I: pbuilder: network access will be disabled during build I: Current time: Thu Feb 13 17:07:57 -12 2025 I: pbuilder-time-stamp: 1739509677 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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 [snpeff_5.1+d+dfsg-3.dsc] I: copying [./snpeff_5.1+d+dfsg.orig.tar.xz] I: copying [./snpeff_5.1+d+dfsg-3.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Jan 20 20:36:39 2023 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./snpeff_5.1+d+dfsg-3.dsc: no acceptable signature found dpkg-source: info: extracting snpeff in snpeff-5.1+d+dfsg dpkg-source: info: unpacking snpeff_5.1+d+dfsg.orig.tar.xz dpkg-source: info: unpacking snpeff_5.1+d+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying alter_pom_for_debian_packaging.patch dpkg-source: info: applying update_launching_script_and_config_file_for_Debian.patch dpkg-source: info: applying use_fastq_from_biojava6.patch dpkg-source: info: applying omit_unused_junit_classes_and_integration_tests.patch dpkg-source: info: applying exclude_tests_with_missing_data.patch dpkg-source: info: applying lowering_heap_allocation.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/976963/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=16 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='16459a37307a4933b081d8f5105cc91d' 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='976963' 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.k965Tbiq/pbuilderrc_15CJ --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.k965Tbiq/b1 --logfile b1/build.log snpeff_5.1+d+dfsg-3.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://85.184.249.68:3128' I: uname -a Linux ionos15-amd64 6.5.0-0.deb12.4-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.5.10-1~bpo12+1 (2023-11-23) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 23 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 23 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 2023 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 23 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 23 2023 more -rwsr-xr-x 1 root root 59704 Mar 23 2023 mount -rwxr-xr-x 1 root root 18744 Mar 23 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Jul 28 2023 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 23 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar -rwxr-xr-x 1 root root 14520 Jul 28 2023 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 23 2023 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 23 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/976963/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), javahelper, default-jdk, default-jdk-doc, maven-debian-helper, libmaven-assembly-plugin-java, libtrove3-java, libhtsjdk-java, libbiojava6-java, junit5, libcommons-codec-java, libcommons-io-java, libcommons-cli-java, libcommons-math3-java, libfreemarker-java, libjaxb-api-java, libmaven-javadoc-plugin-java, libbiojava6-java-doc, libtrove3-java-doc, libcharts4j-java, libapfloat-java, libdistlib-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 ... 18148 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on javahelper; however: Package javahelper is not installed. pbuilder-satisfydepends-dummy depends on default-jdk; however: Package default-jdk is not installed. pbuilder-satisfydepends-dummy depends on default-jdk-doc; however: Package default-jdk-doc is not installed. pbuilder-satisfydepends-dummy depends on maven-debian-helper; however: Package maven-debian-helper 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 libtrove3-java; however: Package libtrove3-java is not installed. pbuilder-satisfydepends-dummy depends on libhtsjdk-java; however: Package libhtsjdk-java is not installed. pbuilder-satisfydepends-dummy depends on libbiojava6-java; however: Package libbiojava6-java is not installed. pbuilder-satisfydepends-dummy depends on junit5; however: Package junit5 is not installed. pbuilder-satisfydepends-dummy depends on libcommons-codec-java; however: Package libcommons-codec-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-io-java; however: Package libcommons-io-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 libcommons-math3-java; however: Package libcommons-math3-java is not installed. pbuilder-satisfydepends-dummy depends on libfreemarker-java; however: Package libfreemarker-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-javadoc-plugin-java; however: Package libmaven-javadoc-plugin-java is not installed. pbuilder-satisfydepends-dummy depends on libbiojava6-java-doc; however: Package libbiojava6-java-doc is not installed. pbuilder-satisfydepends-dummy depends on libtrove3-java-doc; however: Package libtrove3-java-doc is not installed. pbuilder-satisfydepends-dummy depends on libcharts4j-java; however: Package libcharts4j-java is not installed. pbuilder-satisfydepends-dummy depends on libapfloat-java; however: Package libapfloat-java is not installed. pbuilder-satisfydepends-dummy depends on libdistlib-java; however: Package libdistlib-java is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: