Tue May 7 07:12:58 UTC 2024 I: starting to build libgoby-java/trixie/amd64 on jenkins on '2024-05-07 07:12' Tue May 7 07:12:58 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_30/7992/console.log Tue May 7 07:12:58 UTC 2024 I: Downloading source for trixie/libgoby-java=3.3.1+dfsg2-10 --2024-05-07 07:12:58-- http://deb.debian.org/debian/pool/main/libg/libgoby-java/libgoby-java_3.3.1%2bdfsg2-10.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 3011 (2.9K) [text/prs.lines.tag] Saving to: ‘libgoby-java_3.3.1+dfsg2-10.dsc’ 0K .. 100% 315M=0s 2024-05-07 07:12:58 (315 MB/s) - ‘libgoby-java_3.3.1+dfsg2-10.dsc’ saved [3011/3011] Tue May 7 07:12:58 UTC 2024 I: libgoby-java_3.3.1+dfsg2-10.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+dfsg2-10 Maintainer: Debian Med Packaging Team Uploaders: Pierre Gruet , Andreas Tille Homepage: https://campagnelab.org/software/goby/ Standards-Version: 4.6.2 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, pkg-config, 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 46a6a881da114175ba247880ac918fbd443d60ce 29336 libgoby-java_3.3.1+dfsg2-10.debian.tar.xz Checksums-Sha256: b76b19808f893790e238c91e65680441ff020794cc7708ad6695cf13f0767148 41577532 libgoby-java_3.3.1+dfsg2.orig.tar.xz 89a405303356305fe1c53dafd4cab5ddf599f2d8e73ed203956b648fb1cef8cf 29336 libgoby-java_3.3.1+dfsg2-10.debian.tar.xz Files: 3a8dbf45ef2c54ec3073240850acbc75 41577532 libgoby-java_3.3.1+dfsg2.orig.tar.xz c593b3185449e6d893941b7e40b7daf9 29336 libgoby-java_3.3.1+dfsg2-10.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEM8soQxPpC9J9y0UjYAMWptwndHYFAmVsQ70ACgkQYAMWptwn dHZSGA/9GFdrIyK6c9r7P/KTdd0V7AOwl4p6awbMSE5MhS7N5hb/Vi333JaISTcg TV0t4ApvEnA4wwq9xBjMP52KIO0kWoTHcnRYD8OMaK7QWemEF45l4W2VClaFIyCh YeTPIYHs5JyM5e0RPDCErad84RaG46oHb66LqRk3l1+3IiLcUvhNQCBRFNN2jmsq 9mlL5Nn3TE8cs2IzgVzHN7dy3ak7tdI0oTWmRPfl21X8V4leZ/oQ1wQN9Q/I8CxZ lInN00ghgIUFb8f0sF6ZZfwtAKZ1WcyqvfkRIHEICqSFQ32dw7EulzB/tzN2Y2G5 ZPqbv1kLeFO6pdzknM9yu26s7uNo4KQjgT8J2vm5S6/Fn++jWIqHa8ekPgvggiLB ktunZ055EHMPrPTVpz3h+CnUGhh93FzXgD6BiQXUcH0/5wxNDa+33DLCHe/2JkQH hTXRpIdK7xyAR2a+prd9ygtGjZ+iBRpZIk5w7mM9JFHTWjfmrk9QZVbi/waQkmW/ r4Gdc6kBE/EpLc3cicdV5mWmEEbu3IklcgV/kyLupCwq34mETpNG5bjyZbWUCZvu VgLZ9vOBZXrw1agc8mDNQXcLrTuRxDMf7bv7THH53XlXJ5oeyPAdV5BdCC9mUT6p zFnVT2kMrjlczuNgLmdtdNKi4T6b8vyxzu6OiLCyEzMGLYIAEss= =oxEn -----END PGP SIGNATURE----- Tue May 7 07:12:58 UTC 2024 I: Checking whether the package is not for us Tue May 7 07:12:58 UTC 2024 I: Starting 1st build on remote node ionos15-amd64.debian.net. Tue May 7 07:12:58 UTC 2024 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Tue May 7 07:17:47 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Jun 9 01:36:02 -12 2025 I: pbuilder-time-stamp: 1749476162 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+dfsg2-10.dsc] I: copying [./libgoby-java_3.3.1+dfsg2.orig.tar.xz] I: copying [./libgoby-java_3.3.1+dfsg2-10.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Dec 3 09:00:45 2023 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+dfsg2-10.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+dfsg2-10.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/89880/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=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='ccc4e202b29548e48fda682e7b541549' 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='89880' 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.rFLny5uu/pbuilderrc_MChp --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.rFLny5uu/b1 --logfile b1/build.log libgoby-java_3.3.1+dfsg2-10.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://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 8 17:46 /bin -> usr/bin I: user script /srv/workspace/pbuilder/89880/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, pkg-config, 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 ... 19698 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 pkg-config; however: Package pkg-config 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} 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} gnupg-utils{a} gpg{a} gpg-agent{a} gpg-wks-client{a} gpg-wks-server{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} libarchive-zip-perl{a} libasm-java{a} libasound2-data{a} libasound2t64{a} libassuan0{a} libatinject-jsr330-api-java{a} libatk1.0-0t64{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} libbsd0{a} libbsh-java{a} libbuild-helper-maven-plugin-java{a} libbyte-buddy-java{a} libcairo2{a} libcdi-api-java{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{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} 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-nouveau2{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} 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} 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} libgtk2.0-0t64{a} libgtk2.0-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} libllvm17t64{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} libnspr4{a} libnss3{a} libobjenesis-java{a} libopentest4j-java{a} libopentest4j-reporting-java{a} liboro-java{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} libpython3.11-minimal{a} libpython3.11-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-override-perl{a} libsub-quote-perl{a} libsurefire-java{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} 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} 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} ncbi-vdb-data{a} netbase{a} openjdk-17-jdk{a} openjdk-17-jdk-headless{a} openjdk-17-jre{a} openjdk-17-jre-headless{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} protobuf-compiler{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} r-base-core{a} r-cran-rjava{a} readline-common{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} testng{a} tzdata{a} ucf{a} unzip{a} velocity{a} wdiff{a} x11-common{a} xdg-utils{a} zip{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf ant-optional curl dbus debian-keyring dput dput-ng dupload equivs fonts-dejavu-extra icc-profiles-free krb5-locales libarchive-cpio-perl libatk-wrapper-java-jni libdata-dump-perl libdistlib-java-doc libdistro-info-perl libfile-mimeinfo-perl libgail-common libgdk-pixbuf2.0-bin libgit-wrapper-perl libgitlab-api-v4-perl libgkl-jni libglib2.0-data libgtk2.0-bin libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjson-perl libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl libnet-dbus-perl librsvg2-common libsasl2-modules libsaxon-java libsoap-lite-perl libstring-shellquote-perl libx11-protocol-perl libxstring-perl libxt-dev libyaml-snake-java licensecheck lintian lynx mesa-vulkan-drivers 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 wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 442 newly installed, 0 to remove and 0 not upgraded. Need to get 379 MB of archives. After unpacking 943 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 binfmt-support amd64 2.2.2-7 [64.3 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-3 [255 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-3 [307 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.78.4-7 [1455 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 shared-mime-info amd64 2.4-4 [759 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.3.2-0.4+b1 [108 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.3.2-0.4+b1 [308 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.10+dfsg-3+b3 [138 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 gtk-update-icon-cache amd64 3.24.41-4 [46.6 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 adwaita-icon-theme all 46.0-1 [614 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 java-common all 0.75 [6640 B] Get: 50 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libnspr4 amd64 2:4.35-1.1+b1 [109 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libnss3 amd64 2:3.99-1 [1408 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libpcsclite1 amd64 2.0.3-1 [51.0 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 openjdk-17-jre-headless amd64 17.0.11+9-1 [43.8 MB] Get: 55 http://deb.debian.org/debian trixie/main amd64 default-jre-headless amd64 2:1.17-75 [3068 B] Get: 56 http://deb.debian.org/debian trixie/main amd64 ant all 1.10.14-1 [2162 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 ant-contrib all 1.0~b3+svn177-12 [262 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 at-spi2-common all 2.52.0-1 [166 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 dctrl-tools amd64 2.24-3+b1 [104 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 72 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libgtk2.0-common all 2.24.33-4 [2661 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libatk1.0-0t64 amd64 2.52.0-1 [50.8 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.0-3+b1 [531 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libavahi-common-data amd64 0.8-13+b2 [112 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libavahi-common3 amd64 0.8-13+b2 [43.3 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libdbus-1-3 amd64 1.14.10-4+b1 [203 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libavahi-client3 amd64 0.8-13+b2 [47.0 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1~rc2-1 [22.6 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 106 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libcups2t64 amd64 2.4.7-1.2+b1 [247 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.52.1+ds-1 [216 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.52.1+ds-1 [48.3 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.52.1+ds-1 [35.1 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libxcomposite1 amd64 1:0.4.5-1+b1 [14.9 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libxfixes3 amd64 1:6.0.0-2+b1 [20.3 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libxcursor1 amd64 1:1.2.1-1+b1 [36.2 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libxdamage1 amd64 1:1.1.6-1+b1 [15.5 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.1-1 [79.0 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libxinerama1 amd64 2:1.1.4-3+b1 [16.0 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libxrandr2 amd64 2:1.5.4-1 [36.1 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libgtk2.0-0t64 amd64 2.24.33-4 [1816 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libglvnd0 amd64 1.7.0-1+b1 [56.3 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.120-2 [7688 B] Get: 129 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libglapi-mesa amd64 23.3.5-1 [35.8 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libx11-xcb1 amd64 2:1.8.7-1+b1 [232 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libxcb-dri2-0 amd64 1.15-1 [107 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libxcb-dri3-0 amd64 1.15-1 [107 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libxcb-glx0 amd64 1.15-1 [122 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libxcb-present0 amd64 1.15-1 [105 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libxcb-randr0 amd64 1.15-1 [117 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libxcb-sync1 amd64 1.15-1 [109 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libxcb-xfixes0 amd64 1.15-1 [109 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libxshmfence1 amd64 1.3-1+b1 [8852 B] Get: 140 http://deb.debian.org/debian trixie/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libvulkan1 amd64 1.3.280.0-1 [123 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libdrm-intel1 amd64 2.4.120-2 [62.7 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libdrm-nouveau2 amd64 2.4.120-2 [19.3 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libdrm-radeon1 amd64 2.4.120-2 [22.2 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20230828-1+b1 [93.5 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 libllvm17t64 amd64 1:17.0.6-11 [23.7 MB] Get: 150 http://deb.debian.org/debian trixie/main amd64 libsensors-config all 1:3.6.0-9 [14.6 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 libsensors5 amd64 1:3.6.0-9 [34.6 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 libgl1-mesa-dri amd64 23.3.5-1 [8145 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libglx-mesa0 amd64 23.3.5-1 [150 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libglx0 amd64 1.7.0-1+b1 [35.0 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 libgl1 amd64 1.7.0-1+b1 [89.8 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 libasound2-data all 1.2.11-1 [20.9 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 libasound2t64 amd64 1.2.11-1+b1 [369 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 libgif7 amd64 5.2.2-1 [43.9 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 libxtst6 amd64 2:1.2.3-1.1+b1 [25.9 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 openjdk-17-jre amd64 17.0.11+9-1 [185 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 default-jre amd64 2:1.17-75 [1056 B] Get: 163 http://deb.debian.org/debian trixie/main amd64 openjdk-17-jdk-headless amd64 17.0.11+9-1 [71.4 MB] Get: 164 http://deb.debian.org/debian trixie/main amd64 default-jdk-headless amd64 2:1.17-75 [1108 B] Get: 165 http://deb.debian.org/debian trixie/main amd64 openjdk-17-jdk amd64 17.0.11+9-1 [10.4 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 default-jdk amd64 2:1.17-75 [1068 B] Get: 167 http://deb.debian.org/debian trixie/main amd64 libassuan0 amd64 2.5.6-1+b1 [50.4 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 gpgconf amd64 2.2.40-3 [565 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 libksba8 amd64 1.6.6-1 [131 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 172 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 libnpth0t64 amd64 1.6-3.1 [17.9 kB] Get: 174 http://deb.debian.org/debian trixie/main amd64 dirmngr amd64 2.2.40-3 [793 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 gnupg-l10n all 2.2.40-3 [1094 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 gnupg-utils amd64 2.2.40-3 [928 kB] Get: 177 http://deb.debian.org/debian trixie/main amd64 gpg amd64 2.2.40-3 [950 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 pinentry-curses amd64 1.2.1-3+b2 [78.3 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 gpg-agent amd64 2.2.40-3 [695 kB] Get: 180 http://deb.debian.org/debian trixie/main amd64 gpg-wks-client amd64 2.2.40-3 [541 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 gpg-wks-server amd64 2.2.40-3 [532 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 gpgsm amd64 2.2.40-3 [671 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 gnupg all 2.2.40-3 [847 kB] Get: 184 http://deb.debian.org/debian trixie/main amd64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 185 http://deb.debian.org/debian trixie/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 libfile-touch-perl all 0.12-2 [8816 B] Get: 188 http://deb.debian.org/debian trixie/main amd64 libio-pty-perl amd64 1:1.20-1+b1 [34.4 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 190 http://deb.debian.org/debian trixie/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 191 http://deb.debian.org/debian trixie/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b3 [36.2 kB] Get: 192 http://deb.debian.org/debian trixie/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b1 [10.6 kB] Get: 193 http://deb.debian.org/debian trixie/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 194 http://deb.debian.org/debian trixie/main amd64 libdevel-callchecker-perl amd64 0.009-1 [15.9 kB] Get: 195 http://deb.debian.org/debian trixie/main amd64 libparams-classify-perl amd64 0.015-2+b3 [22.4 kB] Get: 196 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 197 http://deb.debian.org/debian trixie/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 198 http://deb.debian.org/debian trixie/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 199 http://deb.debian.org/debian trixie/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 200 http://deb.debian.org/debian trixie/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 201 http://deb.debian.org/debian trixie/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 202 http://deb.debian.org/debian trixie/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 203 http://deb.debian.org/debian trixie/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 204 http://deb.debian.org/debian trixie/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 205 http://deb.debian.org/debian trixie/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 206 http://deb.debian.org/debian trixie/main amd64 liburi-perl all 5.28-1 [98.6 kB] Get: 207 http://deb.debian.org/debian trixie/main amd64 libhtml-parser-perl amd64 3.82-1 [98.9 kB] Get: 208 http://deb.debian.org/debian trixie/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 209 http://deb.debian.org/debian trixie/main amd64 libclone-perl amd64 0.46-1+b2 [13.7 kB] Get: 210 http://deb.debian.org/debian trixie/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 211 http://deb.debian.org/debian trixie/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 212 http://deb.debian.org/debian trixie/main amd64 libhttp-message-perl all 6.45-1 [82.0 kB] Get: 213 http://deb.debian.org/debian trixie/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 214 http://deb.debian.org/debian trixie/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 215 http://deb.debian.org/debian trixie/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get: 216 http://deb.debian.org/debian trixie/main amd64 libnet-ssleay-perl amd64 1.94-1+b1 [339 kB] Get: 217 http://deb.debian.org/debian trixie/main amd64 libio-socket-ssl-perl all 2.085-1 [218 kB] Get: 218 http://deb.debian.org/debian trixie/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 219 http://deb.debian.org/debian trixie/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 220 http://deb.debian.org/debian trixie/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 221 http://deb.debian.org/debian trixie/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 222 http://deb.debian.org/debian trixie/main amd64 libwww-perl all 6.77-1 [183 kB] Get: 223 http://deb.debian.org/debian trixie/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get: 224 http://deb.debian.org/debian trixie/main amd64 wdiff amd64 1.2.2-6 [119 kB] Get: 225 http://deb.debian.org/debian trixie/main amd64 devscripts all 2.23.7 [1068 kB] Get: 226 http://deb.debian.org/debian trixie/main amd64 fastjar amd64 2:0.98-7 [80.1 