.0 overlapping count 5, 6 0.0 overlapping count 3, 3 0.0 overlapping count 3, 12 5.0 overlapping count -1, 2 0.0 overlapping count 0, 45 6.0 overlapping count 13, 15 0.0 -1 0.0 0 0.0 1 0.0 2 0.0 3 2.0 4 2.0 5 3.0 6 3.0 7 3.0 8 3.0 9 3.0 10 3.0 11 2.0 12 2.0 13 0.0 14 0.0 15 1.0 16 1.0 17 1.0 18 1.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 overlapping count 3, 4 2.0 overlapping count 2, 3 2.0 overlapping count 3, 8 4.0 overlapping count 11, 12 2.0 overlapping count 9, 10 3.0 overlapping count 8, 9 4.0 overlapping count 8, 8 3.0 overlapping count 5, 6 3.0 overlapping count 3, 3 2.0 overlapping count 3, 12 5.0 overlapping count -1, 2 0.0 overlapping count 0, 45 6.0 overlapping count 13, 15 1.0 [main] WARN org.campagnelab.goby.algorithmic.algorithm.EquivalentIndelRegionCalculator - Cannot determine sequence at position 600000000 of reference-index 2 appending (count=0,length=1) appending (count=4,length=3) appending (count=1,length=3) appending (count=0,length=2) appending (count=3,length=1) appending (count=1,length=1) appending (count=0,length=1) appending (count=4,length=3) appending (count=0,length=5) appending (count=3,length=1) appending (count=0,length=2) appending (count=2,length=1) appending (count=0,length=2) appending (count=3,length=1) appending (count=2,length=1) appending (count=0,length=1) loading transition for reader[0] position=0 length=1 count=0 loading transition for reader[1] position=0 length=6 count=1 (0,1) loading transition for reader[0] position=1 length=3 count=3 (0,1)(1,4) loading transition for reader[0] position=4 length=2 count=0 (0,1)(1,4)(4,1) loading transition for reader[0] position=0 length=1 count=0 loading transition for reader[1] position=0 length=4 count=0 (0,0) loading transition for reader[0] position=1 length=1 count=1 (0,0)(1,1) loading transition for reader[0] position=2 length=4 count=0 (0,0)(1,1)(2,0) loading transition for reader[1] position=4 length=10 count=1 (0,0)(1,1)(2,0)(4,1) loading transition for reader[0] position=6 length=2 count=1 (0,0)(1,1)(2,0)(4,1)(6,2) loading transition for reader[0] position=8 length=1 count=0 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1) loading transition for reader[0] position=9 length=1 count=1 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2) loading transition for reader[0] position=10 length=2 count=0 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1) loading transition for reader[0] position=12 length=1 count=1 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2) loading transition for reader[0] position=13 length=3 count=0 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1) (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0) loading transition for reader[0] position=16 length=1 count=1 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0)(16,1) loading transition for reader[0] position=0 length=1 count=0 loading transition for reader[1] position=0 length=4 count=0 loading transition for reader[0] position=1 length=1 count=1 loading transition for reader[0] position=2 length=4 count=0 loading transition for reader[1] position=4 length=10 count=1 loading transition for reader[0] position=6 length=2 count=1 loading transition for reader[0] position=8 length=1 count=0 loading transition for reader[0] position=9 length=1 count=1 loading transition for reader[0] position=10 length=2 count=0 loading transition for reader[0] position=12 length=1 count=1 loading transition for reader[0] position=13 length=3 count=0 loading transition for reader[0] position=16 length=1 count=1 loading transition for reader[0] position=0 length=1 count=0 loading transition for reader[1] position=0 length=6 count=1 (0,1) loading transition for reader[0] position=1 length=3 count=3 (0,1)(1,4) loading transition for reader[0] position=4 length=2 count=0 (0,1)(1,4)(4,1) loading transition for reader[0] position=0 length=1 count=0 loading transition for reader[1] position=0 length=4 count=0 (0,0) loading transition for reader[0] position=1 length=1 count=1 (0,0)(1,1) loading transition for reader[0] position=2 length=4 count=0 (0,0)(1,1)(2,0) loading transition for reader[1] position=4 length=10 count=1 (0,0)(1,1)(2,0)(4,1) loading