adwaita-icon-theme{a} ant{a} ant-optional{a} at-spi2-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} dctrl-tools{a} debhelper{a} default-jdk{a} default-jdk-doc{a} default-jdk-headless{a} default-jre{a} default-jre-headless{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{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} java-common{a} java-wrappers{a} javahelper{a} junit4{a} junit5{a} libactivation-java{a} libantlr4-runtime-java{a} libaopalliance-java{a} libapache-pom-java{a} libapfloat-java{a} libapiguardian-java{a} libarchive-zip-perl{a} libargs4j-java{a} libasm-java{a} libasound2{a} libasound2-data{a} libassuan0{a} libatinject-jsr330-api-java{a} libatk1.0-0{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libb-hooks-op-check-perl{a} libbatik-java{a} libbiojava6-java{a} libbiojava6-java-doc{a} libbrotli1{a} libbsd0{a} libbsh-java{a} libcairo2{a} libcdi-api-java{a} libcharts4j-java{a} libciftools-java{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcodemodel-java{a} libcommons-beanutils-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-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} libcups2{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} libdtd-parser-java{a} libdynaloader-functions-perl{a} libedit2{a} libel-api-java{a} libelf1{a} libencode-locale-perl{a} liberror-prone-java{a} libexec-maven-plugin-java{a} libexpat1{a} libfastinfoset-java{a} libfastutil-java{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} libfontbox2-java{a} libfontconfig1{a} libfop-java{a} libfreemarker-java{a} libfreetype6{a} libfribidi0{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libgif7{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgoogle-gson-java{a} libgraphite2-3{a} libgtk2.0-0{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} libicu72{a} libimport-into-perl{a} libinchi1{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libistack-commons-java{a} libitext1-java{a} libitext5-java{a} libjackson2-annotations-java{a} libjackson2-core-java{a} libjackson2-databind-java{a} libjansi-java{a} libjaxb-api-java{a} libjaxb-java{a} libjaxen-java{a} libjaxp1.3-java{a} libjbig0{a} libjetty9-java{a} libjgrapht-java{a} libjgraphx-java{a} libjheaps-java{a} libjmol-java{a} libjni-inchi-java{a} libjni-inchi-jni{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-jquery-ui-theme-base{a} libjson-simple-java{a} libjsoup-java{a} libjsp-api-java{a} libjsr305-java{a} libjtidy-java{a} libksba8{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libllvm15{a} liblog4j1.2-java{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1{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-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} libmaven3-core-java{a} libmbedcrypto7{a} libmbedtls14{a} libmbedx509-1{a} libmjson-java{a} libmmtf-java{a} libmodule-runtime-perl{a} libmoo-perl{a} libmsgpack-java{a} libnaga-java{a} libncbi-ngs3{a} libncbi-vdb3{a} libnet-http-perl{a} libnet-ssleay-perl{a} libngs-java{a} libngs-jni{a} libnpth0{a} libnspr4{a} libnss3{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} libparams-classify-perl{a} libpciaccess0{a} libpcsclite1{a} libpicocli-java{a} libpipeline1{a} libpixman-1-0{a} libplexus-ant-factory-java{a} libplexus-archiver-java{a} libplexus-bsh-factory-java{a} libplexus-build-api-java{a} libplexus-cipher-java{a} libplexus-classworlds-java{a} libplexus-compiler-java{a} libplexus-component-annotations-java{a} libplexus-container-default-java{a} libplexus-container-default1.5-java{a} libplexus-i18n-java{a} libplexus-interactivity-api-java{a} libplexus-interpolation-java{a} libplexus-io-java{a} libplexus-languages-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libplexus-velocity-java{a} libpng16-16{a} libproc2-0{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqdox-java{a} libqdox2-java{a} libreadline8{a} libregexp-ipv6-perl{a} librelaxng-datatype-java{a} librhino-java{a} librngom-java{a} librole-tiny-perl{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libservlet-api-java{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libstax-ex-java{a} libstreambuffer-java{a} libsub-override-perl{a} libsub-quote-perl{a} libsurefire-java{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtool{a} libtrove3-java{a} libtrove3-java-doc{a} libtry-tiny-perl{a} libtxw2-java{a} libuchardet0{a} libunivocity-parsers-java{a} liburi-perl{a} libvecmath-java{a} libvelocity-tools-java{a} libwagon-file-java{a} libwagon-http-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} libxi6{a} libxinerama1{a} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxml2-utils{a} libxmlgraphics-commons-java{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxsom-java{a} libxtst6{a} libxxf86vm1{a} libxz-java{a} libz3-4{a} m4{a} man-db{a} maven{a} maven-debian-helper{a} maven-repo-helper{a} media-types{a} ncbi-vdb-data{a} netbase{a} openjdk-17-doc{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} po-debconf{a} procps{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} unzip{a} velocity{a} wdiff{a} x11-common{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf curl dbus debian-keyring dput dput-ng dupload equivs fonts-dejavu-extra icc-profiles-free javascript-common libarchive-cpio-perl libatk-wrapper-java-jni libdata-dump-perl libdistlib-java-doc libdistro-info-perl libgail-common libgdk-pixbuf2.0-bin libgit-wrapper-perl libgitlab-api-v4-perl libglib2.0-data libgtk2.0-bin libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl librsvg2-common libsasl2-modules libsaxon-java libsoap-lite-perl libstring-shellquote-perl libxstring-perl libxt-dev licensecheck lintian lynx pristine-tar psmisc python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg strace wget xdg-user-dirs 0 packages upgraded, 403 newly installed, 0 to remove and 0 not upgraded. Need to get 355 MB of archives. After unpacking 1220 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 sgml-base all 1.31 [15.4 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 netbase all 