Fri Oct 11 23:03:07 UTC 2024 I: starting to build libgoby-java/trixie/amd64 on jenkins on '2024-10-11 23:02' Fri Oct 11 23:03:07 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_31/22590/console.log Fri Oct 11 23:03:07 UTC 2024 I: Downloading source for trixie/libgoby-java=3.3.1+dfsg2-11 --2024-10-11 23:03:07-- http://deb.debian.org/debian/pool/main/libg/libgoby-java/libgoby-java_3.3.1%2bdfsg2-11.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 3008 (2.9K) [text/prs.lines.tag] Saving to: ‘libgoby-java_3.3.1+dfsg2-11.dsc’ 0K .. 100% 176M=0s 2024-10-11 23:03:07 (176 MB/s) - ‘libgoby-java_3.3.1+dfsg2-11.dsc’ saved [3008/3008] Fri Oct 11 23:03:07 UTC 2024 I: libgoby-java_3.3.1+dfsg2-11.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libgoby-java Binary: libgoby-io-java, goby-java Architecture: all Version: 3.3.1+dfsg2-11 Maintainer: Debian Med Packaging Team Uploaders: Pierre Gruet , Andreas Tille Homepage: https://campagnelab.org/software/goby/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/libgoby-java/ Vcs-Git: https://salsa.debian.org/med-team/libgoby-java.git Testsuite: autopkgtest Testsuite-Triggers: default-jdk Build-Depends: debhelper-compat (= 13), maven-debian-helper, javahelper, default-jdk Build-Depends-Indep: 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 Package-List: goby-java deb science optional arch=all libgoby-io-java deb science optional arch=all Checksums-Sha1: f9f9b6c1f4e76c9c403e1a9881d2c81f4d371d1c 41577532 libgoby-java_3.3.1+dfsg2.orig.tar.xz b26ff390aa68ce3035d8153bb80f2153382882ec 29428 libgoby-java_3.3.1+dfsg2-11.debian.tar.xz Checksums-Sha256: b76b19808f893790e238c91e65680441ff020794cc7708ad6695cf13f0767148 41577532 libgoby-java_3.3.1+dfsg2.orig.tar.xz db2427807fcc6967f7d3d85e656e4b219bd5af8e88faf8c21bdae07b6f74f468 29428 libgoby-java_3.3.1+dfsg2-11.debian.tar.xz Files: 3a8dbf45ef2c54ec3073240850acbc75 41577532 libgoby-java_3.3.1+dfsg2.orig.tar.xz ee077d346354fb548086bf2a9f9f11e5 29428 libgoby-java_3.3.1+dfsg2-11.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEM8soQxPpC9J9y0UjYAMWptwndHYFAmZDkf4ACgkQYAMWptwn dHbpoxAArW4ZHQHLR2i3CFyUh7icehts0H7Dw1QPOrrFFMGdEM3NxatGcCXLQr/a oeQbInqiDMzD4nypqLL5AMMSu3JH7nsQ5OvFLfw3dYZnZpKsDzhdorwnOmhpwZ8P rpL+rsNHL+Ond8BysNEHJHQzElxKrpOa39ihu/hgciQ3Spj7BdjE0qUyy9rcHH8D uGF75qN0lTwYntDkdRfUg9JbMfqBXyuqpI7l7aPuQqr9AID9dSA6ilHOEyvFn1v7 67RgMq6gFKztHYK2c2bwWzQ+exmoFglxPa77Nx6NuqZDEyRllzami0iUCI7n+E5m FcpGPLCcHypkhqhTU0kvlKiTYmrgTXRvhfGxfhBB5CF4V3LFYzdsie113QWpaSru qLorRzuMHUJgKbtjy/H9aDQfkqeua7+cnz1wGnOlpBrutfxP5TXUiaeJBW4SSy4T tAYOaxCSkHEEoU0/rNUNDuFc0t4z7L5nsD2OEp1H4sAO7LHSBbuU83NH6Ey4qxJm PBNybPD24etHY0KCFbGaGo+Id0z0lTfU+1QKj6irDrZawnh69V4EwU+mhjVHd86i jCMPZd1SbDQrSJvKF4hHWp2e+D+LjdCaW5If6BaxKQyHEgxAhWpFns20FwzugFIg 63JI+KVPPcxzQ9F7fPbFF8u7txqQsHQEkea1h1PjKRSBTVNbb20= =36L5 -----END PGP SIGNATURE----- Fri Oct 11 23:03:07 UTC 2024 I: Checking whether the package is not for us Fri Oct 11 23:03:07 UTC 2024 I: Starting 1st build on remote node ionos11-amd64.debian.net. Fri Oct 11 23:03:07 UTC 2024 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Fri Oct 11 23:13:23 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Oct 11 11:03:10 -12 2024 I: pbuilder-time-stamp: 1728687790 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/733974/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='6f35b144232e4c0ba8149597a89ffe09' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='733974' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ONmzhG9r/pbuilderrc_YU8P --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ONmzhG9r/b1 --logfile b1/build.log libgoby-java_3.3.1+dfsg2-11.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-26-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/733974/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 40s (10.0 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 ... 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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 ... 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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) ... 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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: Running cd /build/reproducible-path/libgoby-java-3.3.1+dfsg2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../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.compression... [WARNING] Loading source files for package org.campagnelab.goby.methylation... [WARNING] Loading source files for package org.campagnelab.goby.readers... [WARNING] Loading source files for package org.campagnelab.goby.readers.sam... [WARNING] Loading source files for package org.campagnelab.goby.readers.vcf... [WARNING] Loading source files for package org.campagnelab.goby.xml... [WARNING] Loading source files for package org.campagnelab.goby... [WARNING] Loading source files for package org.campagnelab.goby.R... [WARNING] Loading source files for package org.campagnelab.goby.parsers... [WARNING] Loading source files for package org.campagnelab.goby.reads... [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.modes... [WARNING] Loading source files for package org.campagnelab.goby.modes.core... [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.exception... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.indels... [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.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.util... [WARNING] Loading source files for package org.campagnelab.goby.util.motifs... [WARNING] Loading source files for package org.campagnelab.goby.util.commits... [WARNING] Loading source files for package org.campagnelab.goby.util.pool... [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.stats... [WARNING] Loading source files for package org.campagnelab.goby.baseinfo... [WARNING] Loading source files for package org.campagnelab.goby.config... [WARNING] Loading source files for package org.campagnelab.goby.alignments... [WARNING] Loading source files for package org.campagnelab.goby.alignments.perms... [WARNING] Loading source files for package org.campagnelab.goby.alignments.htsjdk... [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.predictions... [WARNING] Loading source files for package org.campagnelab.goby.cli... [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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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... 