transition for reader[0] position=6 length=2 count=1 (0,0)(1,1)(2,0)(4,1)(6,2) loading transition for reader[0] position=8 length=1 count=0 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1) loading transition for reader[0] position=9 length=1 count=1 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2) loading transition for reader[0] position=10 length=2 count=0 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1) loading transition for reader[0] position=12 length=1 count=1 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2) loading transition for reader[0] position=13 length=3 count=0 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1) (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0) loading transition for reader[0] position=16 length=1 count=1 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0)(16,1) loading transition for reader[0] position=0 length=1 count=0 loading transition for reader[1] position=0 length=4 count=0 loading transition for reader[0] position=1 length=1 count=1 loading transition for reader[0] position=2 length=4 count=0 loading transition for reader[1] position=4 length=10 count=1 loading transition for reader[0] position=6 length=2 count=1 loading transition for reader[0] position=8 length=1 count=0 loading transition for reader[0] position=9 length=1 count=1 loading transition for reader[0] position=10 length=2 count=0 loading transition for reader[0] position=12 length=1 count=1 loading transition for reader[0] position=13 length=3 count=0 loading transition for reader[0] position=16 length=1 count=1 loading transition for reader[0] position=0 length=1 count=0 (0,0) loading transition for reader[0] position=1 length=3 count=1 (0,0)(1,1) Appending count: 43113 length: 9 Appending count: 6504 length: 1 Appending count: 49428 length: 1 Appending count: 28366 length: 6 Appending count: 4957 length: 5 Appending count: 19942 length: 4 Appending count: 31963 length: 5 Appending count: 6545 length: 9 Appending count: 31011 length: 8 Appending count: 24656 length: 1 Appending count: 30730 length: 5 Appending count: 33918 length: 8 Appending count: 35015 length: 6 Appending count: 14759 length: 8 Appending count: 41591 length: 8 Appending count: 36918 length: 3 Appending count: 21210 length: 2 Appending count: 30619 length: 8 Appending count: 29739 length: 9 Appending count: 8300 length: 9 Appending count: 17774 length: 1 Appending count: 16626 length: 1 Appending count: 25425 length: 8 Appending count: 41492 length: 7 Appending count: 4916 length: 9 Appending count: 48770 length: 4 Appending count: 40261 length: 2 Appending count: 28376 length: 7 Appending count: 35125 length: 1 Appending count: 27842 length: 5 position= 0 count= 43113 position= 1 count= 43113 position= 2 count= 43113 position= 3 count= 43113 position= 4 count= 43113 position= 5 count= 43113 position= 6 count= 43113 position= 7 count= 43113 position= 8 count= 43113 position= 9 count= 6504 position= 10 count= 49428 position= 11 count= 28366 position= 12 count= 28366 position= 13 count= 28366 position= 14 count= 28366 position= 15 count= 28366 position= 16 count= 28366 position= 17 count= 4957 position= 18 count= 4957 position= 19 count= 4957 position= 20 count= 4957 position= 21 count= 4957 position= 22 count= 19942 position= 23 count= 19942 position= 24 count= 19942 position= 25 count= 19942 position= 26 count= 31963 position= 27 count= 31963 position= 28 count= 31963 position= 29 count= 31963 position= 30 count= 31963 position= 31 count= 6545 position= 32 count= 6545 position= 33 count= 6545 position= 34 count= 6545 position= 35 count= 6545 position= 36 count= 6545 position= 37 count= 6545 position= 38 count= 6545 position= 39 count= 6545 position= 40 count= 31011 position= 41 count= 31011 position= 42 count= 31011 position= 43 count= 31011 position= 44 count= 31011 position= 45 count= 31011 position= 46 count= 31011 position= 47 count= 31011 position= 48 count= 24656 position= 49 count= 30730 position= 50 count= 30730 position= 51 count= 30730 position= 52 count= 30730 position= 53 count= 30730 position= 54 count= 33918 position= 55 count= 33918 position= 56 count= 33918 position= 57 count= 