6.4 [12.8 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 libproc2-0 amd64 2:4.0.2-3 [62.8 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 procps amd64 2:4.0.2-3 [709 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.11-1~deb12u2 [1419 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-1 [306 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.3~deb12u1 [687 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 shared-mime-info amd64 2.2-1 [729 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2+deb12u1 [286 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6+deb12u1 [316 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.10+dfsg-1+b1 [139 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 gtk-update-icon-cache amd64 3.24.38-2~deb12u1 [44.0 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 adwaita-icon-theme all 43-1 [5124 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 ca-certificates-java all 20230710~deb12u1 [11.9 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 java-common all 0.74 [6388 B] Get: 46 http://deb.debian.org/debian bookworm/main amd64 libavahi-common-data amd64 0.8-10 [107 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 libavahi-common3 amd64 0.8-10 [41.6 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libdbus-1-3 amd64 1.14.10-1~deb12u1 [201 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 libavahi-client3 amd64 0.8-10 [45.5 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 libcups2 amd64 2.4.2-3+deb12u5 [245 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [399 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libnspr4 amd64 2:4.35-1 [113 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libnss3 amd64 2:3.87.1-1 [1331 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 libasound2-data all 1.2.8-1 [20.5 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 libasound2 amd64 1.2.8-1+b1 [362 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 libpcsclite1 amd64 1.9.9-2 [49.7 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre-headless amd64 17.0.9+9-1~deb12u1 [43.7 MB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 default-jre-headless amd64 2:1.17-74 [2936 B] Get: 66 http://deb.debian.org/debian bookworm/main amd64 ant all 1.10.13-1 [2161 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 ant-optional all 1.10.13-1 [449 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 at-spi2-common all 2.46.0-5 [162 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 dctrl-tools amd64 2.24-3+b1 [104 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 80 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 82 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 libgtk2.0-common all 2.24.33-2 [2700 kB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 libatk1.0-0 amd64 2.46.0-5 [49.6 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2+deb12u2 [760 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 100 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB] Get: 102 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB] Get: 106 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB] Get: 107 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB] Get: 109 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB] Get: 110 http://deb.debian.org/debian bookworm/main amd64 libxcomposite1 amd64 1:0.4.5-1 [16.6 kB] Get: 111 http://deb.debian.org/debian bookworm/main amd64 libxfixes3 amd64 1:6.0.0-2 [22.7 kB] Get: 112 http://deb.debian.org/debian bookworm/main amd64 libxcursor1 amd64 1:1.2.1-1 [40.9 kB] Get: 113 http://deb.debian.org/debian bookworm/main amd64 libxdamage1 amd64 1:1.1.6-1 [15.1 kB] Get: 114 http://deb.debian.org/debian bookworm/main amd64 libxi6 amd64 2:1.8-1+b1 [84.2 kB] Get: 115 http://deb.debian.org/debian bookworm/main amd64 libxinerama1 amd64 2:1.1.4-3 [17.8 kB] Get: 116 http://deb.debian.org/debian bookworm/main amd64 libxrandr2 amd64 2:1.5.2-2+b1 [39.2 kB] Get: 117 http://deb.debian.org/debian bookworm/main amd64 libgtk2.0-0 amd64 2.24.33-2 [1855 kB] Get: 118 http://deb.debian.org/debian bookworm/main amd64 libglvnd0 amd64 1.6.0-1 [51.8 kB] Get: 119 http://deb.debian.org/debian bookworm/main amd64 libdrm-common all 2.4.114-1 [7112 B] Get: 120 http://deb.debian.org/debian bookworm/main amd64 libdrm2 amd64 2.4.114-1+b1 [37.5 kB] Get: 121 http://deb.debian.org/debian bookworm/main amd64 libglapi-mesa amd64 22.3.6-1+deb12u1 [35.7 kB] Get: 122 http://deb.debian.org/debian bookworm/main amd64 libx11-xcb1 amd64 2:1.8.4-2+deb12u2 [192 kB] Get: 123 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri2-0 amd64 1.15-1 [107 kB] Get: 124 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri3-0 amd64 1.15-1 [107 kB] Get: 125 http://deb.debian.org/debian bookworm/main amd64 libxcb-glx0 amd64 1.15-1 [122 kB] Get: 126 http://deb.debian.org/debian bookworm/main amd64 libxcb-present0 amd64 1.15-1 [105 kB] Get: 127 http://deb.debian.org/debian bookworm/main amd64 libxcb-randr0 amd64 1.15-1 [117 kB] Get: 128 http://deb.debian.org/debian bookworm/main amd64 libxcb-sync1 amd64 1.15-1 [109 kB] Get: 129 http://deb.debian.org/debian bookworm/main amd64 libxcb-xfixes0 amd64 1.15-1 [109 kB] Get: 130 http://deb.debian.org/debian bookworm/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get: 131 http://deb.debian.org/debian bookworm/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 132 http://deb.debian.org/debian bookworm/main amd64 libdrm-amdgpu1 amd64 2.4.114-1+b1 [20.9 kB] Get: 133 http://deb.debian.org/debian bookworm/main amd64 