kB] Get: 227 http://deb.debian.org/debian trixie/main amd64 jarwrapper all 0.79 [10.1 kB] Get: 228 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get: 229 http://deb.debian.org/debian trixie/main amd64 java-wrappers all 0.4 [8916 B] Get: 230 http://deb.debian.org/debian trixie/main amd64 javahelper all 0.79 [84.6 kB] Get: 231 http://deb.debian.org/debian trixie/main amd64 libhamcrest-java all 2.2-2 [121 kB] Get: 232 http://deb.debian.org/debian trixie/main amd64 junit4 all 4.13.2-4 [349 kB] Get: 233 http://deb.debian.org/debian trixie/main amd64 libapiguardian-java all 1.1.2-1 [4656 B] Get: 234 http://deb.debian.org/debian trixie/main amd64 libopentest4j-java all 1.2.0-4 [9516 B] Get: 235 http://deb.debian.org/debian trixie/main amd64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 236 http://deb.debian.org/debian trixie/main amd64 libpicocli-java all 4.6.2-2 [390 kB] Get: 237 http://deb.debian.org/debian trixie/main amd64 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 238 http://deb.debian.org/debian trixie/main amd64 junit5 all 5.10.1-1 [2458 kB] Get: 239 http://deb.debian.org/debian trixie/main amd64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 240 http://deb.debian.org/debian trixie/main amd64 libaopalliance-java all 20070526-7 [8572 B] Get: 241 http://deb.debian.org/debian trixie/main amd64 libapache-pom-java all 29-2 [5276 B] Get: 242 http://deb.debian.org/debian trixie/main amd64 libasm-java all 9.7-1 [394 kB] Get: 243 http://deb.debian.org/debian trixie/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 244 http://deb.debian.org/debian trixie/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 245 http://deb.debian.org/debian trixie/main amd64 libcommons-lang3-java all 3.14.0-1 [621 kB] Get: 246 http://deb.debian.org/debian trixie/main amd64 libfreemarker-java all 2.3.32-2 [1546 kB] Get: 247 http://deb.debian.org/debian trixie/main amd64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 248 http://deb.debian.org/debian trixie/main amd64 libjoptsimple-java all 5.0.4-4 [73.1 kB] Get: 249 http://deb.debian.org/debian trixie/main amd64 libcommons-codec-java all 1.16.0-1 [297 kB] Get: 250 http://deb.debian.org/debian trixie/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 251 http://deb.debian.org/debian trixie/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 252 http://deb.debian.org/debian trixie/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 253 http://deb.debian.org/debian trixie/main amd64 liblightcouch-java all 0.2.0-1 [75.0 kB] Get: 254 http://deb.debian.org/debian trixie/main amd64 libmongodb-java all 3.6.3-2 [1901 kB] Get: 255 http://deb.debian.org/debian trixie/main amd64 libslf4j-java all 1.7.32-1 [144 kB] Get: 256 http://deb.debian.org/debian trixie/main amd64 liblog4j2-java all 2.19.0-2 [2310 kB] Get: 257 http://deb.debian.org/debian trixie/main amd64 libbarclay-java all 5.0.0+dfsg-1 [108 kB] Get: 258 http://deb.debian.org/debian trixie/main amd64 libjaxp1.3-java all 1.3.05-6 [227 kB] Get: 259 http://deb.debian.org/debian trixie/main amd64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 260 http://deb.debian.org/debian trixie/main amd64 libcommons-io-java all 2.16.1-1 [480 kB] Get: 261 http://deb.debian.org/debian trixie/main amd64 libxmlgraphics-commons-java all 2.8-2 [623 kB] Get: 262 http://deb.debian.org/debian trixie/main amd64 libbatik-java all 1.17+dfsg-1 [3923 kB] Get: 263 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get: 264 http://deb.debian.org/debian trixie/main amd64 libbsh-java all 2.0b4-20 [291 kB] Get: 265 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-utils-java all 3.3.4-1 [138 kB] Get: 266 http://deb.debian.org/debian trixie/main amd64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 267 http://deb.debian.org/debian trixie/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 268 http://deb.debian.org/debian trixie/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 269 http://deb.debian.org/debian trixie/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 270 http://deb.debian.org/debian trixie/main amd64 libguava-java all 32.0.1-1 [2708 kB] Get: 271 http://deb.debian.org/debian trixie/main amd64 libguice-java all 4.2.3-2 [1435 kB] Get: 272 http://deb.debian.org/debian trixie/main amd64 libmaven-parent-java all 35-1 [6140 B] Get: 273 http://deb.debian.org/debian trixie/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 274 http://deb.debian.org/debian trixie/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 275 http://deb.debian.org/debian trixie/main amd64 libmaven-resolver-java all 1.6.3-1 [548 kB] Get: 276 http://deb.debian.org/debian trixie/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 277 http://deb.debian.org/debian trixie/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 278 http://deb.debian.org/debian trixie/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 279 http://deb.debian.org/debian trixie/main amd64 libplexus-interpolation-java all 1.26-1 [76.8 kB] Get: 280 http://deb.debian.org/debian trixie/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 281 http://deb.debian.org/debian trixie/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 282 http://deb.debian.org/debian trixie/main amd64 libcdi-api-java all 1.2-3 [54.3 kB] Get: 283 http://deb.debian.org/debian trixie/main amd64 libsisu-inject-java all 0.3.4-2 [347 kB] Get: 284 http://deb.debian.org/debian trixie/main amd64 libsisu-plexus-java all 0.3.4-3 [181 kB] Get: 285 http://deb.debian.org/debian trixie/main amd64 libmaven3-core-java all 3.8.7-2 [1573 kB] Get: 286 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 287 http://deb.debian.org/debian trixie/main amd64 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 288 http://deb.debian.org/debian trixie/main amd64 libbuild-helper-maven-plugin-java all 3.3.0-1 [59.5 kB] Get: 289 http://deb.debian.org/debian trixie/main amd64 libbyte-buddy-java all 1.14.13-1 [4709 kB] Get: 290 http://deb.debian.org/debian trixie/main amd64 libcolt-free-java all 1.2.0+dfsg-8 [440 kB] Get: 291 http://deb.debian.org/debian trixie/main amd64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 292 http://deb.debian.org/debian trixie/main amd64 libcommons-beanutils-java all 1.9.4-2 [233 kB] Get: 293 http://deb.debian.org/debian trixie/main amd64 libcommons-collections4-java all 4.4-2 [682 kB] Get: 294 http://deb.debian.org/debian trixie/main amd64 libcommons-compress-java all 1.25.0-1 [635 kB] Get: 295 http://deb.debian.org/debian trixie/main amd64 libcommons-lang-java all 2.6-10 [273 kB] Get: 296 http://deb.debian.org/debian trixie/main amd64 libcommons-configuration-java all 1.10-6 [347 kB] Get: 297 http://deb.debian.org/debian trixie/main amd64 libcommons-digester-java all 1.8.1-6 [137 kB] Get: 298 http://deb.debian.org/debian trixie/main amd64 libcommons-exec-java all 1.3-2 [48.1 kB] Get: 299 http://deb.debian.org/debian trixie/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get: 300 http://deb.debian.org/debian trixie/main amd64 libcommons-math-java all 2.2-8 [926 kB] Get: 301 http://deb.debian.org/debian trixie/main amd64 libcommons-math3-java all 3.6.1-3 [2018 kB] Get: 302 http://deb.debian.org/debian trixie/main amd64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 303 http://deb.debian.org/debian trixie/main amd64 libsnappy1v5 amd64 1.2.0-2 [29.0 kB] Get: 304 http://deb.debian.org/debian trixie/main amd64 libsnappy-jni amd64 1.1.10.5-2 [6396 B] Get: 305 http://deb.debian.org/debian trixie/main amd64 libsnappy-java all 1.1.10.5-2 [87.5 kB] Get: 306 http://deb.debian.org/debian trixie/main amd64 libxz-java all 1.9-1 [143 kB] Get: 307 http://deb.debian.org/debian trixie/main amd64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 308 http://deb.debian.org/debian trixie/main amd64 libmaven-archiver-java all 3.6.0-1 [25.1 kB] Get: 309 http://deb.debian.org/debian trixie/main amd64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 310 http://deb.debian.org/debian trixie/main amd64 libcommons-text-java all 1.11.0-1 [217 kB] Get: 311 http://deb.debian.org/debian trixie/main amd64 libcommons-validator-java all 1:1.7-1 [181 kB] Get: 312 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 313 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 314 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 315 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 316 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.7.1-3 [441 kB] Get: 317 http://deb.debian.org/debian trixie/main amd64 libdistlib-java all 1.0-4 [72.1 kB] Get: 318 http://deb.debian.org/debian trixie/main amd64 libjaxen-java all 1.1.6-4 [214 kB] Get: 319 http://deb.debian.org/debian trixie/main amd64 libdom4j-java all 2.1.4-1 [312 kB] Get: 320 http://deb.debian.org/debian trixie/main amd64 libdoxia-core-java all 1.12.0-1 [213 kB] Get: 321 http://deb.debian.org/debian trixie/main amd64 libfontbox2-java all 2.0.29-1 [1510 kB] Get: 322 http://deb.debian.org/debian trixie/main amd64 libqdox-java all 1.12.1-3 [172 kB] Get: 323 http://deb.debian.org/debian trixie/main amd64 libfop-java all 1:2.8-3 [10.1 MB] Get: 324 http://deb.debian.org/debian trixie/main amd64 libitext1-java all 1.4-7 [1257 kB] Get: 325 http://deb.debian.org/debian trixie/main amd64 libxbean-reflect-java all 4.5-8 [133 kB] Get: 326 http://deb.debian.org/debian trixie/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 327 http://deb.debian.org/debian trixie/main amd64 libdoxia-java all 1.12.0-1 [459 kB] Get: 328 http://deb.debian.org/debian trixie/main amd64 libmaven-reporting-api-java all 3.1.1-1 [7240 B] Get: 329 http://deb.debian.org/debian trixie/main amd64 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB] Get: 330 http://deb.debian.org/debian trixie/main amd64 velocity all 1.7-7 [431 kB] Get: 331 http://deb.debian.org/debian trixie/main amd64 libplexus-velocity-java all 1.2-3.1 [10.5 kB] Get: 332 http://deb.debian.org/debian trixie/main amd64 liboro-java all 2.0.8a-14 [70.5 kB] Get: 333 http://deb.debian.org/debian trixie/main amd64 libvelocity-tools-java all 2.0-9 [311 kB] Get: 334 http://deb.debian.org/debian trixie/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 335 http://deb.debian.org/debian trixie/main amd64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 336 http://deb.debian.org/debian trixie/main amd64 libxalan2-java all 2.7.2-4 [3419 kB] Get: 337 http://deb.debian.org/debian trixie/main amd64 libdoxia-sitetools-java all 1.11.1-1 [202 kB] Get: 338 http://deb.debian.org/debian trixie/main amd64 libfastutil-java all 8.5.12+dfsg-1 [19.6 MB] Get: 339 http://deb.debian.org/debian trixie/main amd64 libxpp3-java all 1.1.4c-3 [292 kB] Get: 340 http://deb.debian.org/debian trixie/main amd64 libxstream-java all 1.4.20-1 [565 kB] Get: 341 http://deb.debian.org/debian trixie/main amd64 libjsap-java all 2.1-5 [102 kB] Get: 342 http://deb.debian.org/debian trixie/main amd64 liblogback-java all 1:1.2.11-5 [701 kB] Get: 343 http://deb.debian.org/debian trixie/main amd64 libdsiutils-java all 2.7.3+dfsg-1 [524 kB] Get: 344 http://deb.debian.org/debian trixie/main amd64 libobjenesis-java all 3.3-3 [41.3 kB] Get: 345 http://deb.debian.org/debian trixie/main amd64 libeasymock-java all 5.2.0-1 [131 kB] Get: 346 http://deb.debian.org/debian trixie/main amd64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 347 http://deb.debian.org/debian trixie/main amd64 libexec-maven-plugin-java all 3.1.0-2 [66.7 kB] Get: 348 http://deb.debian.org/debian trixie/main amd64 libgatk-native-bindings-java all 1.0.0+dfsg-2 [8024 B] Get: 349 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14-20240330-1 [836 kB] Get: 350 http://deb.debian.org/debian trixie/main amd64 libmjson-java all 1.4.0-3 [60.4 kB] Get: 351 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB] Get: 352 http://deb.debian.org/debian trixie/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB] Get: 353 http://deb.debian.org/debian trixie/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB] Get: 354 http://deb.debian.org/debian trixie/main amd64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB] Get: 355 http://deb.debian.org/debian trixie/main amd64 libncbi-vdb3 amd64 3.0.2+dfsg-2+b1 [1049 kB] Get: 356 http://deb.debian.org/debian trixie/main amd64 libncbi-ngs3 amd64 3.0.3+dfsg-6+b1 [155 kB] Get: 357 http://deb.debian.org/debian trixie/main amd64 libngs-jni amd64 3.0.3+dfsg-6+b1 [23.7 kB] Get: 358 http://deb.debian.org/debian trixie/main amd64 libngs-java amd64 3.0.3+dfsg-6+b1 [111 kB] Get: 359 http://deb.debian.org/debian trixie/main amd64 librhino-java all 1.7.14-2.1 [1357 kB] Get: 360 http://deb.debian.org/debian trixie/main amd64 libhtsjdk-java all 4.1.0+dfsg-1 [1833 kB] Get: 361 http://deb.debian.org/debian trixie/main amd64 libgkl-java all 0.8.11+dfsg-2 [24.7 kB] Get: 362 http://deb.debian.org/debian trixie/main amd64 libicu4j-java all 73.2-1 [16.4 MB] Get: 363 http://deb.debian.org/debian trixie/main amd64 liblog4j1.2-java all 1.2.17-11 [444 kB] Get: 364 http://deb.debian.org/debian trixie/main amd64 libicb-utils-java all 2.0.1+git20161002.afee1d9-5 [81.5 kB] Get: 365 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.0.10-1+b1 [56.7 kB] Get: 366 http://deb.debian.org/debian trixie/main amd64 libjansi-java all 2.4.1-2 [100 kB] Get: 367 http://deb.debian.org/debian trixie/main amd64 libjavassist-java all 1:3.27.0-1 [731 kB] Get: 368 http://deb.debian.org/debian trixie/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 369 http://deb.debian.org/debian trixie/main amd64 libjboss-logging-java all 3.5.3-1 [56.2 kB] Get: 370 http://deb.debian.org/debian trixie/main amd64 libjboss-vfs-java all 3.2.15.Final-3 [130 kB] Get: 371 http://deb.debian.org/debian trixie/main amd64 libjbzip2-java all 0.9.1-8 [42.7 kB] Get: 372 http://deb.debian.org/debian trixie/main amd64 libjcommander-java all 1.71-4 [73.0 kB] Get: 373 http://deb.debian.org/debian trixie/main amd64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 374 http://deb.debian.org/debian trixie/main amd64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 375 http://deb.debian.org/debian trixie/main amd64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 376 http://deb.debian.org/debian trixie/main amd64 libjetty9-java all 9.4.54-1 [2980 kB] Get: 377 http://deb.debian.org/debian trixie/main amd64 libjsoup-java all 1.15.3-1 [431 kB] Get: 378 http://deb.debian.org/debian trixie/main amd64 libjtidy-java all 7+svn20110807-5 [250 kB] Get: 379 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 380 http://deb.debian.org/debian trixie/main amd64 libmaven-antrun-plugin-java all 3.1.0-1 [36.9 kB] Get: 381 http://deb.debian.org/debian trixie/main amd64 libmaven-common-artifact-filters-java all 3.3.2-1 [48.2 kB] Get: 382 http://deb.debian.org/debian trixie/main amd64 libmaven-artifact-transfer-java all 0.13.1-2 [158 kB] Get: 383 http://deb.debian.org/debian trixie/main amd64 libplexus-build-api-java all 0.0.7-4 [10.3 kB] Get: 384 http://deb.debian.org/debian trixie/main amd64 libmaven-filtering-java all 3.3.0-1 [50.2 kB] Get: 385 http://deb.debian.org/debian trixie/main amd64 libmaven-assembly-plugin-java all 3.4.2-1 [242 kB] Get: 386 http://deb.debian.org/debian trixie/main amd64 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB] Get: 387 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-incremental-java all 1.1-4 [9924 B] Get: 388 http://deb.debian.org/debian trixie/main amd64 libplexus-compiler-java all 2.12.1-2 [99.0 kB] Get: 389 http://deb.debian.org/debian trixie/main amd64 libqdox2-java all 2.0.3-1 [296 kB] Get: 390 http://deb.debian.org/debian trixie/main amd64 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 391 http://deb.debian.org/debian trixie/main amd64 libmaven-compiler-plugin-java all 3.10.1-2 [59.0 kB] Get: 392 http://deb.debian.org/debian trixie/main amd64 libmaven-dependency-analyzer-java all 1.13.0-1 [30.4 kB] Get: 393 http://deb.debian.org/debian trixie/main amd64 libmaven-dependency-tree-java all 3.2.1-1 [34.7 kB] Get: 394 http://deb.debian.org/debian trixie/main amd64 libmaven-reporting-impl-java all 3.2.0-2 [15.2 kB] Get: 395 http://deb.debian.org/debian trixie/main amd64 libmaven-dependency-plugin-java all 3.5.0-1 [173 kB] Get: 396 http://deb.debian.org/debian trixie/main amd64 libmaven-invoker-java all 3.2.0-1 [28.1 kB] Get: 397 http://deb.debian.org/debian trixie/main amd64 libplexus-interactivity-api-java all 1.1-2 [11.0 kB] Get: 398 http://deb.debian.org/debian trixie/main amd64 libmaven-javadoc-plugin-java all 3.4.1-3 [454 kB] Get: 399 http://deb.debian.org/debian trixie/main amd64 libplexus-container-default1.5-java all 2.1.1-1 [4476 B] Get: 400 http://deb.debian.org/debian trixie/main amd64 libplexus-ant-factory-java all 1.0~alpha2.1-4 [11.4 kB] Get: 401 http://deb.debian.org/debian trixie/main amd64 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B] Get: 402 http://deb.debian.org/debian trixie/main amd64 libmaven-plugin-tools-java all 3.7.1-1 [265 kB] Get: 403 http://deb.debian.org/debian trixie/main amd64 libmaven-reporting-exec-java all 1.6.0-1 [26.8 kB] Get: 404 http://deb.debian.org/debian trixie/main amd64 libmaven-resources-plugin-java all 3.3.0-1 [28.4 kB] Get: 405 http://deb.debian.org/debian trixie/main amd64 libmaven-site-plugin-java all 3.12.1-2 [107 kB] Get: 406 http://deb.debian.org/debian trixie/main amd64 libmaven-source-plugin-java all 3.2.1-2 [27.6 kB] Get: 407 http://deb.debian.org/debian trixie/main amd64 libpaper1 amd64 1.1.29+b1 [12.9 kB] Get: 408 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 1.1.29+b1 [9176 B] Get: 409 http://deb.debian.org/debian trixie/main amd64 libpicard-java all 3.1.1+dfsg-1 [1743 kB] Get: 410 http://deb.debian.org/debian trixie/main amd64 libpj-java all 0.0~20150107+dfsg-5 [1389 kB] Get: 411 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-1+b2 [36.4 kB] Get: 412 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Get: 413 http://deb.debian.org/debian trixie/main amd64 libprotobuf32t64 amd64 3.21.12-8.2 [963 kB] Get: 414 http://deb.debian.org/debian trixie/main amd64 libprotobuf-lite32t64 amd64 3.21.12-8.2 [273 kB] Get: 415 http://deb.debian.org/debian trixie/main amd64 libprotobuf-dev amd64 3.21.12-8.2 [1306 kB] Get: 416 http://deb.debian.org/debian trixie/main amd64 libprotobuf-java all 3.21.12-8.2 [1260 kB] Get: 417 http://deb.debian.org/debian trixie/main amd64 libprotoc32t64 amd64 3.21.12-8.2 [864 kB] Get: 418 http://deb.debian.org/debian trixie/main amd64 libreflections-java all 0.10.2+dfsg-2 [125 kB] Get: 419 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.3-1+b1 [33.6 kB] Get: 420 http://deb.debian.org/debian trixie/main amd64 libsurefire-java all 2.22.3-2 [1169 kB] Get: 421 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1 [1034 kB] Get: 422 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 423 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get: 424 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get: 425 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b1 [17.0 kB] Get: 426 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.14-1 [784 kB] Get: 427 http://deb.debian.org/debian trixie/main amd64 libwagon-file-java all 3.5.3-1 [8388 B] Get: 428 http://deb.debian.org/debian trixie/main amd64 libwagon-http-shaded-java all 3.5.3-1 [1341 kB] Get: 429 http://deb.debian.org/debian trixie/main amd64 libxml2-utils amd64 2.9.14+dfsg-1.3+b3 [99.0 kB] Get: 430 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get: 431 http://deb.debian.org/debian trixie/main amd64 maven all 3.8.7-2 [19.3 kB] Get: 432 http://deb.debian.org/debian trixie/main amd64 maven-repo-helper all 1.11 [142 kB] Get: 433 http://deb.debian.org/debian trixie/main amd64 maven-debian-helper all 2.6.4 [108 kB] Get: 434 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-1+b2 [29.7 kB] Get: 435 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-1+b2 [26.2 kB] Get: 436 http://deb.debian.org/debian trixie/main amd64 pkg-config amd64 1.8.1-1+b2 [14.0 kB] Get: 437 http://deb.debian.org/debian trixie/main amd64 protobuf-compiler amd64 3.21.12-8.2 [84.4 kB] Get: 438 http://deb.debian.org/debian trixie/main amd64 zip amd64 3.0-13 [230 kB] Get: 439 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 440 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.3.2-1 [26.8 MB] Get: 441 http://deb.debian.org/debian trixie/main amd64 r-cran-rjava amd64 1.0-11-1 [702 kB] Get: 442 http://deb.debian.org/debian trixie/main amd64 testng all 6.9.12-4 [795 kB] Fetched 379 MB in 10s (38.