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[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.compression... [WARNING] Loading source files for package org.campagnelab.goby.methylation... [WARNING] Loading source files for package org.campagnelab.goby.readers... [WARNING] Loading source files for package org.campagnelab.goby.readers.sam... [WARNING] Loading source files for package org.campagnelab.goby.readers.vcf... [WARNING] Loading source files for package org.campagnelab.goby.xml... [WARNING] Loading source files for package org.campagnelab.goby... [WARNING] Loading source files for package org.campagnelab.goby.R... [WARNING] Loading source files for package org.campagnelab.goby.parsers... [WARNING] Loading source files for package org.campagnelab.goby.reads... [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.modes... [WARNING] Loading source files for package org.campagnelab.goby.modes.core... [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.exception... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.indels... [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.data... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data.xml... 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[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... 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[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... 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[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... 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[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... 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[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... 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[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... 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[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... 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[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... 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[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. 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[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 [ 0.087 s] [INFO] Goby I/O ........................................... SUCCESS [ 41.431 s] [INFO] Goby Full Distribution ............................. SUCCESS [ 45.618 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:27 min [INFO] Finished at: 2024-10-11T11:09:35-12:00 [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 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 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] 11:10:23.168 WARN MessageChunksWriter - Using chunk-size=10000 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 11:10:23.384 WARN GobyVersion - Version number UNKNOWN not recognized. Assuming this version is the most recent. 11:10:24.286 INFO RLoggerMainLoopCallback - 11:10:24.287 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 11:10:24.287 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. 11:10:24.287 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. 11:10:24.287 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. 11:10:24.730 WARN MessageChunksWriter - Using chunk-size=9 11:10:24.747 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 11:10:24.761 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 11:10:24.778 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 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 AGCloading 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 peak : start :5 count :13 length :100010 peak : start :100020 count :10 length :1 11:10:34.016 WARN WiggleWindow - Not writing 101 7 11:10:34.016 WARN WiggleWindow - Not writing 111 7 11:10:34.016 WARN WiggleWindow - Not writing 131 8 11:10:34.016 WARN WiggleWindow - Not writing 141 8 11:10:34.017 WARN WiggleWindow - Not writing 151 8 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) appending (count=10,length=4) appending (count=1,length=0) appending (count=2,length=8) Hello appending (count=10,length=4) 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: 46391 length: 9 Appending count: 49211 length: 8 Appending count: 32047 length: 4 Appending count: 15652 length: 3 Appending count: 23870 length: 2 Appending count: 44943 length: 7 Appending count: 3824 length: 8 Appending count: 44456 length: 7 Appending count: 17404 length: 9 Appending count: 11411 length: 6 Appending count: 43431 length: 5 Appending count: 49261 length: 5 Appending count: 33159 length: 2 Appending count: 20708 length: 9 Appending count: 38802 length: 2 Appending count: 40979 length: 7 Appending count: 40292 length: 7 Appending count: 35637 length: 5 Appending count: 6814 length: 3 Appending count: 11882 length: 5 Appending count: 44812 length: 2 Appending count: 17783 length: 3 Appending count: 48863 length: 1 Appending count: 24760 length: 4 Appending count: 4185 length: 10 Appending count: 21361 length: 7 Appending count: 44024 length: 10 Appending count: 30274 length: 3 Appending count: 23369 length: 3 Appending count: 30376 length: 5 position= 0 count= 46391 position= 1 count= 46391 position= 2 count= 46391 position= 3 count= 46391 position= 4 count= 46391 position= 5 count= 46391 position= 6 count= 46391 position= 7 count= 46391 position= 8 count= 46391 