33918 position= 58 count= 33918 position= 59 count= 33918 position= 60 count= 33918 position= 61 count= 33918 position= 62 count= 35015 position= 63 count= 35015 position= 64 count= 35015 position= 65 count= 35015 position= 66 count= 35015 position= 67 count= 35015 position= 68 count= 14759 position= 69 count= 14759 position= 70 count= 14759 position= 71 count= 14759 position= 72 count= 14759 position= 73 count= 14759 position= 74 count= 14759 position= 75 count= 14759 position= 76 count= 41591 position= 77 count= 41591 position= 78 count= 41591 position= 79 count= 41591 position= 80 count= 41591 position= 81 count= 41591 position= 82 count= 41591 position= 83 count= 41591 position= 84 count= 36918 position= 85 count= 36918 position= 86 count= 36918 position= 87 count= 21210 position= 88 count= 21210 position= 89 count= 30619 position= 90 count= 30619 position= 91 count= 30619 position= 92 count= 30619 position= 93 count= 30619 position= 94 count= 30619 position= 95 count= 30619 position= 96 count= 30619 position= 97 count= 29739 position= 98 count= 29739 position= 99 count= 29739 position= 100 count= 29739 position= 101 count= 29739 position= 102 count= 29739 position= 103 count= 29739 position= 104 count= 29739 position= 105 count= 29739 position= 106 count= 8300 position= 107 count= 8300 position= 108 count= 8300 position= 109 count= 8300 position= 110 count= 8300 position= 111 count= 8300 position= 112 count= 8300 position= 113 count= 8300 position= 114 count= 8300 position= 115 count= 17774 position= 116 count= 16626 position= 117 count= 25425 position= 118 count= 25425 position= 119 count= 25425 position= 120 count= 25425 position= 121 count= 25425 position= 122 count= 25425 position= 123 count= 25425 position= 124 count= 25425 position= 125 count= 41492 position= 126 count= 41492 position= 127 count= 41492 position= 128 count= 41492 position= 129 count= 41492 position= 130 count= 41492 position= 131 count= 41492 position= 132 count= 4916 position= 133 count= 4916 position= 134 count= 4916 position= 135 count= 4916 position= 136 count= 4916 position= 137 count= 4916 position= 138 count= 4916 position= 139 count= 4916 position= 140 count= 4916 position= 141 count= 48770 position= 142 count= 48770 position= 143 count= 48770 position= 144 count= 48770 position= 145 count= 40261 position= 146 count= 40261 position= 147 count= 28376 position= 148 count= 28376 position= 149 count= 28376 position= 150 count= 28376 position= 151 count= 28376 position= 152 count= 28376 position= 153 count= 28376 position= 154 count= 35125 position= 155 count= 27842 position= 156 count= 27842 position= 157 count= 27842 position= 158 count= 27842 position= 159 count= 27842 appending (count=10,length=4) appending (count=1,length=0) appending (count=2,length=8) Hello appending (count=10,length=4) 19:41:42.591 WARN WiggleWindow - Not writing 101 7 19:41:42.592 WARN WiggleWindow - Not writing 111 7 19:41:42.592 WARN WiggleWindow - Not writing 131 8 19:41:42.592 WARN WiggleWindow - Not writing 141 8 19:41:42.592 WARN WiggleWindow - Not writing 151 8 peak : start :5 count :13 length :100010 peak : start :100020 count :10 length :1 original GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: GGTGT original G----GTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: G original GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGT mapped: GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGT original G--GTGTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: GGT qPhred=1 qPhred=2 qPhred=3 qPhred=4 qPhred=5 qPhred=6 qPhred=7 qPhred=8 qPhred=9 qPhred=10 qPhred=11 qPhred=12 qPhred=13 qPhred=14 qPhred=15 qPhred=16 qPhred=17 qPhred=18 qPhred=19 qPhred=20 qPhred=21 qPhred=22 qPhred=23 qPhred=24 qPhred=25 qPhred=26 qPhred=27 qPhred=28 qPhred=29 qPhred=30 qPhred=31 qPhred=32 qPhred=33 qPhred=34 qPhred=35 qPhred=36 qPhred=37 qPhred=38 qPhred=39 qPhred=40 qPhred=41 qPhred=42 qPhred=43 qPhred=44 qPhred=45 qPhred=46 qPhred=47 qPhred=48 qPhred=49 qPhred=50 qPhred=51 qPhred=52 qPhred=53 qPhred=54 qPhred=55 qPhred=56 qPhred=57 qPhred=58 qPhred=59 qPhred=60 qPhred=61 0 AAC 3 ACC 6 ATC 9 AGC 12 AAC 15 ACC 18 ATC 21 AGC 24 AAC 27 ACC 30 ATC 33 AGC 36 AAC 