libpciaccess0 amd64 0.17-2 [51.4 kB] Get: 134 http://deb.debian.org/debian bookworm/main amd64 libdrm-intel1 amd64 2.4.114-1+b1 [64.0 kB] Get: 135 http://deb.debian.org/debian bookworm/main amd64 libdrm-nouveau2 amd64 2.4.114-1+b1 [19.1 kB] Get: 136 http://deb.debian.org/debian bookworm/main amd64 libdrm-radeon1 amd64 2.4.114-1+b1 [21.8 kB] Get: 137 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get: 138 http://deb.debian.org/debian bookworm/main amd64 libz3-4 amd64 4.8.12-3.1 [7216 kB] Get: 139 http://deb.debian.org/debian bookworm/main amd64 libllvm15 amd64 1:15.0.6-4+b1 [23.1 MB] Get: 140 http://deb.debian.org/debian bookworm/main amd64 libsensors-config all 1:3.6.0-7.1 [14.3 kB] Get: 141 http://deb.debian.org/debian bookworm/main amd64 libsensors5 amd64 1:3.6.0-7.1 [34.2 kB] Get: 142 http://deb.debian.org/debian bookworm/main amd64 libgl1-mesa-dri amd64 22.3.6-1+deb12u1 [7239 kB] Get: 143 http://deb.debian.org/debian bookworm/main amd64 libglx-mesa0 amd64 22.3.6-1+deb12u1 [147 kB] Get: 144 http://deb.debian.org/debian bookworm/main amd64 libglx0 amd64 1.6.0-1 [34.4 kB] Get: 145 http://deb.debian.org/debian bookworm/main amd64 libgl1 amd64 1.6.0-1 [88.4 kB] Get: 146 http://deb.debian.org/debian bookworm/main amd64 libgif7 amd64 5.2.1-2.5 [46.9 kB] Get: 147 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 148 http://deb.debian.org/debian bookworm/main amd64 libxtst6 amd64 2:1.2.3-1.1 [28.0 kB] Get: 149 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre amd64 17.0.9+9-1~deb12u1 [184 kB] Get: 150 http://deb.debian.org/debian bookworm/main amd64 default-jre amd64 2:1.17-74 [1056 B] Get: 151 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jdk-headless amd64 17.0.9+9-1~deb12u1 [71.3 MB] Get: 152 http://deb.debian.org/debian bookworm/main amd64 default-jdk-headless amd64 2:1.17-74 [1108 B] Get: 153 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jdk amd64 17.0.9+9-1~deb12u1 [2777 kB] Get: 154 http://deb.debian.org/debian bookworm/main amd64 default-jdk amd64 2:1.17-74 [1068 B] Get: 155 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 156 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 157 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-ui-theme-base all 1.12.1+dfsg-1.1 [44.3 kB] Get: 158 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-doc all 17.0.9+9-1~deb12u1 [12.8 MB] Get: 159 http://deb.debian.org/debian bookworm/main amd64 default-jdk-doc amd64 2:1.17-74 [3020 B] Get: 160 http://deb.debian.org/debian bookworm/main amd64 libassuan0 amd64 2.5.5-5 [48.5 kB] Get: 161 http://deb.debian.org/debian bookworm/main amd64 gpgconf amd64 2.2.40-1.1 [564 kB] Get: 162 http://deb.debian.org/debian bookworm/main amd64 libksba8 amd64 1.6.3-2 [128 kB] Get: 163 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 164 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 165 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 166 http://deb.debian.org/debian bookworm/main amd64 libnpth0 amd64 1.6-3 [19.0 kB] Get: 167 http://deb.debian.org/debian bookworm/main amd64 dirmngr amd64 2.2.40-1.1 [792 kB] Get: 168 http://deb.debian.org/debian bookworm/main amd64 gnupg-l10n all 2.2.40-1.1 [1093 kB] Get: 169 http://deb.debian.org/debian bookworm/main amd64 gnupg-utils amd64 2.2.40-1.1 [927 kB] Get: 170 http://deb.debian.org/debian bookworm/main amd64 gpg amd64 2.2.40-1.1 [949 kB] Get: 171 http://deb.debian.org/debian bookworm/main amd64 pinentry-curses amd64 1.2.1-1 [77.4 kB] Get: 172 http://deb.debian.org/debian bookworm/main amd64 gpg-agent amd64 2.2.40-1.1 [695 kB] Get: 173 http://deb.debian.org/debian bookworm/main amd64 gpg-wks-client amd64 2.2.40-1.1 [541 kB] Get: 174 http://deb.debian.org/debian bookworm/main amd64 gpg-wks-server amd64 2.2.40-1.1 [531 kB] Get: 175 http://deb.debian.org/debian bookworm/main amd64 gpgsm amd64 2.2.40-1.1 [671 kB] Get: 176 http://deb.debian.org/debian bookworm/main amd64 gnupg all 2.2.40-1.1 [846 kB] Get: 177 http://deb.debian.org/debian bookworm/main amd64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 178 http://deb.debian.org/debian bookworm/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 179 http://deb.debian.org/debian bookworm/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 180 http://deb.debian.org/debian bookworm/main amd64 libfile-touch-perl all 0.12-2 [8816 B] Get: 181 http://deb.debian.org/debian bookworm/main amd64 libio-pty-perl amd64 1:1.17-1 [34.9 kB] Get: 182 http://deb.debian.org/debian bookworm/main amd64 libipc-run-perl all 20220807.0-1 [104 kB] Get: 183 http://deb.debian.org/debian bookworm/main amd64 libclass-method-modifiers-perl all 2.14-1 [18.1 kB] Get: 184 http://deb.debian.org/debian bookworm/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b1 [36.4 kB] Get: 185 http://deb.debian.org/debian bookworm/main amd64 libb-hooks-op-check-perl amd64 0.22-2+b1 [10.5 kB] Get: 186 http://deb.debian.org/debian bookworm/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 187 http://deb.debian.org/debian bookworm/main amd64 libdevel-callchecker-perl amd64 0.008-2 [15.8 kB] Get: 188 http://deb.debian.org/debian bookworm/main amd64 libparams-classify-perl amd64 0.015-2+b1 [23.1 kB] Get: 189 http://deb.debian.org/debian bookworm/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 190 http://deb.debian.org/debian bookworm/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 191 http://deb.debian.org/debian bookworm/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 192 http://deb.debian.org/debian bookworm/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 