position= 9 count= 49211 position= 10 count= 49211 position= 11 count= 49211 position= 12 count= 49211 position= 13 count= 49211 position= 14 count= 49211 position= 15 count= 49211 position= 16 count= 49211 position= 17 count= 32047 position= 18 count= 32047 position= 19 count= 32047 position= 20 count= 32047 position= 21 count= 15652 position= 22 count= 15652 position= 23 count= 15652 position= 24 count= 23870 position= 25 count= 23870 position= 26 count= 44943 position= 27 count= 44943 position= 28 count= 44943 position= 29 count= 44943 position= 30 count= 44943 position= 31 count= 44943 position= 32 count= 44943 position= 33 count= 3824 position= 34 count= 3824 position= 35 count= 3824 position= 36 count= 3824 position= 37 count= 3824 position= 38 count= 3824 position= 39 count= 3824 position= 40 count= 3824 position= 41 count= 44456 position= 42 count= 44456 position= 43 count= 44456 position= 44 count= 44456 position= 45 count= 44456 position= 46 count= 44456 position= 47 count= 44456 position= 48 count= 17404 position= 49 count= 17404 position= 50 count= 17404 position= 51 count= 17404 position= 52 count= 17404 position= 53 count= 17404 position= 54 count= 17404 position= 55 count= 17404 position= 56 count= 17404 position= 57 count= 11411 position= 58 count= 11411 position= 59 count= 11411 position= 60 count= 11411 position= 61 count= 11411 position= 62 count= 11411 position= 63 count= 43431 position= 64 count= 43431 position= 65 count= 43431 position= 66 count= 43431 position= 67 count= 43431 position= 68 count= 49261 position= 69 count= 49261 position= 70 count= 49261 position= 71 count= 49261 position= 72 count= 49261 position= 73 count= 33159 position= 74 count= 33159 position= 75 count= 20708 position= 76 count= 20708 position= 77 count= 20708 position= 78 count= 20708 position= 79 count= 20708 position= 80 count= 20708 position= 81 count= 20708 position= 82 count= 20708 position= 83 count= 20708 position= 84 count= 38802 position= 85 count= 38802 position= 86 count= 40979 position= 87 count= 40979 position= 88 count= 40979 position= 89 count= 40979 position= 90 count= 40979 position= 91 count= 40979 position= 92 count= 40979 position= 93 count= 40292 position= 94 count= 40292 position= 95 count= 40292 position= 96 count= 40292 position= 97 count= 40292 position= 98 count= 40292 position= 99 count= 40292 position= 100 count= 35637 position= 101 count= 35637 position= 102 count= 35637 position= 103 count= 35637 position= 104 count= 35637 position= 105 count= 6814 position= 106 count= 6814 position= 107 count= 6814 position= 108 count= 11882 position= 109 count= 11882 position= 110 count= 11882 position= 111 count= 11882 position= 112 count= 11882 position= 113 count= 44812 position= 114 count= 44812 position= 115 count= 17783 position= 116 count= 17783 position= 117 count= 17783 position= 118 count= 48863 position= 119 count= 24760 position= 120 count= 24760 position= 121 count= 24760 position= 122 count= 24760 position= 123 count= 4185 position= 124 count= 4185 position= 125 count= 4185 position= 126 count= 4185 position= 127 count= 4185 position= 128 count= 4185 position= 129 count= 4185 position= 130 count= 4185 position= 131 count= 4185 position= 132 count= 4185 position= 133 count= 21361 position= 134 count= 21361 position= 135 count= 21361 position= 136 count= 21361 position= 137 count= 21361 position= 138 count= 21361 position= 139 count= 21361 position= 140 count= 44024 position= 141 count= 44024 position= 142 count= 44024 position= 143 count= 44024 position= 144 count= 44024 position= 145 count= 44024 position= 146 count= 44024 position= 147 count= 44024 position= 148 count= 44024 position= 149 count= 44024 position= 150 count= 30274 position= 151 count= 30274 position= 152 count= 30274 position= 153 count= 23369 position= 154 count= 23369 position= 155 count= 23369 position= 156 count= 30376 position= 157 count= 30376 position= 158 count= 30376 position= 159 count= 30376 position= 160 count= 30376 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 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 11:10:36.655 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 11:10:36.660 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 11:10:36.664 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 11:10:36.666 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 11:10:36.670 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 11:10:36.673 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 11:10:36.675 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 11:10:36.678 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 11:10:36.680 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 11:10:36.682 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 11:10:36.869 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 11:10:36.871 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 11:10:36.873 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 11:10:36.875 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 11:10:36.877 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 11:10:36.879 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 11:10:36.881 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 11:10:36.883 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 11:10:36.885 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 11:10:36.888 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 11:10:37.038 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 11:10:37.040 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 11:10:37.043 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 11:10:37.045 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 11:10:37.047 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 11:10:37.053 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 11:10:37.057 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 11:10:37.061 