39 ACC 42 ATC 45 AGC 48 AAC 51 ACC 54 ATC 57 AGC 60 AAC 63 ACC 66 ATC 69 AGC 72 AAC 75 ACC 78 ATC 81 AGC19:41:46.289 WARN MessageChunksWriter - Using chunk-size=9 19:41:46.291 WARN MessageChunksWriter - Using chunk-size=9 Total logical entries written: 39 Total bytes written: 660 Average bytes/logical entry: 16.923077 Number of bits/base 3.6590436 19:41:46.292 WARN MessageChunksWriter - Using chunk-size=9 Total logical entries written: 39 Total bytes written: 685 Average bytes/logical entry: 17.564102 Number of bits/base 3.797644 19:41:46.294 WARN MessageChunksWriter - Using chunk-size=9 Total logical entries written: 39 Total bytes written: 660 Average bytes/logical entry: 16.923077 Number of bits/base 3.6590436 >1 NNTGAATGAGACCTA [WARNING] Tests run: 512, Failures: 0, Errors: 0, Skipped: 46, Time elapsed: 64.137 s - in TestSuite 19:41:46.600 INFO GobyRengine - Shutdown hook is terminating R [INFO] [INFO] Results: [INFO] [WARNING] Tests run: 512, Failures: 0, Errors: 0, Skipped: 46 [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Goby Framework 3.3.1: [INFO] [INFO] Goby Framework ..................................... SUCCESS [ 0.034 s] [INFO] Goby I/O ........................................... SUCCESS [ 5.552 s] [INFO] Goby Full Distribution ............................. SUCCESS [01:14 min] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:19 min [INFO] Finished at: 2025-11-14T19:41:52+14:00 [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2' 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/libgoby-java-3.3.1\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian -Dmaven.repo.local=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian/maven-repo --batch-mode -Ddebian.dir=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian -Ddebian.package=libgoby-io-java -Dmaven.repo.local=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/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.campagnelab.goby:goby-distribution:jar:3.3.1 [WARNING] 'dependencies.dependency.systemPath' for org.rosuda.REngine:REngine:jar should use a variable instead of a hard-coded path /usr/lib/R/site-library/rJava/jri/JRI.jar @ line 227, column 16 [WARNING] 'dependencies.dependency.systemPath' for com.github.broadinstitute:picard:jar should use a variable instead of a hard-coded path /usr/share/java/picard.jar @ line 293, column 16 [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: it.unimi.dsi:dsiutils:jar -> duplicate declaration of version debian @ line 295, column 15 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-io:jar:3.3.1 [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: com.google.protobuf:protobuf-java:jar -> duplicate declaration of version debian @ line 350, column 15 [WARNING] 'dependencies.dependency.systemPath' for org.itadaki:bzip2:jar should use a variable instead of a hard-coded path /usr/share/java/jbzip2-0.9.1.jar @ line 391, column 16 [WARNING] 'build.plugins.plugin.(groupId:artifactId)' must be unique but found duplicate declaration of plugin org.apache.maven.plugins:maven-antrun-plugin @ line 291, column 12 [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] Goby Framework [pom] [INFO] Goby I/O [jar] [INFO] Goby Full Distribution [jar] [INFO] [INFO] ----------------< org.campagnelab.goby:goby-framework >----------------- [INFO] Building Goby Framework 3.3.1 [1/3] [INFO] from pom.xml [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ goby-framework --- [INFO] Cleaning pom file: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/pom.xml.save with options: [INFO] --keep-pom-version --package=libgoby-io-java --has-package-version [INFO] --rules=/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven.publishedRules [INFO] [INFO] --------------------< org.campagnelab.goby:goby-io >-------------------- [INFO] Building Goby I/O 3.3.1 [2/3] [INFO] from goby-io/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ goby-io --- [INFO] Cleaning pom file: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/pom.xml.save with options: [INFO] --keep-pom-version --package=libgoby-io-java [INFO] --rules=/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven.publishedRules [INFO] Install