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1: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 ... 19698 files and directories currently installed.) Preparing to unpack .../libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package binfmt-support. Preparing to unpack .../binfmt-support_2.2.2-7_amd64.deb ... Unpacking binfmt-support (2.2.2-7) ... Selecting previously unselected package libpython3.11-minimal:amd64. 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(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 ... 20037 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up libgoogle-gson-java (2.10.1-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libmjson-java (1.4.0-3) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up unzip (6.0-28) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:amd64 (1.1.0-2+b3) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libpicocli-java (4.6.2-2) ... Setting up libasm-java (9.7-1) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libtry-tiny-perl (0.31-2) ... Setting up libsensors-config (1:3.6.0-9) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.61.0-1+b1) ... Setting up libdeflate0:amd64 (1.20-1) ... Setting up perl-openssl-defaults:amd64 (7+b2) ... Setting up liblog4j1.2-java (1.2.17-11) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libel-api-java (3.0.0-3) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libplexus-component-annotations-java (2.1.1-1) ... Setting up libcom-err2:amd64 (1.47.1~rc2-1) ... Setting up file (1:5.45-3) ... Setting up libjboss-logging-java (3.5.3-1) ... Setting up libassuan0:amd64 (2.5.6-1+b1) ... Setting up libunivocity-parsers-java (2.9.1-1) ... Setting up libjbig0:amd64 (2.1-6.1+b1) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up liboro-java (2.0.8a-14) ... Setting up libsnappy1v5:amd64 (1.2.0-2) ... Setting up libkrb5support0:amd64 (1.20.1-6+b1) ... Setting up libexec-maven-plugin-java (3.1.0-2) ... Setting up libfontbox2-java (2.0.29-1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Jun 9 13:37:43 UTC 2025. Universal Time is now: Mon Jun 9 13:37:43 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... Setting up libgeronimo-interceptor-3.0-spec-java (1.0.1-4) ... Setting up libcommons-collections3-java (3.2.2-3) ... Setting up libasound2-data (1.2.11-1) ... Setting up libjavassist-java (1:3.27.0-1) ... Setting up zip (3.0-13) ... Setting up librhino-java (1.7.14-2.1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.8.12-3.1+b2) ... Setting up libglib2.0-0t64:amd64 (2.78.4-7) ... No schema files found: doing nothing. Setting up libblas3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libpkgconf3:amd64 (1.8.1-1+b2) ... Setting up libasound2t64:amd64 (1.2.11-1+b1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3) ... Setting up libjaxen-java (1.1.6-4) ... Setting up libapiguardian-java (1.1.2-1) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libnspr4:amd64 (2:4.35-1.1+b1) ... Setting up gnupg-l10n (2.2.40-3) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libjtidy-java (7+svn20110807-5) ... Setting up libjansi-java (2.4.1-2) ... Setting up libapache-pom-java (29-2) ... Setting up libavahi-common-data:amd64 (0.8-13+b2) ... Setting up libxpp3-java (1.1.4c-3) ... Setting up libatinject-jsr330-api-java (1.0+ds1-5) ... Setting up libdbus-1-3:amd64 (1.14.10-4+b1) ... Setting up libwebsocket-api-java (1.1-2) ... Setting up libfribidi0:amd64 (1.0.13-3+b1) ... Setting up libproc2-0:amd64 (2:4.0.4-4) ... Setting up libplexus-interpolation-java (1.26-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.43-5) ... Setting up libxml-commons-resolver1.1-java (1.2-11) ... Setting up libxz-java (1.9-1) ... Setting up libitext1-java (1.4-7) ... Setting up libio-html-perl (1.004-3) ... Setting up libtcl8.6:amd64 (8.6.14+dfsg-1) ... Setting up autopoint (0.21-14) ... Setting up binfmt-support (2.2.2-7) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libb-hooks-op-check-perl:amd64 (0.22-3+b1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libjbzip2-java (0.9.1-8) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up libpcsclite1:amd64 (2.0.3-1) ... Setting up pkgconf-bin (1.8.1-1+b2) ... Setting up libsensors5:amd64 (1:3.6.0-9) ... Setting up libmongodb-java (3.6.3-2) ... Setting up libk5crypto3:amd64 (1.20.1-6+b1) ... Setting up libactivation-java (1.2.0-2) ... Setting up libhamcrest-java (2.2-2) ... Setting up libglapi-mesa:amd64 (23.3.5-1) ... Setting up libbsh-java (2.0b4-20) ... Setting up libjsp-api-java (2.3.4-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Setting up libgfortran5:amd64 (14-20240330-1) ... Setting up libvulkan1:amd64 (1.3.280.0-1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:amd64 (1.3.2-0.4+b1) ... Setting up libcolt-free-java (1.2.0+dfsg-8) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libgif7:amd64 (5.2.2-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up libfreemarker-java (2.3.32-2) ... Setting up sensible-utils (0.0.22) ... Setting up libxshmfence1:amd64 (1.3-1+b1) ... Setting up libjsoup-java (1.15.3-1) ... Setting up at-spi2-common (2.52.0-1) ... Setting up libcommons-math-java (2.2-8) ... Setting up libtiff6:amd64 (4.5.1+git230720-4) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libxml-commons-external-java (1.4.01-6) ... Setting up procps (2:4.0.4-4) ... Setting up libxbean-reflect-java (4.5-8) ... Setting up libservlet-api-java (4.0.1-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libopentest4j-java (1.2.0-4) ... Setting up libsub-override-perl (0.10-1) ... Setting up ncbi-vdb-data (3.0.2+dfsg-2) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up libcommons-math3-java (3.6.1-3) ... Setting up sgml-base (1.31) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b3) ... Setting up libgtk2.0-common (2.24.33-4) ... Setting up libkrb5-3:amd64 (1.20.1-6+b1) ... Setting up libwagon-http-shaded-java (3.5.3-1) ... Setting up libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Setting up libhttpcore-java (4.4.16-1) ... Setting up libjoptsimple-java (5.0.4-4) ... Setting up libprotoc32t64:amd64 (3.21.12-8.2) ... Setting up libxerces2-java (2.12.2-1) ... Setting up libfile-dirlist-perl (0.05-3) ... 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 (3.2.1-3) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up libdrm-common (2.4.120-2) ... Setting up libcdi-api-java (1.2-3) ... Setting up libsnappy-jni (1.1.10.5-2) ... Setting up readline-common (8.2-4) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... 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 (5.28-1) ... Setting up libfile-touch-perl (0.12-2) ... Setting up dctrl-tools (2.24-3+b1) ... 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 (1.2.1-3+b2) ... Setting up libdom4j-java (2.1.4-1) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libwagon-provider-api-java (3.5.3-1) ... 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 libxdmcp6:amd64 (1:1.1.2-3+b1) ... 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 libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-14+b1) ... Setting up libmbedx509-1t64:amd64 (2.28.8-1) ... Setting up libjetty9-java (9.4.54-1) ... Setting up libxcb-xfixes0:amd64 (1.15-1) ... Setting up java-wrappers (0.4) ... Setting up libatk1.0-0t64:amd64 (2.52.0-1) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libplexus-languages-java (1.1.1-2) ... Setting up protobuf-compiler (3.21.12-8.2) ... Setting up libjboss-vfs-java (3.2.15.Final-3) ... Setting up jarwrapper (0.79) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libxcb-glx0:amd64 (1.15-1) ... Setting up libmaven-parent-java (35-1) ... Setting up libedit2:amd64 (3.1-20230828-1+b1) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-13+b2) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libnet-http-perl (6.23-1) ... Setting up libsisu-inject-java (0.3.4-2) ... Setting up libnss3:amd64 (2:3.99-1) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libdevel-callchecker-perl:amd64 (0.009-1) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up pkgconf:amd64 (1.8.1-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libprotobuf-dev:amd64 (3.21.12-8.2) ... Setting up libxcb-present0:amd64 (1.15-1) ... 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 libllvm17t64:amd64 (1:17.0.6-11) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Setting up libxcb-sync1:amd64 (1.15-1) ... Setting up libxalan2-java (2.7.2-4) ... Setting up testng (6.9.12-4) ... Setting up shared-mime-info (2.4-4) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up libcommons-collections4-java (4.4-2) ... Setting up pkg-config:amd64 (1.8.1-1+b2) ... Setting up ucf (3.0043+nmu1) ... Setting up libcommons-lang3-java (3.14.0-1) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up libxcb-dri2-0:amd64 (1.15-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libdrm2:amd64 (2.4.120-2) ... Setting up libmaven-common-artifact-filters-java (3.3.2-1) ... Setting up libmbedtls14t64:amd64 (2.28.8-1) ... Setting up groff-base (1.23.0-4) ... Setting up libxcb-randr0:amd64 (1.15-1) ... Setting up libhtml-parser-perl:amd64 (3.82-1) ... Setting up gpgconf (2.2.40-3) ... Setting up libcommons-beanutils-java (1.9.4-2) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2+b1) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-3+b3) ... Setting up libsnappy-java (1.1.10.5-2) ... 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 (2.9.14+dfsg-1.3+b3) ... Setting up libcommons-codec-java (1.16.0-1) ... Setting up libxcomposite1:amd64 (1:0.4.5-1+b1) ... 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 (2.085-1) ... Setting up gpg (2.2.40-3) ... Setting up gnupg-utils (2.2.40-3) ... Setting up libhttp-message-perl (6.45-1) ... Setting up libdrm-amdgpu1:amd64 (2.4.120-2) ... Setting up libxcb-dri3-0:amd64 (1.15-1) ... Setting up libpaper1:amd64 (1.1.29+b1) ... Creating config file /etc/papersize with new version Setting up gtk-update-icon-cache (3.24.41-4) ... Setting up libx11-xcb1:amd64 (2:1.8.7-1+b1) ... 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 libdrm-nouveau2:amd64 (2.4.120-2) ... Setting up libxdamage1:amd64 (1:1.1.6-1+b1) ... Setting up gpg-agent (2.2.40-3) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up libcommons-compress-java (1.25.0-1) ... Setting up libcurl4t64:amd64 (8.7.1-3) ... 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 (2.4.120-2) ... Setting up libcommons-digester-java (1.8.1-6) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up libdistlib-java (1.0-4) ... Setting up libparams-classify-perl:amd64 (0.015-2+b3) ... Setting up gpgsm (2.2.40-3) ... Setting up libpango-1.0-0:amd64 (1.52.1+ds-1) ... Setting up libdrm-intel1:amd64 (2.4.120-2) ... Setting up libgl1-mesa-dri:amd64 (23.3.5-1) ... Setting up libncbi-vdb3:amd64 (3.0.2+dfsg-2+b1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libxmlgraphics-commons-java (2.8-2) ... Setting up libpaper-utils (1.1.29+b1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.18.0-3+b1) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up dirmngr (2.2.40-3) ... Setting up libmaven-filtering-java (3.3.0-1) ... Setting up libmaven-resolver-java (1.6.3-1) ... Setting up adwaita-icon-theme (46.0-1) ... 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 libxfixes3:amd64 (1:6.0.0-2+b1) ... Setting up libxinerama1:amd64 (2:1.1.4-3+b1) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2) ... Setting up libxrandr2:amd64 (2:1.5.4-1) ... Setting up openjdk-17-jre-headless:amd64 (17.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up gpg-wks-server (2.2.40-3) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up libmaven-dependency-tree-java (3.2.1-1) ... Setting up liblightcouch-java (0.2.0-1) ... Setting up libmaven-shared-utils-java (3.3.4-1) ... Setting up libxss1:amd64 (1:1.2.3-1+b1) ... Setting up libpangoft2-1.0-0:amd64 (1.52.1+ds-1) ... Setting up libmaven-resources-plugin-java (3.3.0-1) ... Setting up libcups2t64:amd64 (2.4.7-1.2+b1) ... Setting up libpangocairo-1.0-0:amd64 (1.52.1+ds-1) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up libncbi-ngs3:amd64 (3.0.3+dfsg-6+b1) ... Setting up python3.11 (3.11.9-1) ... Setting up libngs-jni:amd64 (3.0.3+dfsg-6+b1) ... Setting up libxft2:amd64 (2.3.6-1+b1) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up libglx-mesa0:amd64 (23.3.5-1) ... Setting up libxi6:amd64 (2:1.8.1-1) ... Setting up gpg-wks-client (2.2.40-3) ... Setting up libglx0:amd64 (1.7.0-1+b1) ... Setting up libcommons-validator-java (1:1.7-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libxtst6:amd64 (2:1.2.3-1.1+b1) ... 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 libtk8.6:amd64 (8.6.14-1) ... Setting up libxcursor1:amd64 (1:1.2.1-1+b1) ... Setting up libmaven-invoker-java (3.2.0-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up libgl1:amd64 (1.7.0-1+b1) ... Setting up r-base-core (4.3.2-1) ... Creating config file /etc/R/Renviron with new version Setting up libgtk2.0-0t64:amd64 (2.24.33-4) ... Setting up libmaven-clean-plugin-java (3.2.0-2) ... Setting up gnupg (2.2.40-3) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libngs-java:amd64 (3.0.3+dfsg-6+b1) ... Setting up libhtsjdk-java (4.1.0+dfsg-1) ... Setting up libbarclay-java (5.0.0+dfsg-1) ... Setting up libfop-java (1:2.8-3) ... Setting up libgkl-java (0.8.11+dfsg-2) ... Setting up libmaven-archiver-java (3.6.0-1) ... Setting up libpicard-java (3.1.1+dfsg-1) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libwww-perl (6.77-1) ... Setting up devscripts (2.23.7) ... Setting up libguava-java (32.0.1-1) ... Setting up javahelper (0.79) ... Setting up libprotobuf-java (3.21.12-8.2) ... Setting up libplexus-container-default-java (2.1.1-1) ... 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 (3.8.7-2) ... 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 libmaven-dependency-analyzer-java (1.13.0-1) ... Setting up libplexus-compiler-java (2.12.1-2) ... 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 (1.14.13-1) ... 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 (2.38-7) ... 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-repo-helper (1.11) ... Setting up maven (3.8.7-2) ... update-alternatives: using /usr/share/maven/bin/mvn to provide /usr/bin/mvn (mvn) in auto mode Setting up openjdk-17-jdk-headless:amd64 (17.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up ant (1.10.14-1) ... Setting up junit4 (4.13.2-4) ... Setting up default-jre-headless (2:1.17-75) ... Setting up ant-contrib (1.0~b3+svn177-12) ... Setting up openjdk-17-jre:amd64 (17.0.11+9-1) ... Setting up default-jre (2:1.17-75) ... Setting up openjdk-17-jdk:amd64 (17.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up libmaven-antrun-plugin-java (3.1.0-1) ... Setting up libplexus-ant-factory-java (1.0~alpha2.1-4) ... Setting up default-jdk-headless (2:1.17-75) ... 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 (5.10.1-1) ... Setting up default-jdk (2:1.17-75) ... 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+dfsg2-10_source.changes dpkg-buildpackage: info: source package libgoby-java dpkg-buildpackage: info: source version 3.3.1+dfsg2-10 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] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --------------------< org.campagnelab.goby:goby-io >-------------------- [INFO] Building Goby I/O 3.3.1 [2/3] [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:3.3.0 [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:3.3.0: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:3.3.0: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 org.campagnelab.goby.R... [WARNING] Loading source files for package org.campagnelab.goby.alignments... [WARNING] Loading source files for package org.campagnelab.goby.alignments.filters... [WARNING] Loading source files for package org.campagnelab.goby.alignments.htsjdk... [WARNING] Loading source files for package org.campagnelab.goby.alignments.processors... [WARNING] Loading source files for package org.campagnelab.goby.alignments.perms... [WARNING] Loading source files for package org.campagnelab.goby.baseinfo... [WARNING] Loading source files for package org.campagnelab.goby... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.algorithm... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.algorithm.dmr... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.indels... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data.xml... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data.ranges... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.compression... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.dsv... [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.barcode... [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.stats... [WARNING] Loading source files for package org.campagnelab.goby.modes... [WARNING] Loading source files for package org.campagnelab.goby.modes.formats... [WARNING] Loading source files for package org.campagnelab.goby.modes.core... [WARNING] Loading source files for package org.campagnelab.goby.modes.dsv... [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.readers... [WARNING] Loading source files for package org.campagnelab.goby.xml... [WARNING] Loading source files for package org.campagnelab.goby.predictions... [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.exception... [WARNING] Loading source files for package org.campagnelab.goby.cli... [WARNING] Loading source files for package org.campagnelab.goby.compression... [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.config... [WARNING] Loading source files for package org.campagnelab.goby.methylation... [WARNING] Loading source files for package samples... [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/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/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/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/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/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/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/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/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/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/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/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/PercentMismatchesQualityFilter.java:23: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:39: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.IntegerForLoop; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:40: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.ParallelRegion; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:41: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.ParallelTeam; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:53: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBContext; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:54: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBException; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:55: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.Marshaller; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:106: error: cannot find symbol [WARNING] private ParallelTeam team; [WARNING] ^ [WARNING] symbol: class ParallelTeam [WARNING] location: class CompactAlignmentToAnnotationCountsMode [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:325: error: cannot find symbol [WARNING] protected synchronized ParallelTeam getParallelTeam() { [WARNING] ^ [WARNING] symbol: class ParallelTeam [WARNING] location: class CompactAlignmentToAnnotationCountsMode [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/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/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/MethylStatsMode.java:34: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBContext; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:35: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBException; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:36: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.Marshaller; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/xml/MethylStats.java:21: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlRootElement; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/xml/MethylStats.java:31: error: cannot find symbol [WARNING] @XmlRootElement [WARNING] ^ [WARNING] symbol: class XmlRootElement [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:696: error: cannot find symbol [WARNING] private void writeXml(PrintWriter output, String[] samples, MethylStats[] methylStats) throws JAXBException { [WARNING] ^ [WARNING] symbol: class JAXBException [WARNING] location: class MethylStatsMode [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:30: error: package org.apache.commons.exec does not exist [WARNING] import org.apache.commons.exec.CommandLine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:31: error: package org.apache.commons.exec does not exist [WARNING] import org.apache.commons.exec.DefaultExecutor; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:32: error: package org.apache.commons.exec does not exist [WARNING] import org.apache.commons.exec.PumpStreamHandler; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/CompareGroupsVCFOutputFormat.java:42: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/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/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/FoldChangeForExonPairs.java:22: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/PlantIndels.java:22: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/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/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 17.0.11+9-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... 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylSimilarityScan.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationData.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/DifferentiallyMethylatedRegion.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationRegion.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/HitBoundedPriorityQueue.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSimilarityMatch.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSiteIterator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/class-use/ParseReadsCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/class-use/ParseAlignmentEntriesCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/class-use/ParseAlignmentEntriesWithIndexCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/class-use/IterateAlignmentsCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/class-use/ModifyAlignmentsCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.ReferencePosition.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.ReferencePosition.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.ReferencePositionOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.Base.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.Base.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.BaseOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.Sample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.Sample.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SampleOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformation.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformationOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformationCollection.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformationCollection.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformationCollectionOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SomaticOutput.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SomaticOutput.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SomaticOutputOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.NumberWithFrequency.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.NumberWithFrequency.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.NumberWithFrequencyOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.CountInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.CountInfo.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.CountInfoOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SampleInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SampleInfo.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SampleInfoOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformation.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformationOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformationCollection.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformationCollection.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformationCollectionOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/package-use.html... 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[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... 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[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/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] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0: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:3.3.0: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 org.campagnelab.goby.R... [WARNING] Loading source files for package org.campagnelab.goby.alignments... [WARNING] Loading source files for package org.campagnelab.goby.alignments.filters... [WARNING] Loading source files for package org.campagnelab.goby.alignments.htsjdk... [WARNING] Loading source files for package org.campagnelab.goby.alignments.processors... [WARNING] Loading source files for package org.campagnelab.goby.alignments.perms... [WARNING] Loading source files for package org.campagnelab.goby.baseinfo... [WARNING] Loading source files for package org.campagnelab.goby... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.algorithm... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.algorithm.dmr... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.indels... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data.xml... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data.ranges... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.compression... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.dsv... [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.barcode... [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.stats... [WARNING] Loading source files for package org.campagnelab.goby.modes... [WARNING] Loading source files for package org.campagnelab.goby.modes.formats... [WARNING] Loading source files for package org.campagnelab.goby.modes.core... [WARNING] Loading source files for package org.campagnelab.goby.modes.dsv... [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.readers... [WARNING] Loading source files for package org.campagnelab.goby.xml... [WARNING] Loading source files for package org.campagnelab.goby.predictions... [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.exception... [WARNING] Loading source files for package org.campagnelab.goby.cli... [WARNING] Loading source files for package org.campagnelab.goby.compression... [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.config... [WARNING] Loading source files for package org.campagnelab.goby.methylation... [WARNING] Loading source files for package samples... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.11+9-Debian-1 [WARNING] Building tree for all the packages and classes... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/AbstractAlignmentEntryFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AbstractAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AbstractAlignmentToCompactMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AbstractAlignmentToCompactMode.TransferIds.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AbstractCommandLineMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AbstractConcatAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AbstractGobyMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/AbstractMethylationAdapter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/AbstractOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/AddTrueGenotypeHelperI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/AddTrueGenotypeHelperI.WillKeepI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AggregatePeaksByPeakDistanceMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AggregatePeaksByRPKMDifferenceMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/AlignedCountNormalization.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignedSequence.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentCollectionHandler.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentCollectionHandler.CombinedLists.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/AlignmentHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentPositionComparator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/AlignmentProcessorFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/AlignmentProcessorInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/AlignmentQualityFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentReader.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderFactoryBase.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderImpl.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentSliceHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentStats.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentTooManyHitsReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentTooManyHitsWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AlignmentToPileupMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AlignmentToPileupMode.OutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AlignmentToTextMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentToTextWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentWriterImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/AlleleFrequencyOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Annotation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/AnnotationAveragingWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCountInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCountIterateAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AnnotationPenaltyMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/AnnotationRPKM.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AnnotationsToCountsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationWeightCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/AnyTransitionCountsIterator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ATGCCorrectionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/AtLeastAQuarterFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ATProportionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/AverageCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/AverageFisherRCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/BarcodeDecoderMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/BarcodeMatcher.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/BarcodeMatcherResult.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/BasenameUtils.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/BaseProportionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/BaseStatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/BaseToStringHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/BenjaminiHochbergAdjustment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/BestScoreAmbiguityAlignmentFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/BestScoreOnlyAlignmentFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/BetweenGroupSequenceVariationOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/BisulfiteConversionMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/BonferroniAdjustment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/BufferedSortingAlignmentWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/BufferedSortingSamBamWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/BuggyDeltaStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/BuildSequenceCacheMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/By5BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/BZip2ChunkCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CachingCountsArchiveReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/ChiSquareTestAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/ChiSquareTestCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/ChromosomeMapper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/ChunkCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/ChunkCodecHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/CodecHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ColorSpaceConverter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnField.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnFields.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnMetaInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/Columns.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnType.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/CommitPropertiesStatAccumulator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/commits/CommitPropertyHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/CommonIndelArtifactFilter.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/dsv/CommonIndelArtifactFilter.java:17: warning: invalid input: '<' [WARNING] * larger than expected (P<0.05, with Poisson cumulative distribution) from prior observations (most of them are assumed to be errors). [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToCountsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToReadSetMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToTranscriptCountsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactFileStatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactToFastaMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactToFastaMode.OutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactToSAMMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompareAlignmentToGenomeMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/CompareGroupsVCFOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDataInput.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDataOutput.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDirectoryEntry.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileTool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileTool.PROGRAM_MODE.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/CompressedRead.