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 11:10:37.063 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 11:10:37.066 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 11:10:37.171 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 11:10:37.175 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 11:10:37.177 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 11:10:37.179 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 11:10:37.181 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 11:10:37.183 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 11:10:37.185 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 11:10:37.186 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 11:10:37.188 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 11:10:37.190 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 11:10:37.324 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 11:10:37.326 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 11:10:37.329 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 11:10:37.331 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 11:10:37.335 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 11:10:37.337 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 11:10:37.339 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 11:10:37.342 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 11:10:37.344 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 11:10:37.346 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 11:10:37.458 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 11:10:37.460 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 11:10:37.462 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 11:10:37.464 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 11:10:37.466 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 11:10:37.468 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 11:10:37.471 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 11:10:37.473 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 11:10:37.475 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 11:10:37.477 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 11:10:37.588 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 11:10:37.590 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 11:10:37.592 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 11:10:37.594 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 11:10:37.597 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 11:10:37.599 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 11:10:37.600 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 11:10:37.602 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 11:10:37.605 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 11:10:37.607 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 11:10:37.692 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 11:10:37.693 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 11:10:37.695 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 11:10:37.696 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 11:10:37.698 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 11:10:37.699 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 11:10:37.701 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 11:10:37.702 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 11:10:37.704 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 11:10:37.705 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 11:10:37.787 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 11:10:37.789 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 11:10:37.790 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 11:10:37.792 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 11:10:37.793 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 11:10:37.795 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 11:10:37.797 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 11:10:37.798 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 11:10:37.800 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 11:10:37.801 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 11:10:37.888 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 11:10:37.890 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 11:10:37.892 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 11:10:37.893 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 11:10:37.895 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 11:10:37.897 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 11:10:37.899 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 11:10:37.901 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 11:10:37.903 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 11:10:37.904 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 11:10:38.030 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 11:10:38.032 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 11:10:38.033 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 11:10:38.035 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 11:10:38.036 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 11:10:38.038 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 11:10:38.040 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 11:10:38.041 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 11:10:38.042 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 11:10:38.044 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 11:10:38.144 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 11:10:38.146 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 11:10:38.149 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 11:10:38.152 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 11:10:38.153 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 11:10:38.154 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 