193 http://deb.debian.org/debian bookworm/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 194 http://deb.debian.org/debian bookworm/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 195 http://deb.debian.org/debian bookworm/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 196 http://deb.debian.org/debian bookworm/main amd64 libhttp-date-perl all 6.05-2 [10.5 kB] Get: 197 http://deb.debian.org/debian bookworm/main amd64 libfile-listing-perl all 6.15-1 [12.6 kB] Get: 198 http://deb.debian.org/debian bookworm/main amd64 libhtml-tagset-perl all 3.20-6 [11.7 kB] Get: 199 http://deb.debian.org/debian bookworm/main amd64 libregexp-ipv6-perl all 0.03-3 [5212 B] Get: 200 http://deb.debian.org/debian bookworm/main amd64 liburi-perl all 5.17-1 [90.4 kB] Get: 201 http://deb.debian.org/debian bookworm/main amd64 libhtml-parser-perl amd64 3.81-1 [101 kB] Get: 202 http://deb.debian.org/debian bookworm/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 203 http://deb.debian.org/debian bookworm/main amd64 libclone-perl amd64 0.46-1 [13.7 kB] Get: 204 http://deb.debian.org/debian bookworm/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 205 http://deb.debian.org/debian bookworm/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 206 http://deb.debian.org/debian bookworm/main amd64 libhttp-message-perl all 6.44-1 [81.7 kB] Get: 207 http://deb.debian.org/debian bookworm/main amd64 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get: 208 http://deb.debian.org/debian bookworm/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 209 http://deb.debian.org/debian bookworm/main amd64 perl-openssl-defaults amd64 7+b1 [7924 B] Get: 210 http://deb.debian.org/debian bookworm/main amd64 libnet-ssleay-perl amd64 1.92-2+b1 [317 kB] Get: 211 http://deb.debian.org/debian bookworm/main amd64 libio-socket-ssl-perl all 2.081-2 [219 kB] Get: 212 http://deb.debian.org/debian bookworm/main amd64 libnet-http-perl all 6.22-1 [25.3 kB] Get: 213 http://deb.debian.org/debian bookworm/main amd64 liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get: 214 http://deb.debian.org/debian bookworm/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 215 http://deb.debian.org/debian bookworm/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 216 http://deb.debian.org/debian bookworm/main amd64 libwww-perl all 6.68-1 [186 kB] Get: 217 http://deb.debian.org/debian bookworm/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get: 218 http://deb.debian.org/debian bookworm/main amd64 wdiff amd64 1.2.2-5 [119 kB] Get: 219 http://deb.debian.org/debian bookworm/main amd64 devscripts amd64 2.23.4+deb12u1 [1073 kB] Get: 220 http://deb.debian.org/debian bookworm/main amd64 unzip amd64 6.0-28 [166 kB] Get: 221 http://deb.debian.org/debian bookworm/main amd64 java-wrappers all 0.4 [8916 B] Get: 222 http://deb.debian.org/debian bookworm/main amd64 javahelper all 0.78 [97.2 kB] Get: 223 http://deb.debian.org/debian bookworm/main amd64 libhamcrest-java all 2.2-1 [121 kB] Get: 224 http://deb.debian.org/debian bookworm/main amd64 junit4 all 4.13.2-3 [348 kB] Get: 225 http://deb.debian.org/debian bookworm/main amd64 libapiguardian-java all 1.1.2-1 [4656 B] Get: 226 http://deb.debian.org/debian bookworm/main amd64 libopentest4j-java all 1.2.0-4 [9516 B] Get: 227 http://deb.debian.org/debian bookworm/main amd64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 228 http://deb.debian.org/debian bookworm/main amd64 libpicocli-java all 4.6.2-2 [390 kB] Get: 229 http://deb.debian.org/debian bookworm/main amd64 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 230 http://deb.debian.org/debian bookworm/main amd64 junit5 all 5.9.2-1 [2398 kB] Get: 231 http://deb.debian.org/debian bookworm/main amd64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 232 http://deb.debian.org/debian bookworm/main amd64 libantlr4-runtime-java all 4.7.2-5 [315 kB] Get: 233 http://deb.debian.org/debian bookworm/main amd64 libaopalliance-java all 20070526-7 [8572 B] Get: 234 http://deb.debian.org/debian bookworm/main amd64 libapache-pom-java all 29-2 [5276 B] Get: 235 http://deb.debian.org/debian bookworm/main amd64 libapfloat-java all 1.10.1-2 [620 kB] Get: 236 http://deb.debian.org/debian bookworm/main amd64 libargs4j-java all 2.33-2 [138 kB] Get: 237 http://deb.debian.org/debian bookworm/main amd64 libasm-java all 9.4-1 [389 kB] Get: 238 http://deb.debian.org/debian bookworm/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 239 http://deb.debian.org/debian bookworm/main amd64 libjaxp1.3-java all 1.3.05-6 [227 kB] Get: 240 http://deb.debian.org/debian bookworm/main amd64 libxml-commons-external-java all 1.4.01-5 [240 kB] Get: 241 http://deb.debian.org/debian bookworm/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 242 http://deb.debian.org/debian bookworm/main amd64 libcommons-io-java all 2.11.0-2 [319 kB] Get: 243 http://deb.debian.org/debian bookworm/main amd64 libcommons-logging-java all 1.2-3 [62.4 kB] Get: 244 http://deb.debian.org/debian bookworm/main amd64 libxmlgraphics-commons-java all 2.8-2 [623 kB] Get: 245 http://deb.debian.org/debian bookworm/main amd64 libbatik-java all 1.16+dfsg-1+deb12u1 [3949 kB] Get: 246 http://deb.debian.org/debian bookworm/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 247 http://deb.debian.org/debian bookworm/main amd64 libgoogle-gson-java all 2.10-1 [261 kB] Get: 248 http://deb.debian.org/debian bookworm/main amd64 libciftools-java all 4.0.5-1 [2139 kB] Get: 249 http://deb.debian.org/debian bookworm/main amd64 libcommons-codec-java all 1.15-1 [292 kB] Get: 250 http://deb.debian.org/debian bookworm/main amd64 libcommons-math-java all 2.2-8 [926 kB] Get: 251 http://deb.debian.org/debian bookworm/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 252 http://deb.debian.org/debian bookworm/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 253 http://deb.debian.org/debian bookworm/main amd64 libguava-java all 31.1-1 [2613 kB] Get: 254 http://deb.debian.org/debian bookworm/main amd64 libitext5-java all 5.5.13.3-2 [2665 kB] Get: 255 http://deb.debian.org/debian bookworm/main amd64 libjackson2-annotations-java all 2.14.0-1 [68.8 kB] Get: 256 http://deb.debian.org/debian bookworm/main amd64 libjackson2-core-java all 2.14.1-1 [447 kB] Get: 257 http://deb.debian.org/debian bookworm/main amd64 libjackson2-databind-java all 2.14.0-1 [1584 kB] Get: 258 http://deb.debian.org/debian bookworm/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 259 http://deb.debian.org/debian bookworm/main amd64 libjaxen-java all 1.1.6-4 [214 kB] Get: 260 http://deb.debian.org/debian bookworm/main amd64 libdom4j-java all 2.1.3-2 [310 kB] Get: 261 http://deb.debian.org/debian bookworm/main amd64 libmaven-shared-utils-java all 3.3.4-1 [138 kB] Get: 262 http://deb.debian.org/debian bookworm/main amd64 libcommons-cli-java all 1.5.0-1 [60.0 kB] Get: 263 http://deb.debian.org/debian bookworm/main amd64 libcommons-lang3-java all 3.12.0-2 [561 kB] Get: 264 http://deb.debian.org/debian bookworm/main amd64 libguice-java all 4.2.3-2 [1435 kB] Get: 265 http://deb.debian.org/debian bookworm/main amd64 libmaven-parent-java all 35-1 [6140 B] Get: 266 http://deb.debian.org/debian bookworm/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 267 http://deb.debian.org/debian bookworm/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 268 http://deb.debian.org/debian bookworm/main amd64 libmaven-resolver-java all 1.6.3-1 [548 kB] Get: 269 http://deb.debian.org/debian bookworm/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 270 http://deb.debian.org/debian bookworm/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 271 http://deb.debian.org/debian bookworm/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 272 http://deb.debian.org/debian bookworm/main amd64 libplexus-interpolation-java all 1.26-1 [76.8 kB] Get: 273 http://deb.debian.org/debian bookworm/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 274 http://deb.debian.org/debian bookworm/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 275 http://deb.debian.org/debian bookworm/main amd64 libcdi-api-java all 1.2-3 [54.3 kB] Get: 276 http://deb.debian.org/debian bookworm/main amd64 libslf4j-java all 1.7.32-1 [144 kB] Get: 277 http://deb.debian.org/debian bookworm/main amd64 libsisu-inject-java all 0.3.4-2 [347 kB] Get: 278 http://deb.debian.org/debian bookworm/main amd64 libsisu-plexus-java all 0.3.4-3 [181 kB] Get: 279 http://deb.debian.org/debian bookworm/main amd64 libmaven3-core-java all 3.8.7-1 [1572 kB] Get: 280 http://deb.debian.org/debian bookworm/main amd64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 281 http://deb.debian.org/debian bookworm/main amd64 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 282 http://deb.debian.org/debian bookworm/main amd64 libcommons-compress-java all 1.22-1 [615 kB] Get: 283 http://deb.debian.org/debian bookworm/main amd64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 284 http://deb.debian.org/debian bookworm/main amd64 libsnappy1v5 amd64 1.1.9-3 [26.0 kB] Get: 285 http://deb.debian.org/debian bookworm/main amd64 libsnappy-jni amd64 1.1.8.3-1 [7152 B] Get: 286 http://deb.debian.org/debian bookworm/main amd64 libsnappy-java all 1.1.8.3-1 [98.9 kB] Get: 287 http://deb.debian.org/debian bookworm/main amd64 libxz-java all 1.9-1 [143 kB] Get: 288 http://deb.debian.org/debian bookworm/main amd64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 289 http://deb.debian.org/debian bookworm/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 290 http://deb.debian.org/debian bookworm/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 291 http://deb.debian.org/debian bookworm/main amd64 libjsoup-java all 1.15.3-1 [431 kB] Get: 292 http://deb.debian.org/debian bookworm/main amd64 libwagon-http-java all 3.5.3-1 [49.5 kB] Get: 293 http://deb.debian.org/debian bookworm/main amd64 libistack-commons-java all 3.0.6-5 [145 kB] Get: 294 http://deb.debian.org/debian bookworm/main amd64 libcodemodel-java all 2.6+jaxb2.3.0.1-10.1 [164 kB] Get: 295 http://deb.debian.org/debian bookworm/main amd64 librelaxng-datatype-java all 1.0+ds1-3.1 [11.7 kB] Get: 296 http://deb.debian.org/debian bookworm/main amd64 librngom-java all 2.3.0.1-10.1 [290 kB] Get: 297 http://deb.debian.org/debian bookworm/main amd64 libxsom-java all 2.3.0.1-10.1 [400 kB] Get: 298 http://deb.debian.org/debian bookworm/main amd64 libtxw2-java all 2.3.0.1-10.1 [134 kB] Get: 299 http://deb.debian.org/debian bookworm/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 300 http://deb.debian.org/debian bookworm/main amd64 libdtd-parser-java all 1.2-1 [64.9 kB] Get: 301 http://deb.debian.org/debian bookworm/main amd64 libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 302 http://deb.debian.org/debian bookworm/main amd64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB] Get: 303 http://deb.debian.org/debian bookworm/main amd64 libfastinfoset-java all 1.2.12-3 [343 kB] Get: 304 http://deb.debian.org/debian bookworm/main amd64 libjaxb-java all 2.3.0.1-10.1 [1973 kB] Get: 305 http://deb.debian.org/debian bookworm/main amd64 libmaven-archiver-java