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeCountInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeStartCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeWeightCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ConcatAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ConcatenateAlignmentMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ConcatenateCompactReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/ConcatenatePermutations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ConcatSortedAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/ConstantAccumulator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/ConversionConfig.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/ConvertSamBAMReadToGobyAlignment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountAdaptiveBinningAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CountArchiveToPeakAnnotationsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountBinningAdapterI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountBinningAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/CountCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/CountFixer.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/CountFixerInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/CountFixerNoThresholdingEffect.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountIndexBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/CountRawSampleIdsCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsAggregatorI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsArchiveReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CountsArchiveToBedGraphMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CountsArchiveToUnionPeaksAnnotationMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CountsArchiveToWiggleMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsArchiveWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsReaderI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsWriter.html... 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[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... 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[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/HybridChunkCodec1.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/HybridChunkCodec2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/IndelCountOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/InferSexFromAlignmentsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/InfoForTarget.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/InformativeColumns.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/InformativeDouble.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/InformativeNonZeroNonNaN.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Interval.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/InvalidChecksumException.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/IOUtil.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/IsDone.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/IterateAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/IterateAlignmentsCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/IterateSortedAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/IterateSortedAlignmentsListImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/IterateSortedAlignmentsListImpl2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/IterateSortedAlignmentsListImpl2.PositionBaseInfo2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/IterateSortedAlignmentsToPileup.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/KnownIndelSet.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/LastParser.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/LastToCompactMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/LeftOverFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/LinearBinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/LocalSortProcessor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Log10BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Log2BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/Log2FoldChangeCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/LogGCCorrectionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/LoggingOutputStream.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/LogIsConfigured.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/LongNamedCounter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/MakeBisulfiteFastaExample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/MaxCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/MedianCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/Merge.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/MergeCompactAlignmentsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/MergeIndelFrom.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/MergeIndelFrom.SplitIndel.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/MessageChunksReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/MessageChunksWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationData.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/MethylationFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/MethylationRateDifferenceStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/MethylationRateVCFOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationRegion.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/MethylationRegionsOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationSimilarityMatch.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationSite.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationSiteIterator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/MethylCountInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/MethylCountProvider.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/MethylCountProviderFromRegionsOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/MethylCountProviderTestSupport.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/MethylRateInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylSimilarityScan.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/xml/MethylStats.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/MethylStatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/MinCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/ModifyAlignmentsCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/MotifMatcher.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/MoveToFrontCoder.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/MoveToFrontCoder.java:42: warning: invalid input: '<' [WARNING] * @param symbol Symbol to encode with move to front (precondition: 0<= symbol ?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/QualityEncoding.java:41: warning: invalid input: '<' [WARNING] * !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/QualityScoreFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/QueryIndexPermutation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/QueryIndexPermutationInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/QueueResettableObjectPool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/RandomAccessAnnotations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/RandomAccessSequenceCache.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/RandomAccessSequenceInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/RandomAccessSequenceTestSupport.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/Range.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/Ranges.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Read.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Read.ReadSortByEnd.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Read.ReadSortByStart.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadCodec2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadCodecImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/ReaderFastaParser.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ReadGroupHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ReadIndexStats.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/ReadNameToIndex.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ReadOriginInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadProtobuffCollectionHandler.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ReadQualityStatsMode.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:193: warning: invalid input: '<' [WARNING] * Number of reads observed because of sampleFraction value < 1.0d. If sampleFraction == 1.0d [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:185: warning: invalid input: '<' [WARNING] * Number of reads skipped because of sampleFraction value < 1.0d. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:185: warning: invalid input: '<' [WARNING] * Number of reads skipped because of sampleFraction value < 1.0d. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:193: warning: invalid input: '<' [WARNING] * Number of reads observed because of sampleFraction value < 1.0d. If sampleFraction == 1.0d [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadSet.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ReadSetToTextMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsLoader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/ReadsToText.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsToTextWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ReadsToWeightsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsWriterImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ReadWithIndex.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/RealignmentProcessor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ReferenceLocation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ReformatCompactReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/RegionAveragingWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/RegionWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/RegisterThis.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/Release1_9_7_2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/RemoveBasesMatchingIndelsGenotypeFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/RemoveIndelArtifactsFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/RenameWeights.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/RepositionableInputStream.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/Resettable.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/ResettableObjectPoolInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/RpkmLikeNormalizationMethod.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/RunParallelMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SamComparison.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/readers/sam/SamComparison.java:233: warning: @return tag cannot be used in method with void return type. [WARNING] public void setCountComparisonFailures(final boolean countComparisonFailures) { [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/readers/sam/SamComparison.java:275: warning: @return tag cannot be used in method with void return type. [WARNING] public void setAllowSourceNs(boolean allowSourceNs) { [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SamComparisonInterface.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/readers/sam/SamComparisonInterface.java:130: warning: @return tag cannot be used in method with void return type. [WARNING] public void setAllowSourceNs(boolean allowSourceNs); [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SAMComparisonMode.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMComparisonMode.java:214: warning: @return tag cannot be used in method with void return type. [WARNING] public void setCheckMate(final boolean checkMate) { [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SamExtractReadsMode.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/SamExtractReadsMode.java:44: warning: invalid input: '<' [WARNING] * WARNING: If the file contains pairs, the source SAM/BAM file >>MUST<< be sorted by read name. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/SamExtractReadsMode.java:44: warning: invalid input: '<' [WARNING] * WARNING: If the file contains pairs, the source SAM/BAM file >>MUST<< be sorted by read name. [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/SamHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SamPerPositionComparison.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/SampleCountCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/SampleCountInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/SamplePair.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/SamplePairEnumerator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SampleQualityScoresMode.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/SampleQualityScoresMode.java:176: warning: invalid input: '<' [WARNING] * Set to <= 0 to process the entire file. [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/SampleStats.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/SamRecordGenomicPositionComparator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SAMRecordIterable.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SamRecordParser.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/SamSequenceVariation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SAMToCompactMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SAMToCompactOldMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SAMToCompactSamHelperMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ScanReferenceSequence.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Segment.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/Segment.java:137: warning: invalid input: '&' [WARNING] * Determine if the segment overlaps with position. This method evaluates to position>=start && position<=end; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/Segment.java:137: warning: invalid input: '&' [WARNING] * Determine if the segment overlaps with position. This method evaluates to position>=start && position<=end; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/Segment.java:137: warning: invalid input: '<' [WARNING] * Determine if the segment overlaps with position. This method evaluates to position>=start && position<=end; [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/SequenceBaseInfoCollectionHandler.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/SequenceBaseInformationOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/SequenceBaseInformationReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/SequenceBaseInformationWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/SequenceDigests.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/SequenceEncoder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/SequenceSegmentInfoCollectionHandler.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/SequenceSegmentInformationReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/SequenceSegmentInformationWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/SequenceVariationOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SequenceVariationPool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SequenceVariationPool.ReadIndexInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SequenceVariationPool.Variation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SequenceVariationStats2Mode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SequenceVariationStatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/SimulateBisulfiteReads.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SimulateReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/SitesInFixedWindow.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/SkipToListIterator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/SkipToSortedReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/SlidingCountArray.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/SmallAndLog10BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/SomaticPredictor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/SomaticVariationOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/Sort1Mode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SortedAnnotations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/SortIterateAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SortMode.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/SortMode.java:142: warning: invalid input: '<' [WARNING] * Set to < 0 for auto-detect number of cores. [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplicedSamHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplicedSamHelper.Limits.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplitCompactReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplitFastaMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplitTranscriptsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat3StatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat4StatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat5MciProviderStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat5StatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorBaseQuality.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorDistancesToReadVariations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorDistanceToEndOfRead.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorDistanceToStartOfRead.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorInsertSizes.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorNumVariationsInRead.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorPairFlags.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorQueryAlignedLength.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorQueryPosition.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorReadMappingQuality.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorTargetAlignedLength.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/StatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/StatisticCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/StatisticComparator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/StatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/StrandBiasFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/StreamSignal.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/SubSequenceMotifMatcher.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SuggestPositionSlicesMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SummedCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TabToColumnInfoMode.