11:10:38.156 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 11:10:38.158 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 11:10:38.159 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 11:10:38.161 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} 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 TTC[27]->CGT[27] / qual=1:2:3 A[15]->G[20] / qual=20 A[15]->G[20] / qual=20 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 [ {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 [main] WARN org.campagnelab.goby.algorithmic.algorithm.EquivalentIndelRegionCalculator - Cannot determine sequence at position 600000000 of reference-index 2 Annotations loaded Annotations loaded Annotations loaded Annotations loaded Annotations loaded 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 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 11:12:08.660 INFO TestPostBarcodeMatcher - Num matches = 200, Num Ambiguous = 0, Num no matches = 0 11:12:08.661 INFO TestPostBarcodeMatcher - Time to parse 8 million reads 0 seconds 11:12:08.721 INFO BullardUpperQuartileNormalization - normalization denominator 54080.2 for sample B-7 11:12:08.722 INFO BullardUpperQuartileNormalization - normalization denominator 53206.8 for sample B-3 11:12:08.722 INFO BullardUpperQuartileNormalization - normalization denominator 109107 for sample A-3 11:12:08.722 INFO BullardUpperQuartileNormalization - normalization denominator 110999 for sample A-12 11:12:08.722 INFO BullardUpperQuartileNormalization - normalization denominator 54880.9 for sample B-15 11:12:08.722 INFO BullardUpperQuartileNormalization - normalization denominator 53570.7 for sample B-14 11:12:08.722 INFO BullardUpperQuartileNormalization - normalization denominator 53934.6 for sample B-11 11:12:08.722 INFO BullardUpperQuartileNormalization - normalization denominator 109179 for sample A-17 11:12:08.722 INFO BullardUpperQuartileNormalization - normalization denominator 55754.3 for sample B-2 11:12:08.722 INFO BullardUpperQuartileNormalization - normalization denominator 55390.4 for sample B-10 11:12:08.722 INFO BullardUpperQuartileNormalization - normalization denominator 108888 for sample A-16 11:12:08.723 INFO BullardUpperQuartileNormalization - normalization denominator 55463.1 for sample B-8 11:12:08.723 INFO BullardUpperQuartileNormalization - normalization denominator 56045.4 for sample B-4 11:12:08.723 INFO BullardUpperQuartileNormalization - normalization denominator 108524 for sample A-2 11:12:08.723 INFO BullardUpperQuartileNormalization - normalization denominator 108379 for sample A-0 11:12:08.723 INFO BullardUpperQuartileNormalization - normalization denominator 55681.5 for sample B-6 11:12:08.723 INFO BullardUpperQuartileNormalization - normalization denominator 109179 for sample A-9 11:12:08.723 INFO BullardUpperQuartileNormalization - normalization denominator 110708 for sample A-8 11:12:08.723 INFO BullardUpperQuartileNormalization - normalization denominator 108597 for sample A-5 11:12:08.723 INFO BullardUpperQuartileNormalization - normalization denominator 111145 for sample A-4 11:12:08.723 INFO BullardUpperQuartileNormalization - normalization denominator 110562 for sample A-6 11:12:08.724 INFO BullardUpperQuartileNormalization - normalization denominator 109179 for sample A-7 11:12:08.724 INFO BullardUpperQuartileNormalization - normalization denominator 52842.8 for sample B-5 11:12:08.724 INFO BullardUpperQuartileNormalization - normalization denominator 106923 for sample A-10 11:12:08.724 INFO BullardUpperQuartileNormalization - normalization denominator 107214 for sample A-14 11:12:08.724 INFO BullardUpperQuartileNormalization - normalization denominator 54007.4 for sample B-9 11:12:08.724 INFO BullardUpperQuartileNormalization - normalization denominator 109834 for sample A-1 11:12:08.724 INFO BullardUpperQuartileNormalization - normalization denominator 56045.4 for sample B-0 11:12:08.724 INFO BullardUpperQuartileNormalization - normalization denominator 54444.1 for sample B-12 11:12:08.724 INFO BullardUpperQuartileNormalization - normalization denominator 54735.3 for sample B-13 11:12:08.725 INFO BullardUpperQuartileNormalization - normalization denominator 106268 for sample A-19 11:12:08.725 INFO BullardUpperQuartileNormalization - normalization denominator 108597 for sample A-18 11:12:08.725 INFO BullardUpperQuartileNormalization - normalization denominator 108233 for sample A-15 11:12:08.725 INFO BullardUpperQuartileNormalization - normalization denominator 55681.5 for sample B-1 11:12:08.725 INFO BullardUpperQuartileNormalization - normalization denominator 107433 for sample A-13 11:12:08.725 INFO BullardUpperQuartileNormalization - normalization denominator 110198 for sample A-11 11:12:08.725 INFO BullardUpperQuartileNormalization - normalization denominator 53716.3 for sample B-16 11:12:08.725 INFO BullardUpperQuartileNormalization - normalization denominator 54662.5 for sample B-17 11:12:08.725 INFO BullardUpperQuartileNormalization - normalization denominator 55972.6 for sample B-19 11:12:08.725 INFO BullardUpperQuartileNormalization - normalization denominator 55972.6 for sample B-18 11:12:08.820 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value 11:12:08.876 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. 11:12:08.876 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value 11:12:08.899 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. 11:12:08.899 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value 11:12:09.070 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. 11:12:09.127 INFO FDRAdjustment - ... statistic t-test-P-value-Bonferroni-adjusted was found, FDR adjustment executed. 11:12:09.127 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value 11:12:09.278 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. 