all 3.6.0-1 [25.1 kB] Get: 306 http://deb.debian.org/debian bookworm/main amd64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 307 http://deb.debian.org/debian bookworm/main amd64 libcommons-text-java all 1.10.0-1 [211 kB] Get: 308 http://deb.debian.org/debian bookworm/main amd64 libfastutil-java all 8.5.11+dfsg-1 [19.6 MB] Get: 309 http://deb.debian.org/debian bookworm/main amd64 libjheaps-java all 0.14-2 [144 kB] Get: 310 http://deb.debian.org/debian bookworm/main amd64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 311 http://deb.debian.org/debian bookworm/main amd64 libjgraphx-java all 2.1.0.7-3 [807 kB] Get: 312 http://deb.debian.org/debian bookworm/main amd64 libjgrapht-java all 1.5.1-3 [1584 kB] Get: 313 http://deb.debian.org/debian bookworm/main amd64 libinchi1 amd64 1.03+dfsg-4+b2 [436 kB] Get: 314 http://deb.debian.org/debian bookworm/main amd64 libjni-inchi-jni amd64 0.8+dfsg-7 [9064 B] Get: 315 http://deb.debian.org/debian bookworm/main amd64 libcommons-exec-java all 1.3-2 [48.1 kB] Get: 316 http://deb.debian.org/debian bookworm/main amd64 libexec-maven-plugin-java all 3.1.0-1 [66.2 kB] Get: 317 http://deb.debian.org/debian bookworm/main amd64 libmaven-shared-incremental-java all 1.1-3 [9524 B] Get: 318 http://deb.debian.org/debian bookworm/main amd64 libcommons-lang-java all 2.6-10 [273 kB] Get: 319 http://deb.debian.org/debian bookworm/main amd64 libxbean-reflect-java all 4.5-8 [133 kB] Get: 320 http://deb.debian.org/debian bookworm/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 321 http://deb.debian.org/debian bookworm/main amd64 libplexus-compiler-java all 2.12.1-1 [99.8 kB] Get: 322 http://deb.debian.org/debian bookworm/main amd64 libqdox2-java all 2.0.3-1 [296 kB] Get: 323 http://deb.debian.org/debian bookworm/main amd64 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 324 http://deb.debian.org/debian bookworm/main amd64 libmaven-compiler-plugin-java all 3.10.1-2 [59.0 kB] Get: 325 http://deb.debian.org/debian bookworm/main amd64 liblog4j1.2-java all 1.2.17-11 [444 kB] Get: 326 http://deb.debian.org/debian bookworm/main amd64 libjni-inchi-java all 0.8+dfsg-7 [33.2 kB] Get: 327 http://deb.debian.org/debian bookworm/main amd64 libnaga-java all 3.0+svn80-5 [43.5 kB] Get: 328 http://deb.debian.org/debian bookworm/main amd64 libjmol-java all 14.32.83+dfsg-2 [8699 kB] Get: 329 http://deb.debian.org/debian bookworm/main amd64 libjson-simple-java all 2.3.0-1 [63.8 kB] Get: 330 http://deb.debian.org/debian bookworm/main amd64 libmsgpack-java all 0.9.3-1 [155 kB] Get: 331 http://deb.debian.org/debian bookworm/main amd64 libmmtf-java all 1.0.11-1 [187 kB] Get: 332 http://deb.debian.org/debian bookworm/main amd64 libvecmath-java all 1.5.2-7 [97.0 kB] Get: 333 http://deb.debian.org/debian bookworm/main amd64 libbiojava6-java all 6.1.0+dfsg-4 [5367 kB] Get: 334 http://deb.debian.org/debian bookworm/main amd64 libbiojava6-java-doc all 6.1.0+dfsg-4 [2241 kB] Get: 335 http://deb.debian.org/debian bookworm/main amd64 libbsh-java all 2.0b4-20 [291 kB] Get: 336 http://deb.debian.org/debian bookworm/main amd64 libcharts4j-java all 1.3-4 [162 kB] Get: 337 http://deb.debian.org/debian bookworm/main amd64 libcommons-collections3-java all 3.2.2-2 [526 kB] Get: 338 http://deb.debian.org/debian bookworm/main amd64 libcommons-beanutils-java all 1.9.4-1 [232 kB] Get: 339 http://deb.debian.org/debian bookworm/main amd64 libcommons-configuration-java all 1.10-6 [347 kB] Get: 340 http://deb.debian.org/debian bookworm/main amd64 libcommons-digester-java all 1.8.1-5 [168 kB] Get: 341 http://deb.debian.org/debian bookworm/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get: 342 http://deb.debian.org/debian bookworm/main amd64 libcommons-math3-java all 3.6.1-3 [2018 kB] Get: 343 http://deb.debian.org/debian bookworm/main amd64 libcommons-validator-java all 1:1.7-1 [181 kB] Get: 344 http://deb.debian.org/debian bookworm/main amd64 libdistlib-java all 1.0-4 [72.1 kB] Get: 345 http://deb.debian.org/debian bookworm/main amd64 libdoxia-core-java all 1.12.0-1 [213 kB] Get: 346 http://deb.debian.org/debian bookworm/main amd64 libfontbox2-java all 2.0.27-2 [1510 kB] Get: 347 http://deb.debian.org/debian bookworm/main amd64 libqdox-java all 1.12.1-3 [172 kB] Get: 348 http://deb.debian.org/debian bookworm/main amd64 libfop-java all 1:2.8-2 [10.1 MB] Get: 349 http://deb.debian.org/debian bookworm/main amd64 libitext1-java all 1.4-7 [1257 kB] Get: 350 http://deb.debian.org/debian bookworm/main amd64 libdoxia-java all 1.12.0-1 [459 kB] Get: 351 http://deb.debian.org/debian bookworm/main amd64 libmaven-reporting-api-java all 3.1.1-1 [7240 B] Get: 352 http://deb.debian.org/debian bookworm/main amd64 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB] Get: 353 http://deb.debian.org/debian bookworm/main amd64 velocity all 1.7-6 [429 kB] Get: 354 http://deb.debian.org/debian bookworm/main amd64 libplexus-velocity-java all 1.2-3.1 [10.5 kB] Get: 355 http://deb.debian.org/debian bookworm/main amd64 liboro-java all 2.0.8a-14 [70.5 kB] Get: 356 http://deb.debian.org/debian bookworm/main amd64 libvelocity-tools-java all 2.0-8 [308 kB] Get: 357 http://deb.debian.org/debian bookworm/main amd64 libxalan2-java all 2.7.2-4 [3419 kB] Get: 358 http://deb.debian.org/debian bookworm/main amd64 libdoxia-sitetools-java all 1.11.1-1 [202 kB] Get: 359 http://deb.debian.org/debian bookworm/main amd64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 360 http://deb.debian.org/debian bookworm/main amd64 libfreemarker-java all 2.3.31-2 [1528 kB] Get: 361 