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:186: warning: invalid input: '<' [WARNING] * Get the number of input lines to read or set to <= 0 to read the entire file. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:194: warning: invalid input: '<' [WARNING] * Set the number of input lines to read or set to <= 0 to read the entire file. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:186: warning: invalid input: '<' [WARNING] * Get the number of input lines to read or set to <= 0 to read the entire file. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:194: warning: invalid input: '<' [WARNING] * Set the number of input lines to read or set to <= 0 to read the entire file. [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:216: warning: invalid input: '<' [WARNING] * Get the number of input lines to read or set to <= 0 to read the entire file. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:224: warning: invalid input: '<' [WARNING] * Set the number of input lines to read or set to <= 0 to read the entire file. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:216: warning: invalid input: '<' [WARNING] * Get the number of input lines to read or set to <= 0 to read the entire file. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:224: warning: invalid input: '<' [WARNING] * Set the number of input lines to read or set to <= 0 to read the entire file. [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TallyBasesMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TallyReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TestRConnectionMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/TestSkipTo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/Timer.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/TranscriptBestScoreAlignmentFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/TranscriptsAlignmentFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TrimMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/TSVWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/TTestCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/UnboundedFifoPool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/UnionAlgorithmSkeleton.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/UnionDumpIterator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/UpgradeMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/UpgradeModeCore.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/UpgradeTo1_9_6.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/Variant.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/Variant.FromTo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/Variant.GobyIndelFromVCF.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/VariantMapCreator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/VariantMapHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VCFCompareMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VCFCompareMode.VCFPosition.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/VCFParser.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/readers/vcf/VCFParser.java:179: warning: invalid input: '<' [WARNING] * Set to <= 0 to scan the entire file. This must be set before calling readHeader() for the value to be used. [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/VCFParser.SyntaxException.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VCFSubsetMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VCFToGenotypeMapMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VCFToKnownIndelsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VcfToTabMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/VCFWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VersionMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/WarningCounter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/WeightCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/WeightParameters.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/WeightsInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/WiggleWindow.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/WithinGroupVariabilityMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/compression/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/compression/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/package-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/package-summary.html... 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/HitBoundedPriorityQueue.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSimilarityMatch.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:127: warning: Tag @link: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore [WARNING] * Dequeues a document from the queue, returning an instance of {@link [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSiteIterator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/class-use/ParseReadsCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/class-use/ParseAlignmentEntriesCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/class-use/ParseAlignmentEntriesWithIndexCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/class-use/IterateAlignmentsCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/class-use/ModifyAlignmentsCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/compression/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/indels/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/htsjdk/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/config/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/exception/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/commits/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/xml/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/deprecated-list.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/allclasses-index.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/index-all.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:127: warning: Tag @link: 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: Tag @link: 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: Tag @link: 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: Tag @link: 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/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 [ 0.034 s] [INFO] Goby I/O ........................................... SUCCESS [ 17.067 s] [INFO] Goby Full Distribution ............................. SUCCESS [ 19.087 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 36.277 s [INFO] Finished at: 2025-06-09T01:38:49-12:00 [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] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --------------------< org.campagnelab.goby:goby-io >-------------------- [INFO] Building Goby I/O 3.3.1 [2/3] [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:3.3.0 [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:3.3.0: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:3.3.0: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] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0: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:3.3.0: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 01:39:01.712 INFO RLoggerMainLoopCallback - 01:39:01.716 INFO RLoggerMainLoopCallback - R version 4.3.2 (2023-10-31) -- "Eye Holes" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) 01:39:01.716 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. 01:39:01.717 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. 01:39:01.717 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. 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] 01:39:01.913 WARN MessageChunksWriter - Using chunk-size=10000 01:39:01.939 WARN MessageChunksWriter - Using chunk-size=1000 01:39:02.013 WARN MessageChunksWriter - Using chunk-size=1000 01:39:02.017 WARN MessageChunksWriter - Using chunk-size=1000 01:39:02.047 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 01:39:02.079 WARN MessageChunksWriter - Using chunk-size=1000 01:39:02.081 WARN MessageChunksWriter - Using chunk-size=1000 01:39:02.098 WARN GobyVersion - Version number UNKNOWN not recognized. Assuming this version is the most recent. 01:39:02.109 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. 01:39:02.165 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. 01:39:02.165 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 01:39:02.166 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: 7ms; used/avail/free/total/max mem: 55.98M/21.03G/1.30G/1.36G/21.09G 01:39:02.209 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 01:39:02.305 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. 01:39:02.310 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. 01:39:02.362 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. 01:39:02.362 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. 01:39:02.362 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. 01:39:02.363 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 01:39:02.363 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. 01:39:02.363 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: 48.85M/21.04G/1.31G/1.36G/21.09G 01:39:02.368 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. 01:39:02.384 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. 01:39:02.419 WARN MessageChunksWriter - Using chunk-size=1000 01:39:02.444 WARN MessageChunksWriter - Using chunk-size=1000 01:39:02.446 WARN MessageChunksWriter - Using chunk-size=1000 01:39:02.470 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 01:39:02.494 WARN MessageChunksWriter - Using chunk-size=1000 01:39:02.496 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: 2ms [2 items, 2,000.00 items/s, 500.00 ?s/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item]; used/avail/free/total/max mem: 141.13M/20.95G/1.22G/1.36G/21.09G found entry: query_index: 2 target_index: 1999 position: 19993 score: 20022.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 3 target_index: 1999 position: 19994 score: 20023.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 4 target_index: 1999 position: 19995 score: 20024.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 5 target_index: 1999 position: 19996 score: 20025.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 6 target_index: 1999 position: 19997 score: 20026.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 7 target_index: 1999 position: 19998 score: 20027.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 8 target_index: 1999 position: 19999 score: 20028.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 9 target_index: 1999 position: 20000 score: 20029.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 2 target_index: 3999 position: 19993 score: 20022.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 3 target_index: 3999 position: 19994 score: 20023.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 4 target_index: 3999 position: 19995 score: 20024.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 5 target_index: 3999 position: 19996 score: 20025.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 6 target_index: 3999 position: 19997 score: 20026.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 7 target_index: 3999 position: 19998 score: 20027.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 8 target_index: 3999 position: 19999 score: 20028.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 9 target_index: 3999 position: 20000 score: 20029.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 01:39:02.622 WARN MessageChunksWriter - Using chunk-size=1000 01:39:02.648 WARN MessageChunksWriter - Using chunk-size=1000 01:39:02.650 WARN MessageChunksWriter - Using chunk-size=1000 01:39:02.673 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 01:39:02.696 WARN MessageChunksWriter - Using chunk-size=1000 01:39:02.697 WARN MessageChunksWriter - Using chunk-size=1000 01:39:02.700 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. 01:39:02.718 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. 01:39:02.719 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 01:39:02.719 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [1 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 41.46M/21.05G/1.32G/1.36G/21.09G 01:39:02.722 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 01:39:02.734 WARN MessageChunksWriter - Using chunk-size=1000 01:39:02.757 WARN MessageChunksWriter - Using chunk-size=1000 01:39:02.758 WARN MessageChunksWriter - Using chunk-size=1000 01:39:02.782 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 01:39:02.806 WARN MessageChunksWriter - Using chunk-size=1000 01:39:02.807 WARN MessageChunksWriter - Using chunk-size=1000 01:39:02.810 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. 01:39:02.812 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. 01:39:02.815 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. 01:39:02.816 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. 01:39:02.816 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. 01:39:02.816 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 01:39:02.816 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. 01:39:02.816 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 65.37M/21.02G/219.84M/285.21M/21.09G 01:39:02.819 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. 01:39:02.821 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. 01:39:02.826 WARN MessageChunksWriter - Using chunk-size=1000 01:39:02.850 WARN MessageChunksWriter - Using chunk-size=1000 01:39:02.851 WARN MessageChunksWriter - Using chunk-size=1000 01:39:02.875 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 01:39:02.899 WARN MessageChunksWriter - Using chunk-size=1000 01:39:02.900 WARN MessageChunksWriter - Using chunk-size=1000 Finding max number of reads... Found input file with 2 target(s) 01:39:02.902 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) 01:39:02.905 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. 01:39:02.908 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. 01:39:02.908 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. 01:39:02.908 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. 01:39:02.908 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 01:39:02.909 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. 01:39:02.909 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 98.93M/20.99G/186.29M/285.21M/21.09G Second pass: writing the merged alignment. 01:39:02.911 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. 01:39:02.913 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 01:39:02.918 WARN MessageChunksWriter - Using chunk-size=1000 01:39:02.942 WARN MessageChunksWriter - Using chunk-size=1000 01:39:02.943 WARN MessageChunksWriter - Using chunk-size=1000 01:39:02.967 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 01:39:02.989 WARN MessageChunksWriter - Using chunk-size=1000 01:39:02.990 WARN MessageChunksWriter - Using chunk-size=1000 01:39:02.993 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. 01:39:02.995 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. 01:39:02.995 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 01:39:02.995 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: 132.48M/20.96G/152.73M/285.21M/21.09G 01:39:02.998 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 01:39:03.004 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.027 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.029 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.052 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 01:39:03.075 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.076 WARN MessageChunksWriter - Using chunk-size=1000 [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item]; used/avail/free/total/max mem: 182.81M/20.91G/102.40M/285.21M/21.09G found entry: query_index: 2 target_index: 1999 position: 19993 score: 20022.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 3 target_index: 1999 position: 19994 score: 20023.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 4 target_index: 1999 position: 19995 score: 20024.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 5 target_index: 1999 position: 19996 score: 20025.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 6 target_index: 1999 position: 19997 score: 20026.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 7 target_index: 1999 position: 19998 score: 20027.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 8 target_index: 1999 position: 19999 score: 20028.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 9 target_index: 1999 position: 20000 score: 20029.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 2 target_index: 3999 position: 19993 score: 20022.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 3 target_index: 3999 position: 19994 score: 20023.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 4 target_index: 3999 position: 19995 score: 20024.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 5 target_index: 3999 position: 19996 score: 20025.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 6 target_index: 3999 position: 19997 score: 20026.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 7 target_index: 3999 position: 19998 score: 20027.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 8 target_index: 3999 position: 19999 score: 20028.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 9 target_index: 3999 position: 20000 score: 20029.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 01:39:03.181 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.215 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.217 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.242 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 01:39:03.265 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.267 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.271 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. 01:39:03.274 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. 01:39:03.302 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. 01:39:03.302 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. 01:39:03.302 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. 01:39:03.303 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 01:39:03.303 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. 01:39:03.303 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: 108.40M/20.98G/696.91M/805.31M/21.09G 01:39:03.306 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. 