11:12:09.312 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 [0.9988225176027525, 0.5039216928000868, -0.001699748923964364, -0.9887285321667536, 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 20 threads. [main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 20 threads. [main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 20 threads. [main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 20 threads. ##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 Creating base test directory: test-results/stats-writer allele: A ref: [CC] alt: [T]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. [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. Setting quality threshold to 0.02 [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. 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' 11:12:24.625 WARN MessageChunksWriter - Using chunk-size=1 11:12:24.632 WARN MessageChunksWriter - Using chunk-size=1 11:12:24.798 WARN MessageChunksWriter - Using chunk-size=1 11:12:24.890 WARN MessageChunksWriter - Using chunk-size=1 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 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 11:12:25.084 WARN MessageChunksWriter - Using chunk-size=1000 11:12:25.087 WARN MessageChunksWriter - Using chunk-size=1000 11:12:25.097 WARN MessageChunksWriter - Using chunk-size=1000 11:12:25.178 WARN MessageChunksWriter - Using chunk-size=1000 0 23 11:12:25.776 WARN MessageChunksWriter - Using chunk-size=1000 11:12:25.781 WARN MessageChunksWriter - Using chunk-size=1000 11:12:25.782 WARN MessageChunksWriter - Using chunk-size=1000 11:12:25.783 WARN MessageChunksWriter - Using chunk-size=1000 11:12:25.866 WARN MessageChunksWriter - Using chunk-size=1000 11:12:26.081 WARN MessageChunksWriter - Using chunk-size=1000 11:12:26.257 WARN MessageChunksWriter - Using chunk-size=1000 11:12:26.455 WARN MessageChunksWriter - Using chunk-size=1000 11:12:26.580 WARN MessageChunksWriter - Using chunk-size=1000 11:12:26.581 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 11:12:26.649 WARN MessageChunksWriter - Using chunk-size=1000 11:12:26.778 WARN MessageChunksWriter - Using chunk-size=1000 11:12:26.960 WARN MessageChunksWriter - Using chunk-size=1000 11:12:27.133 WARN MessageChunksWriter - Using chunk-size=1000 11:12:27.317 WARN MessageChunksWriter - Using chunk-size=1000 11:12:27.484 WARN MessageChunksWriter - Using chunk-size=1000 11:12:27.587 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 11:12:27.589 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 11:12:27.591 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 11:12:27.595 WARN MessageChunksWriter - Using chunk-size=1000 11:12:27.732 WARN MessageChunksWriter - Using chunk-size=1000 11:12:27.733 WARN MessageChunksWriter - Using chunk-size=1000 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 } 11:12:27.916 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 11:12:27.927 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 11:12:27.935 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 11:12:27.943 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 11:12:27.949 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 11:12:28.051 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 11:12:28.317 WARN MessageChunksWriter - Using chunk-size=1000 11:12:28.551 WARN MessageChunksWriter - Using chunk-size=1000 11:12:28.553 WARN MessageChunksWriter - Using chunk-size=1000 11:12:28.770 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 11:12:28.805 WARN MessageChunksWriter - Using chunk-size=1000 11:12:28.807 WARN MessageChunksWriter - Using chunk-size=1000 11:12:28.817 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. 11:12:29.005 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. 11:12:29.005 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 11:12:29.005 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: 111ms; used/avail/free/total/max mem: 687.57M/20.54G/50.63M/738.20M/21.22G 11:12:29.123 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 11:12:29.285 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. 11:12:29.291 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. 11:12:29.342 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. 11:12:29.342 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. 11:12:29.343 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. 11:12:29.343 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 11:12:29.343 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. 11:12:29.343 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: 40ms; used/avail/free/total/max mem: 51.13M/21.17G/703.84M/754.97M/21.22G 11:12:29.387 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. 11:12:29.407 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. 11:12:29.655 WARN MessageChunksWriter - Using chunk-size=1000 11:12:29.945 WARN MessageChunksWriter - Using chunk-size=1000 11:12:30.219 WARN MessageChunksWriter - Using chunk-size=1000 11:12:30.540 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 11:12:30.853 WARN MessageChunksWriter - Using chunk-size=1000 11:12:31.162 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: 151.79M/21.07G/603.18M/754.97M/21.22G 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 11:12:31.499 WARN MessageChunksWriter - Using chunk-size=1000 11:12:31.793 WARN MessageChunksWriter - Using chunk-size=1000 11:12:32.080 WARN MessageChunksWriter - Using chunk-size=1000 11:12:32.379 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 11:12:32.605 WARN MessageChunksWriter - Using chunk-size=1000 11:12:32.816 WARN MessageChunksWriter - Using chunk-size=1000 11:12:32.959 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. 11:12:32.966 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. 