jar for goby-io into /usr/share/java [INFO] [INFO] ---------------< org.campagnelab.goby:goby-distribution >--------------- [INFO] Building Goby Full Distribution 3.3.1 [3/3] [INFO] from goby-distribution/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ goby-distribution --- [INFO] Cleaning pom file: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/pom.xml.save with options: [INFO] --keep-pom-version --package=goby-java [INFO] --rules=/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven.publishedRules [INFO] Install jar for goby-distribution into /usr/share/java [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Goby Framework 3.3.1: [INFO] [INFO] Goby Framework ..................................... SUCCESS [ 0.601 s] [INFO] Goby I/O ........................................... SUCCESS [ 0.047 s] [INFO] Goby Full Distribution ............................. SUCCESS [ 0.178 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.948 s [INFO] Finished at: 2025-11-14T19:41:54+14:00 [INFO] ------------------------------------------------------------------------ mh_resolve_dependencies --non-interactive --offline --build -plibgoby-io-java --base-directory=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2 --non-explore Analysing pom.xml... Analysing goby-distribution/pom.xml... Checking the parent dependency in the sub project goby-distribution/pom.xml Analysing goby-io/pom.xml... Checking the parent dependency in the sub project goby-io/pom.xml > dpkg --search /usr/share/maven-repo/org/rosuda/REngine/REngine/*/* dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/maven-repo/org/rosuda/REngine/REngine Nov 14, 2025 7:42:00 PM org.debian.maven.packager.DependenciesSolver$ToResolve resolve SEVERE: Cannot resolve dependencies in /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/pom.xml: Dependency not found org.rosuda.REngine:REngine:jar:debian > dpkg --search /usr/share/maven-repo/org/itadaki/bzip2/*/* dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/maven-repo/org/itadaki/bzip2 Nov 14, 2025 7:42:05 PM org.debian.maven.packager.DependenciesSolver$ToResolve resolve SEVERE: Cannot resolve dependencies in /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/pom.xml: Dependency not found org.itadaki:bzip2:jar:debian ERROR: goby-distribution/pom.xml: dependency is not packaged in the Maven repository for Debian: org.rosuda.REngine:REngine:debian goby-io/pom.xml: dependency is not packaged in the Maven repository for Debian: org.itadaki:bzip2:debian -------- Some problems were found in this project, exiting... mh_unpatchpoms -plibgoby-io-java dh_install jh_installjavadoc dh_installdocs dh_installchangelogs dh_installman dh_lintian dh_perl dh_link jh_installlibs jh_classpath jh_manifest jh_exec jh_depends dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package goby-java: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package goby-java: substitution variable ${maven:Depends} used, but is not defined dpkg-gencontrol: warning: Recommends field of package goby-java: substitution variable ${maven:OptionalDepends} used, but is not defined dpkg-gencontrol: warning: Depends field of package libgoby-io-java: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package goby-java: substitution variable ${java:Depends} unused, but is defined dpkg-gencontrol: warning: package libgoby-io-java: substitution variable ${java:Depends} unused, but is defined dpkg-gencontrol: warning: package libgoby-io-java: substitution variable ${maven:CompileDepends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'libgoby-io-java' in '../libgoby-io-java_3.3.1+dfsg2-11_all.deb'. dpkg-deb: building package 'goby-java' in '../goby-java_3.3.1+dfsg2-11_all.deb'. dpkg-genbuildinfo --build=binary -O../libgoby-java_3.3.1+dfsg2-11_amd64.buildinfo dpkg-genchanges --build=binary -O../libgoby-java_3.3.1+dfsg2-11_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: user script /srv/workspace/pbuilder/1730115/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1730115/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1730115 and its subdirectories I: Current time: Fri Nov 14 19:42:14 +14 2025 I: pbuilder-time-stamp: 1763098934