01:39:03.320 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 01:39:03.571 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 01:39:03.580 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 01:39:03.598 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 01:39:03.601 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 01:39:03.604 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 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 01:39:03.662 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 } 01:39:03.683 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 01:39:03.762 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.765 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 01:39:03.772 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.773 WARN MessageChunksWriter - Using chunk-size=1000 entry: score=30.0000 readOriginIndex=0 entry: score=30.0000 readOriginIndex=0 Scanned 2 entries 01:39:03.777 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.778 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.783 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.784 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.789 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.790 WARN MessageChunksWriter - Using chunk-size=1000 0 2 01:39:03.796 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.798 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 01:39:03.804 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.805 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.836 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.837 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.842 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.843 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 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' 01:39:03.889 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.890 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.890 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.898 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.899 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.900 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.907 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.908 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.909 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 01:39:03.916 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.917 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.918 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.924 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.925 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.926 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.928 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 01:39:03.929 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 01:39:03.931 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 01:39:03.934 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.935 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.936 WARN MessageChunksWriter - Using chunk-size=1000 01:39:03.948 WARN MessageChunksWriter - Using chunk-size=1 01:39:03.952 WARN MessageChunksWriter - Using chunk-size=1 01:39:03.955 WARN MessageChunksWriter - Using chunk-size=1 01:39:03.958 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 [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. 01:39:03.986 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 01:39:03.989 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 01:39:03.991 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 01:39:03.994 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 01:39:03.997 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 01:39:03.999 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 01:39:04.002 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 Setting quality threshold to 0.02 01:39:04.028 WARN MessageChunksWriter - Using chunk-size=1000 01:39:04.030 WARN MessageChunksWriter - Using chunk-size=1000 01:39:04.037 WARN MessageChunksWriter - Using chunk-size=1000 01:39:04.038 WARN MessageChunksWriter - Using chunk-size=1000 0 23 Total logical entries written: 4 Total bytes written: 0 Average bytes/logical entry: 0.0 Min query index: 1 Max query index: 1 Number of queries: 1 Number of targets: 2 Total logical entries written: 4 Total bytes written: 62 Average bytes/logical entry: 15.5 Min query index: 1 Max query index: 1 Number of queries: 1 Number of targets: 2 Annotations loaded Annotations loaded Annotations loaded Annotations loaded Annotations loaded count perbase{0=>0, 13=>0, 11=>2, 3=>2, 5=>3} count keys [0, 3, 5, 11, 13] -1 0.0 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 overlapping count 3, 4 0.0 overlapping count 15, 17 0.0 overlapping count 9, 18 2.0 overlapping count 3, 8 2.0 overlapping count 11, 12 0.0 overlapping count 9, 10 1.0 overlapping count 8, 9 0.0 overlapping count 8, 8 0.0 overlapping count 5, 6 0.0 overlapping count 3, 3 0.0 overlapping count 3, 12 5.0 overlapping count -1, 2 0.0 overlapping count 0, 45 6.0 overlapping count 13, 15 0.0 -1 0.0 0 0.0 1 0.0 2 0.0 3 2.0 4 2.0 5 3.0 6 3.0 7 3.0 8 3.0 9 3.0 10 3.0 11 2.0 12 2.0 13 0.0 14 0.0 15 1.0 16 1.0 17 1.0 18 1.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 overlapping count 3, 4 2.0 overlapping count 2, 3 2.0 overlapping count 3, 8 4.0 overlapping count 11, 12 2.0 overlapping count 9, 10 3.0 overlapping count 8, 9 4.0 overlapping count 8, 8 3.0 overlapping count 5, 6 3.0 overlapping count 3, 3 2.0 overlapping count 3, 12 5.0 overlapping count -1, 2 0.0 overlapping count 0, 45 6.0 overlapping count 13, 15 1.0 [main] WARN org.campagnelab.goby.algorithmic.algorithm.EquivalentIndelRegionCalculator - Cannot determine sequence at position 600000000 of reference-index 2 [ {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 01:39:53.644 INFO TestPostBarcodeMatcher - Num matches = 200, Num Ambiguous = 0, Num no matches = 0 01:39:53.644 INFO TestPostBarcodeMatcher - Time to parse 8 million reads 0 seconds 01:39:53.697 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value 01:39:53.730 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. 01:39:53.730 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value 01:39:53.742 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. 01:39:53.742 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value 01:39:53.833 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. 01:39:53.860 INFO FDRAdjustment - ... statistic t-test-P-value-Bonferroni-adjusted was found, FDR adjustment executed. 01:39:53.860 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value 01:39:53.937 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. 01:39:53.946 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 [0.9968909711873614, 0.49875859218382285, -0.00449236752427049, -1.003586399829636, 0.0, 0.0] ] truncated fdr=3.53108e-05 original=3.53108e-05 truncated fdr=0.00128842 original=0.00128842 truncated fdr=0.00128842 original=0.00128842 truncated fdr=0.00284140 original=0.00284140 truncated fdr=0.00284140 original=0.00284140 truncated fdr=0.00284140 original=0.00284140 truncated fdr=0.00284140 original=0.00284140 truncated fdr=0.00294094 original=0.00294094 truncated fdr=0.00375760 original=0.00375760 truncated fdr=0.00569307 original=0.00569307 truncated fdr=0.00833856 original=0.00833856 truncated fdr=0.0201744 original=0.0201744 truncated fdr=0.0379108 original=0.0379108 truncated fdr=0.0379108 original=0.0379108 truncated fdr=0.0523700 original=0.0523700 truncated fdr=0.0622873 original=0.0622873 truncated fdr=0.0622873 original=0.0622873 truncated fdr=0.0733761 original=0.0733761 truncated fdr=0.0742187 original=0.0742187 truncated fdr=0.0847349 original=0.0847349 truncated fdr=0.151073 original=0.151073 truncated fdr=0.335641 original=0.335641 truncated fdr=0.391390 original=0.391390 truncated fdr=0.391390 original=0.391390 truncated fdr=0.443709 original=0.443709 truncated fdr=0.477756 original=0.477756 truncated fdr=0.479630 original=0.479630 truncated fdr=0.637850 original=0.637850 truncated fdr=0.977998 original=0.977998 truncated fdr=1.00000 original=1.00000 truncated fdr=1.00000 original=1.00000 truncated fdr=1.00000 original=1.00000 truncated fdr=1.00000 original=1.00000 [main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 42 threads. [main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 42 threads. [main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 42 threads. [main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 42 threads. Creating base test directory: test-results/stats-writer allele: A ref: [CC] alt: [T]##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 01:40:05.917 INFO BullardUpperQuartileNormalization - normalization denominator 44190.5 for sample B-7 01:40:05.917 INFO BullardUpperQuartileNormalization - normalization denominator 44249.6 for sample B-3 01:40:05.917 INFO BullardUpperQuartileNormalization - normalization denominator 89150.0 for sample A-3 01:40:05.917 INFO BullardUpperQuartileNormalization - normalization denominator 90155.7 for sample A-12 01:40:05.917 INFO BullardUpperQuartileNormalization - normalization denominator 45018.7 for sample B-15 01:40:05.917 INFO BullardUpperQuartileNormalization - normalization denominator 44722.9 for sample B-14 01:40:05.917 INFO BullardUpperQuartileNormalization - normalization denominator 43717.2 for sample B-11 01:40:05.917 INFO BullardUpperQuartileNormalization - normalization denominator 86192.2 for sample A-17 01:40:05.917 INFO BullardUpperQuartileNormalization - normalization denominator 43894.7 for sample B-2 01:40:05.917 INFO BullardUpperQuartileNormalization - normalization denominator 44486.3 for sample B-10 01:40:05.917 INFO BullardUpperQuartileNormalization - normalization denominator 88262.7 for sample A-16 01:40:05.917 INFO BullardUpperQuartileNormalization - normalization denominator 43658.1 for sample B-8 01:40:05.918 INFO BullardUpperQuartileNormalization - normalization denominator 44013.0 for sample B-4 01:40:05.918 INFO BullardUpperQuartileNormalization - normalization denominator 87020.4 for sample A-2 01:40:05.918 INFO BullardUpperQuartileNormalization - normalization denominator 89800.8 for sample A-0 01:40:05.918 INFO BullardUpperQuartileNormalization - normalization denominator 44131.3 for sample B-6 01:40:05.918 INFO BullardUpperQuartileNormalization - normalization denominator 87848.6 for sample A-9 01:40:05.918 INFO BullardUpperQuartileNormalization - normalization denominator 88262.7 for sample A-8 01:40:05.918 INFO BullardUpperQuartileNormalization - normalization denominator 89623.3 for sample A-5 01:40:05.918 INFO BullardUpperQuartileNormalization - normalization denominator 85364.0 for sample A-4 01:40:05.918 INFO BullardUpperQuartileNormalization - normalization denominator 89386.7 for sample A-6 01:40:05.918 INFO BullardUpperQuartileNormalization - normalization denominator 91989.6 for sample A-7 01:40:05.918 INFO BullardUpperQuartileNormalization - normalization denominator 44013.0 for sample B-5 01:40:05.918 INFO BullardUpperQuartileNormalization - normalization denominator 89090.9 for sample A-10 01:40:05.918 INFO BullardUpperQuartileNormalization - normalization denominator 88972.6 for sample A-14 01:40:05.918 INFO BullardUpperQuartileNormalization - normalization denominator 44841.2 for sample B-9 01:40:05.919 INFO BullardUpperQuartileNormalization - normalization denominator 87848.6 for sample A-1 01:40:05.919 INFO BullardUpperQuartileNormalization - normalization denominator 43598.9 for sample B-0 01:40:05.919 INFO BullardUpperQuartileNormalization - normalization denominator 44486.3 for sample B-12 01:40:05.919 INFO BullardUpperQuartileNormalization - normalization denominator 43717.2 for sample B-13 01:40:05.919 INFO BullardUpperQuartileNormalization - normalization denominator 89268.3 for sample A-19 01:40:05.919 INFO BullardUpperQuartileNormalization - normalization denominator 87138.7 for sample A-18 01:40:05.919 INFO BullardUpperQuartileNormalization - normalization denominator 87552.8 for sample A-15 01:40:05.919 INFO BullardUpperQuartileNormalization - normalization denominator 43362.3 for sample B-1 01:40:05.919 INFO BullardUpperQuartileNormalization - normalization denominator 85364.0 for sample A-13 01:40:05.919 INFO BullardUpperQuartileNormalization - normalization denominator 90688.1 for sample A-11 01:40:05.919 INFO BullardUpperQuartileNormalization - normalization denominator 44308.8 for sample B-16 01:40:05.919 INFO BullardUpperQuartileNormalization - normalization denominator 45610.3 for sample B-17 01:40:05.919 INFO BullardUpperQuartileNormalization - normalization denominator 42948.2 for sample B-19 01:40:05.919 INFO BullardUpperQuartileNormalization - normalization denominator 43717.2 for sample B-18 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. 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 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 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 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences 1/1 ..T 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 01:40:07.122 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 01:40:07.123 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 01:40:07.124 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 01:40:07.125 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 01:40:07.126 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 01:40:07.128 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 01:40:07.129 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 01:40:07.130 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 01:40:07.131 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 01:40:07.132 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 01:40:07.191 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 01:40:07.192 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 01:40:07.193 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 01:40:07.194 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 01:40:07.195 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 01:40:07.196 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 01:40:07.198 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 01:40:07.199 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 01:40:07.200 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 01:40:07.201 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 01:40:07.258 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 01:40:07.259 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 01:40:07.260 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 01:40:07.261 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 01:40:07.261 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 01:40:07.262 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 01:40:07.263 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 01:40:07.264 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 01:40:07.265 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 01:40:07.266 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 01:40:07.320 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 01:40:07.321 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 01:40:07.322 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 01:40:07.323 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 01:40:07.324 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 01:40:07.325 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 01:40:07.326 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 01:40:07.327 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 01:40:07.328 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 01:40:07.329 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 01:40:07.374 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 01:40:07.375 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 01:40:07.376 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 01:40:07.377 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 01:40:07.378 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 01:40:07.379 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 01:40:07.379 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 01:40:07.380 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 01:40:07.382 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 01:40:07.383 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 01:40:07.425 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 01:40:07.426 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 01:40:07.427 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 01:40:07.428 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 01:40:07.429 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 01:40:07.430 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 01:40:07.431 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 01:40:07.432 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 01:40:07.433 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 01:40:07.434 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 01:40:07.507 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 01:40:07.508 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 01:40:07.509 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 01:40:07.510 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 01:40:07.511 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 01:40:07.512 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 01:40:07.513 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 01:40:07.514 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 01:40:07.515 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 01:40:07.516 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 01:40:07.556 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 01:40:07.557 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 01:40:07.558 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 01:40:07.559 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 01:40:07.559 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 01:40:07.560 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 01:40:07.562 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 01:40:07.563 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 01:40:07.564 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 01:40:07.565 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 