11:12:32.966 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 11:12:32.966 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: 2ms; used/avail/free/total/max mem: 210.52M/21.01G/544.46M/754.97M/21.22G 11:12:32.968 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 11:12:33.030 WARN MessageChunksWriter - Using chunk-size=1000 11:12:33.481 WARN MessageChunksWriter - Using chunk-size=1000 11:12:33.719 WARN MessageChunksWriter - Using chunk-size=1000 11:12:33.950 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 11:12:34.168 WARN MessageChunksWriter - Using chunk-size=1000 11:12:34.301 WARN MessageChunksWriter - Using chunk-size=1000 11:12:34.304 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. 11:12:34.306 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. 11:12:34.309 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. 11:12:34.309 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. 11:12:34.309 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. 11:12:34.309 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 11:12:34.309 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. 11:12:34.309 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: 36ms; used/avail/free/total/max mem: 235.75M/20.99G/519.22M/754.97M/21.22G 11:12:34.349 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. 11:12:34.351 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. 11:12:34.355 WARN MessageChunksWriter - Using chunk-size=1000 11:12:34.409 WARN MessageChunksWriter - Using chunk-size=1000 11:12:34.525 WARN MessageChunksWriter - Using chunk-size=1000 11:12:34.925 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 11:12:35.071 WARN MessageChunksWriter - Using chunk-size=1000 11:12:35.199 WARN MessageChunksWriter - Using chunk-size=1000 Finding max number of reads... Found input file with 2 target(s) 11:12:35.203 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) 11:12:35.203 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. 11:12:35.207 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. 11:12:35.207 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. 11:12:35.207 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. 11:12:35.207 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 11:12:35.207 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. 11:12:35.207 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: 24ms; used/avail/free/total/max mem: 260.84M/20.96G/494.13M/754.97M/21.22G Second pass: writing the merged alignment. 11:12:35.234 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. 11:12:35.235 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 11:12:35.241 WARN MessageChunksWriter - Using chunk-size=1000 11:12:35.532 WARN MessageChunksWriter - Using chunk-size=1000 11:12:35.761 WARN MessageChunksWriter - Using chunk-size=1000 11:12:35.885 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 11:12:36.172 WARN MessageChunksWriter - Using chunk-size=1000 11:12:36.270 WARN MessageChunksWriter - Using chunk-size=1000 11:12:36.273 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. 11:12:36.348 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. 11:12:36.349 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 11:12:36.349 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: 286.05M/20.94G/468.92M/754.97M/21.22G 11:12:36.352 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 11:12:36.542 WARN MessageChunksWriter - Using chunk-size=1000 11:12:36.755 WARN MessageChunksWriter - Using chunk-size=1000 11:12:36.757 WARN MessageChunksWriter - Using chunk-size=1000 11:12:36.841 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 11:12:36.959 WARN MessageChunksWriter - Using chunk-size=1000 11:12:37.086 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: 175ms [2 items, 11.49 items/s, 87.00 ms/item]; used/avail/free/total/max mem: 344.73M/20.88G/410.24M/754.97M/21.22G 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 11:12:37.700 WARN MessageChunksWriter - Using chunk-size=1000 11:12:37.878 WARN MessageChunksWriter - Using chunk-size=1000 11:12:37.947 WARN MessageChunksWriter - Using chunk-size=1000 11:12:38.112 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 11:12:38.282 WARN MessageChunksWriter - Using chunk-size=1000 11:12:38.283 WARN MessageChunksWriter - Using chunk-size=1000 11:12:38.289 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. 11:12:38.294 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. 11:12:38.333 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. 11:12:38.334 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. 11:12:38.334 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. 11:12:38.334 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 11:12:38.334 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. 11:12:38.334 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: 437.02M/20.79G/317.96M/754.97M/21.22G 11:12:38.339 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. 11:12:38.361 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 11:12:38.422 WARN MessageChunksWriter - Using chunk-size=1000 11:12:38.426 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 11:12:38.438 WARN MessageChunksWriter - Using chunk-size=1000 11:12:38.441 WARN MessageChunksWriter - Using chunk-size=1000 entry: score=30.0000 readOriginIndex=0 entry: score=30.0000 readOriginIndex=0 Scanned 2 entries 11:12:38.450 WARN MessageChunksWriter - Using chunk-size=1000 11:12:38.454 WARN MessageChunksWriter - Using chunk-size=1000 11:12:38.465 WARN MessageChunksWriter - Using chunk-size=1000 11:12:38.467 WARN MessageChunksWriter - Using chunk-size=1000 11:12:38.477 WARN MessageChunksWriter - Using chunk-size=1000 11:12:38.481 WARN MessageChunksWriter - Using chunk-size=1000 0 2 11:12:38.492 WARN MessageChunksWriter - Using chunk-size=1000 11:12:38.495 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 11:12:38.504 WARN MessageChunksWriter - Using chunk-size=1000 11:12:38.506 WARN MessageChunksWriter - Using chunk-size=1000 11:12:38.516 WARN MessageChunksWriter - Using chunk-size=1000 11:12:38.518 WARN MessageChunksWriter - Using chunk-size=1000 11:12:38.527 WARN MessageChunksWriter - Using chunk-size=1000 11:12:38.530 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 11:12:38.541 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 11:12:38.549 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 11:12:38.554 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 11:12:38.558 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 11:12:38.562 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 11:12:38.566 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 11:12:38.571 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 original GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: GGTGT original G----GTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: G original GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGT mapped: GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGT original G--GTGTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: GGT [WARNING] Tests run: 512, Failures: 0, Errors: 0, Skipped: 46, Time elapsed: 140.207 s - in TestSuite 11:12:39.428 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 [ 0.080 s] [INFO] Goby I/O ........................................... SUCCESS [ 15.437 s] [INFO] Goby Full Distribution ............................. SUCCESS [02:53 min] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 03:09 min [INFO] Finished at: 2024-10-11T11:12:47-12:00 [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 [ 0.607 s] [INFO] Goby I/O ........................................... SUCCESS [ 0.074 s] [INFO] Goby Full Distribution ............................. SUCCESS [ 0.058 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 1.052 s [INFO] Finished at: 2024-10-11T11:12:50-12:00 [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 Oct 11, 2024 11:12:57 AM 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 Oct 11, 2024 11:13:03 AM 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 libgoby-io-java: substitution variable ${shlibs:Depends} used, but is not 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 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: package goby-java: substitution variable ${java:Depends} 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: 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/733974 and its subdirectories I: Current time: Fri Oct 11 11:13:22 -12 2024 I: pbuilder-time-stamp: 1728688402 Fri Oct 11 23:13:23 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Fri Oct 11 23:13:23 UTC 2024 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Fri Oct 11 23:19:15 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Fri Oct 11 23:19:16 UTC 2024 I: libgoby-java_3.3.1+dfsg2-11_amd64.changes: Format: 1.8 Date: Tue, 14 May 2024 18:17:12 +0200 Source: libgoby-java Binary: goby-java libgoby-io-java Architecture: all Version: 3.3.1+dfsg2-11 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Pierre Gruet Description: goby-java - next-generation sequencing data and results analysis tool libgoby-io-java - IO API for goby Changes: libgoby-java (3.3.1+dfsg2-11) unstable; urgency=medium . * Raising Standards version to 4.7.0 (no change) * Restricting autopkgtest architecture to amd64 and arm64, where sra-sdk packages are installable * Build-depending on pkgconf instead of obsolete pkg-config Checksums-Sha1: 1eb477e28d6fb114e4bec3b52fd19dc800f8d2dd 1575728 goby-java_3.3.1+dfsg2-11_all.deb dd84b9c5cf30b1b3b6d5fdcd821327dccf6a7ae3 979004 libgoby-io-java_3.3.1+dfsg2-11_all.deb 736369a6a9211aa860efdeefc621f5e31c990d7d 19536 libgoby-java_3.3.1+dfsg2-11_amd64.buildinfo Checksums-Sha256: 293898836ebc56dc259caa53cf283a426e5083e103ec18215a9a990ea689a855 1575728 goby-java_3.3.1+dfsg2-11_all.deb 6290b77a340114e206f584b4c3ee85619181ee6317e8c4d7fe4225cf56b8223f 979004 libgoby-io-java_3.3.1+dfsg2-11_all.deb 9b5648f90b261b35a9d9eae62f7de9a22d1ac8f9a61cea019ae28ff0e45b2e98 19536 libgoby-java_3.3.1+dfsg2-11_amd64.buildinfo Files: 6873eaf26693cb5deaa4603ecb55d6f4 1575728 science optional goby-java_3.3.1+dfsg2-11_all.deb 945745f48a2c27cee9b5fa6b1e5c4112 979004 science optional libgoby-io-java_3.3.1+dfsg2-11_all.deb 27a0adcaf5953fc2783b27f26dd1a237 19536 science optional libgoby-java_3.3.1+dfsg2-11_amd64.buildinfo Fri Oct 11 23:19:17 UTC 2024 I: diffoscope 279 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_31-22590.service Warning: program compiled against libxml 212 using older 209 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.ONmzhG9r/libgoby-java_3.3.1+dfsg2-11.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.ONmzhG9r/libgoby-java_3.3.1+dfsg2-11.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.ONmzhG9r/libgoby-java_3.3.1+dfsg2-11.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.ONmzhG9r/b1/libgoby-java_3.3.1+dfsg2-11_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.ONmzhG9r/b2/libgoby-java_3.3.1+dfsg2-11_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.410s) 0.410s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.044s) 0.044s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 761ms CPU time consumed: 763ms Fri Oct 11 23:19:18 UTC 2024 I: diffoscope 279 found no differences in the changes files, and a .buildinfo file also exists. Fri Oct 11 23:19:18 UTC 2024 I: libgoby-java from trixie built successfully and reproducibly on amd64. Fri Oct 11 23:19:19 UTC 2024 I: Submitting .buildinfo files to external archives: Fri Oct 11 23:19:19 UTC 2024 I: Submitting 20K b1/libgoby-java_3.3.1+dfsg2-11_amd64.buildinfo.asc Fri Oct 11 23:19:20 UTC 2024 I: Submitting 20K b2/libgoby-java_3.3.1+dfsg2-11_amd64.buildinfo.asc Fri Oct 11 23:19:21 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Oct 11 23:19:21 UTC 2024 I: Done submitting .buildinfo files. Fri Oct 11 23:19:21 UTC 2024 I: Removing signed libgoby-java_3.3.1+dfsg2-11_amd64.buildinfo.asc files: removed './b1/libgoby-java_3.3.1+dfsg2-11_amd64.buildinfo.asc' removed './b2/libgoby-java_3.3.1+dfsg2-11_amd64.buildinfo.asc'