01:40:07.604 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 01:40:07.605 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 01:40:07.606 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 01:40:07.606 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 01:40:07.607 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 01:40:07.608 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 01:40:07.609 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 01:40:07.610 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 01:40:07.611 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 01:40:07.612 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 01:40:07.650 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 01:40:07.651 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 01:40:07.652 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 01:40:07.653 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 01:40:07.654 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 01:40:07.654 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 01:40:07.655 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 01:40:07.656 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 01:40:07.657 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 01:40:07.659 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 01:40:07.698 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 01:40:07.699 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 01:40:07.700 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 01:40:07.701 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 01:40:07.702 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 01:40:07.703 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 01:40:07.703 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 01:40:07.704 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 01:40:07.705 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 01:40:07.706 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 01:40:07.749 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 01:40:07.750 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 01:40:07.751 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 01:40:07.752 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 01:40:07.753 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 01:40:07.754 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 01:40:07.755 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 01:40:07.756 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 01:40:07.757 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 01:40:07.758 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} TTC[27]->CGT[27] / qual=1:2:3 A[15]->G[20] / qual=20 A[15]->G[20] / qual=20 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 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 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 original GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: GGTGT original G----GTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: G original GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGT mapped: GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGT original G--GTGTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: GGT appending (count=0,length=1) appending (count=4,length=3) appending (count=1,length=3) appending (count=0,length=2) appending (count=3,length=1) appending (count=1,length=1) appending (count=0,length=1) appending (count=4,length=3) appending (count=0,length=5) appending (count=3,length=1) appending (count=0,length=2) appending (count=2,length=1) appending (count=0,length=2) appending (count=3,length=1) appending (count=2,length=1) appending (count=0,length=1) loading transition for reader[0] position=0 length=1 count=0 loading transition for reader[1] position=0 length=6 count=1 (0,1) loading transition for reader[0] position=1 length=3 count=3 (0,1)(1,4) loading transition for reader[0] position=4 length=2 count=0 (0,1)(1,4)(4,1) loading transition for reader[0] position=0 length=1 count=0 loading transition for reader[1] position=0 length=4 count=0 (0,0) loading transition for reader[0] position=1 length=1 count=1 (0,0)(1,1) loading transition for reader[0] position=2 length=4 count=0 (0,0)(1,1)(2,0) loading transition for reader[1] position=4 length=10 count=1 (0,0)(1,1)(2,0)(4,1) loading transition for reader[0] position=6 length=2 count=1 (0,0)(1,1)(2,0)(4,1)(6,2) loading transition for reader[0] position=8 length=1 count=0 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1) loading transition for reader[0] position=9 length=1 count=1 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2) loading transition for reader[0] position=10 length=2 count=0 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1) loading transition for reader[0] position=12 length=1 count=1 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2) loading transition for reader[0] position=13 length=3 count=0 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1) (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0) loading transition for reader[0] position=16 length=1 count=1 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0)(16,1) loading transition for reader[0] position=0 length=1 count=0 loading transition for reader[1] position=0 length=4 count=0 loading transition for reader[0] position=1 length=1 count=1 loading transition for reader[0] position=2 length=4 count=0 loading transition for reader[1] position=4 length=10 count=1 loading transition for reader[0] position=6 length=2 count=1 loading transition for reader[0] position=8 length=1 count=0 loading transition for reader[0] position=9 length=1 count=1 loading transition for reader[0] position=10 length=2 count=0 loading transition for reader[0] position=12 length=1 count=1 loading transition for reader[0] position=13 length=3 count=0 loading transition for reader[0] position=16 length=1 count=1 loading transition for reader[0] position=0 length=1 count=0 loading transition for reader[1] position=0 length=6 count=1 (0,1) loading transition for reader[0] position=1 length=3 count=3 (0,1)(1,4) loading transition for reader[0] position=4 length=2 count=0 (0,1)(1,4)(4,1) loading transition for reader[0] position=0 length=1 count=0 loading transition for reader[1] position=0 length=4 count=0 (0,0) loading transition for reader[0] position=1 length=1 count=1 (0,0)(1,1) loading transition for reader[0] position=2 length=4 count=0 (0,0)(1,1)(2,0) loading transition for reader[1] position=4 length=10 count=1 (0,0)(1,1)(2,0)(4,1) loading transition for reader[0] position=6 length=2 count=1 (0,0)(1,1)(2,0)(4,1)(6,2) loading transition for reader[0] position=8 length=1 count=0 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1) loading transition for reader[0] position=9 length=1 count=1 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2) loading transition for reader[0] position=10 length=2 count=0 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1) loading transition for reader[0] position=12 length=1 count=1 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2) loading transition for reader[0] position=13 length=3 count=0 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1) (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0) loading transition for reader[0] position=16 length=1 count=1 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0)(16,1) loading transition for reader[0] position=0 length=1 count=0 loading transition for reader[1] position=0 length=4 count=0 loading transition for reader[0] position=1 length=1 count=1 loading transition for reader[0] position=2 length=4 count=0 loading transition for reader[1] position=4 length=10 count=1 loading transition for reader[0] position=6 length=2 count=1 loading transition for reader[0] position=8 length=1 count=0 loading transition for reader[0] position=9 length=1 count=1 loading transition for reader[0] position=10 length=2 count=0 loading transition for reader[0] position=12 length=1 count=1 loading transition for reader[0] position=13 length=3 count=0 loading transition for reader[0] position=16 length=1 count=1 loading transition for reader[0] position=0 length=1 count=0 (0,0) loading transition for reader[0] position=1 length=3 count=1 (0,0)(1,1) Appending count: 33146 length: 9 Appending count: 5977 length: 10 Appending count: 10235 length: 3 Appending count: 45889 length: 5 Appending count: 8549 length: 6 Appending count: 23174 length: 4 Appending count: 20325 length: 6 Appending count: 6351 length: 1 Appending count: 15289 length: 10 Appending count: 15856 length: 2 Appending count: 46337 length: 5 Appending count: 10299 length: 1 Appending count: 18671 length: 2 Appending count: 28742 length: 1 Appending count: 13037 length: 1 Appending count: 7432 length: 2 Appending count: 10861 length: 6 Appending count: 22908 length: 9 Appending count: 24507 length: 4 Appending count: 30184 length: 5 Appending count: 13791 length: 5 Appending count: 32696 length: 6 Appending count: 21151 length: 2 Appending count: 17331 length: 10 Appending count: 20498 length: 2 Appending count: 13904 length: 1 Appending count: 16479 length: 7 Appending count: 1361 length: 3 Appending count: 33299 length: 5 Appending count: 10460 length: 2 position= 0 count= 33146 position= 1 count= 33146 position= 2 count= 33146 position= 3 count= 33146 position= 4 count= 33146 position= 5 count= 33146 position= 6 count= 33146 position= 7 count= 33146 position= 8 count= 33146 position= 9 count= 5977 position= 10 count= 5977 position= 11 count= 5977 position= 12 count= 5977 position= 13 count= 5977 position= 14 count= 5977 position= 15 count= 5977 position= 16 count= 5977 position= 17 count= 5977 position= 18 count= 5977 position= 19 count= 10235 position= 20 count= 10235 position= 21 count= 10235 position= 22 count= 45889 position= 23 count= 45889 position= 24 count= 45889 position= 25 count= 45889 position= 26 count= 45889 position= 27 count= 8549 position= 28 count= 8549 position= 29 count= 8549 position= 30 count= 8549 position= 31 count= 8549 position= 32 count= 8549 position= 33 count= 23174 position= 34 count= 23174 position= 35 count= 23174 position= 36 count= 23174 position= 37 count= 20325 position= 38 count= 20325 position= 39 count= 20325 position= 40 count= 20325 position= 41 count= 20325 position= 42 count= 20325 position= 43 count= 6351 position= 44 count= 15289 position= 45 count= 15289 position= 46 count= 15289 position= 47 count= 15289 position= 48 count= 15289 position= 49 count= 15289 position= 50 count= 15289 position= 51 count= 15289 position= 52 count= 15289 position= 53 count= 15289 position= 54 count= 15856 position= 55 count= 15856 position= 56 count= 46337 position= 57 count= 46337 position= 58 count= 46337 position= 59 count= 46337 position= 60 count= 46337 position= 61 count= 10299 position= 62 count= 18671 position= 63 count= 18671 position= 64 count= 28742 position= 65 count= 13037 position= 66 count= 7432 position= 67 count= 7432 position= 68 count= 10861 position= 69 count= 10861 position= 70 count= 10861 position= 71 count= 10861 position= 72 count= 10861 position= 73 count= 10861 position= 74 count= 22908 position= 75 count= 22908 position= 76 count= 22908 position= 77 count= 22908 position= 78 count= 22908 position= 79 count= 22908 position= 80 count= 22908 position= 81 count= 22908 position= 82 count= 22908 position= 83 count= 24507 position= 84 count= 24507 position= 85 count= 24507 position= 86 count= 24507 position= 87 count= 30184 position= 88 count= 30184 position= 89 count= 30184 position= 90 count= 30184 position= 91 count= 30184 position= 92 count= 13791 position= 93 count= 13791 position= 94 count= 13791 position= 95 count= 13791 position= 96 count= 13791 position= 97 count= 32696 position= 98 count= 32696 position= 99 count= 32696 position= 100 count= 32696 position= 101 count= 32696 position= 102 count= 32696 position= 103 count= 21151 position= 104 count= 21151 position= 105 count= 17331 position= 106 count= 17331 position= 107 count= 17331 position= 108 count= 17331 position= 109 count= 17331 position= 110 count= 17331 position= 111 count= 17331 position= 112 count= 17331 position= 113 count= 17331 position= 114 count= 17331 position= 115 count= 20498 position= 116 count= 20498 position= 117 count= 13904 position= 118 count= 16479 position= 119 count= 16479 position= 120 count= 16479 position= 121 count= 16479 position= 122 count= 16479 position= 123 count= 16479 position= 124 count= 16479 position= 125 count= 1361 position= 126 count= 1361 position= 127 count= 1361 position= 128 count= 33299 position= 129 count= 33299 position= 130 count= 33299 position= 131 count= 33299 position= 132 count= 33299 position= 133 count= 10460 position= 134 count= 10460 peak : start :5 count :13 length :100010 peak : start :100020 count :10 length :1 01:40:08.181 WARN WiggleWindow - Not writing 101 7 01:40:08.181 WARN WiggleWindow - Not writing 111 7 01:40:08.181 WARN WiggleWindow - Not writing 131 8 01:40:08.181 WARN WiggleWindow - Not writing 141 8 01:40:08.181 WARN WiggleWindow - Not writing 151 8 appending (count=10,length=4) appending (count=1,length=0) appending (count=2,length=8) Hello appending (count=10,length=4) 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 AGC01:40:08.265 WARN MessageChunksWriter - Using chunk-size=9 01:40:08.266 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 01:40:08.268 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 01:40:08.270 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 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 >1 NNTGAATGAGACCTA [WARNING] Tests run: 512, Failures: 0, Errors: 0, Skipped: 46, Time elapsed: 71.055 s - in TestSuite 01:40:12.083 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 [ 0.036 s] [INFO] Goby I/O ........................................... SUCCESS [ 5.597 s] [INFO] Goby Full Distribution ............................. SUCCESS [01:24 min] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:29 min [INFO] Finished at: 2025-06-09T01:40:20-12:00 [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] --------------------------------[ 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] --------------------------------[ 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] --------------------------------[ 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 [ 0.292 s] [INFO] Goby I/O ........................................... SUCCESS [ 0.177 s] [INFO] Goby Full Distribution ............................. SUCCESS [ 0.030 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.618 s [INFO] Finished at: 2025-06-09T01:40:22-12:00 [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 Jun 09, 2025 1:40:28 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 Jun 09, 2025 1:40:33 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+dfsg2-10_all.deb'. dpkg-deb: building package 'goby-java' in '../goby-java_3.3.1+dfsg2-10_all.deb'. dpkg-genbuildinfo --build=binary -O../libgoby-java_3.3.1+dfsg2-10_amd64.buildinfo dpkg-genchanges --build=binary -O../libgoby-java_3.3.1+dfsg2-10_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/89880 and its subdirectories I: Current time: Mon Jun 9 01:40:46 -12 2025 I: pbuilder-time-stamp: 1749476446 Tue May 7 07:17:48 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Tue May 7 07:17:48 UTC 2024 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Tue May 7 07:47:26 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Tue May 7 07:47:26 UTC 2024 I: libgoby-java_3.3.1+dfsg2-10_amd64.changes: Format: 1.8 Date: Sun, 03 Dec 2023 08:03:09 +0100 Source: libgoby-java Binary: goby-java libgoby-io-java Architecture: all Version: 3.3.1+dfsg2-10 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 Closes: 1045612 Changes: libgoby-java (3.3.1+dfsg2-10) unstable; urgency=medium . * Fixing the clean target (Closes: #1045612) * Update standards version to 4.6.2, no changes needed. Checksums-Sha1: f626e4040f1ffbc8014c00f66541e31384972323 1580036 goby-java_3.3.1+dfsg2-10_all.deb ad8a6d19468824ce212cd0c0db1d15236e77c8ba 977044 libgoby-io-java_3.3.1+dfsg2-10_all.deb 821fd9cec37ef49845a81cce755020345b6b38cb 18983 libgoby-java_3.3.1+dfsg2-10_amd64.buildinfo Checksums-Sha256: 8c841ad040d1b04a02f3c28dd3eee873d8baada2bca45de02117acefe39ef0dd 1580036 goby-java_3.3.1+dfsg2-10_all.deb 10bdc08ef37cc06b8022f477751b394670c7c1f705dd82f261638b37a946b431 977044 libgoby-io-java_3.3.1+dfsg2-10_all.deb 9654ad4e7bb8c08ad92cc0e766b1665ba1c50dfdd0504c676fcc31d11f389467 18983 libgoby-java_3.3.1+dfsg2-10_amd64.buildinfo Files: 32259d996532b05cf3b23de7a9038cb6 1580036 science optional goby-java_3.3.1+dfsg2-10_all.deb 66a18b62a64b6edf85e43a8d8cc70c2b 977044 science optional libgoby-io-java_3.3.1+dfsg2-10_all.deb ebc518ae7a06f5a07946610aff2698e1 18983 science optional libgoby-java_3.3.1+dfsg2-10_amd64.buildinfo Tue May 7 07:47:28 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_30-7992.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.rFLny5uu/libgoby-java_3.3.1+dfsg2-10.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.rFLny5uu/libgoby-java_3.3.1+dfsg2-10.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.rFLny5uu/libgoby-java_3.3.1+dfsg2-10.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.rFLny5uu/b1/libgoby-java_3.3.1+dfsg2-10_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.rFLny5uu/b2/libgoby-java_3.3.1+dfsg2-10_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: 0.385s) 0.385s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.042s) 0.042s 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: 716ms CPU time consumed: 717ms Tue May 7 07:47:29 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Tue May 7 07:47:29 UTC 2024 I: libgoby-java from trixie built successfully and reproducibly on amd64. Tue May 7 07:47:30 UTC 2024 I: Submitting .buildinfo files to external archives: Tue May 7 07:47:30 UTC 2024 I: Submitting 20K b1/libgoby-java_3.3.1+dfsg2-10_amd64.buildinfo.asc Tue May 7 07:47:31 UTC 2024 I: Submitting 20K b2/libgoby-java_3.3.1+dfsg2-10_amd64.buildinfo.asc Tue May 7 07:47:32 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue May 7 07:47:32 UTC 2024 I: Done submitting .buildinfo files. Tue May 7 07:47:32 UTC 2024 I: Removing signed libgoby-java_3.3.1+dfsg2-10_amd64.buildinfo.asc files: removed './b1/libgoby-java_3.3.1+dfsg2-10_amd64.buildinfo.asc' removed './b2/libgoby-java_3.3.1+dfsg2-10_amd64.buildinfo.asc'