http://deb.debian.org/debian bookworm/main amd64 libmjson-java all 1.4.0-3 [60.4 kB] Get: 362 http://deb.debian.org/debian bookworm/main amd64 libmbedcrypto7 amd64 2.28.3-1 [277 kB] Get: 363 http://deb.debian.org/debian bookworm/main amd64 libmbedx509-1 amd64 2.28.3-1 [128 kB] Get: 364 http://deb.debian.org/debian bookworm/main amd64 libmbedtls14 amd64 2.28.3-1 [163 kB] Get: 365 http://deb.debian.org/debian bookworm/main amd64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB] Get: 366 http://deb.debian.org/debian bookworm/main amd64 libncbi-vdb3 amd64 3.0.2+dfsg-2 [1050 kB] Get: 367 http://deb.debian.org/debian bookworm/main amd64 libncbi-ngs3 amd64 3.0.3+dfsg-6~deb12u1 [154 kB] Get: 368 http://deb.debian.org/debian bookworm/main amd64 libngs-jni amd64 3.0.3+dfsg-6~deb12u1 [23.5 kB] Get: 369 http://deb.debian.org/debian bookworm/main amd64 libngs-java amd64 3.0.3+dfsg-6~deb12u1 [110 kB] Get: 370 http://deb.debian.org/debian bookworm/main amd64 librhino-java all 1.7.14-2.1 [1357 kB] Get: 371 http://deb.debian.org/debian bookworm/main amd64 libhtsjdk-java all 3.0.4+dfsg-2 [1813 kB] Get: 372 http://deb.debian.org/debian bookworm/main amd64 libjansi-java all 2.4.0-2 [105 kB] Get: 373 http://deb.debian.org/debian bookworm/main amd64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 374 http://deb.debian.org/debian bookworm/main amd64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 375 http://deb.debian.org/debian bookworm/main amd64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 376 http://deb.debian.org/debian bookworm/main amd64 libjetty9-java all 9.4.50-4+deb12u2 [2981 kB] Get: 377 http://deb.debian.org/debian bookworm/main amd64 libjtidy-java all 7+svn20110807-5 [250 kB] Get: 378 http://deb.debian.org/debian bookworm/main amd64 libmaven-common-artifact-filters-java all 3.3.2-1 [48.2 kB] Get: 379 http://deb.debian.org/debian bookworm/main amd64 libmaven-artifact-transfer-java all 0.13.1-2 [158 kB] Get: 380 http://deb.debian.org/debian bookworm/main amd64 libplexus-build-api-java all 0.0.7-4 [10.3 kB] Get: 381 http://deb.debian.org/debian bookworm/main amd64 libmaven-filtering-java all 3.3.0-1 [50.2 kB] Get: 382 http://deb.debian.org/debian bookworm/main amd64 libmaven-assembly-plugin-java all 3.4.2-1 [242 kB] Get: 383 http://deb.debian.org/debian bookworm/main amd64 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB] Get: 384 http://deb.debian.org/debian bookworm/main amd64 libmaven-invoker-java all 3.2.0-1 [28.1 kB] Get: 385 http://deb.debian.org/debian bookworm/main amd64 libplexus-interactivity-api-java all 1.1-2 [11.0 kB] Get: 386 http://deb.debian.org/debian bookworm/main amd64 libmaven-javadoc-plugin-java all 3.4.1-2 [454 kB] Get: 387 http://deb.debian.org/debian bookworm/main amd64 libmaven-reporting-impl-java all 3.2.0-2 [15.2 kB] Get: 388 http://deb.debian.org/debian bookworm/main amd64 libplexus-container-default1.5-java all 2.1.1-1 [4476 B] Get: 389 http://deb.debian.org/debian bookworm/main amd64 libplexus-ant-factory-java all 1.0~alpha2.1-4 [11.4 kB] Get: 390 http://deb.debian.org/debian bookworm/main amd64 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B] Get: 391 http://deb.debian.org/debian bookworm/main amd64 libmaven-plugin-tools-java all 3.7.1-1 [265 kB] Get: 392 http://deb.debian.org/debian bookworm/main amd64 libmaven-reporting-exec-java all 1.6.0-1 [26.8 kB] Get: 393 http://deb.debian.org/debian bookworm/main amd64 libmaven-resources-plugin-java all 3.3.0-1 [28.4 kB] Get: 394 http://deb.debian.org/debian bookworm/main amd64 libmaven-site-plugin-java all 3.12.1-2 [107 kB] Get: 395 http://deb.debian.org/debian bookworm/main amd64 libsurefire-java all 2.22.3-2 [1169 kB] Get: 396 http://deb.debian.org/debian bookworm/main amd64 libtrove3-java all 3.0.3-5 [2146 kB] Get: 397 http://deb.debian.org/debian bookworm/main amd64 libtrove3-java-doc all 3.0.3-5 [823 kB] Get: 398 http://deb.debian.org/debian bookworm/main amd64 libwagon-file-java all 3.5.3-1 [8388 B] Get: 399 http://deb.debian.org/debian bookworm/main amd64 libwagon-http-shaded-java all 3.5.3-1 [1341 kB] Get: 400 http://deb.debian.org/debian bookworm/main amd64 libxml2-utils amd64 2.9.14+dfsg-1.3~deb12u1 [98.9 kB] Get: 401 http://deb.debian.org/debian bookworm/main amd64 maven all 3.8.7-1 [18.9 kB] Get: 402 http://deb.debian.org/debian bookworm/main amd64 maven-repo-helper all 1.11 [142 kB] Get: 403 http://deb.debian.org/debian bookworm/main amd64 maven-debian-helper all 2.6.3 [108 kB] Fetched 355 MB in 4s (96.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal: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 ... 18148 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. 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Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18898 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... 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Setting up libdeflate0:amd64 (1.14-1) ... Setting up perl-openssl-defaults:amd64 (7+b1) ... Setting up liblog4j1.2-java (1.2.17-11) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... 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 libnpth0:amd64 (1.6-3) ... Setting up libantlr4-runtime-java (4.7.2-5) ... Setting up file (1:5.44-3) ... Setting up libjson-simple-java (2.3.0-1) ... Setting up libassuan0:amd64 (2.5.5-5) ... Setting up libunivocity-parsers-java (2.9.1-1) ... Setting up libjbig0:amd64 (2.1-6.1) ... Setting up liboro-java (2.0.8a-14) ... Setting up libsnappy1v5:amd64 (1.1.9-3) ... Setting up libcharts4j-java (1.3-4) ... Setting up libexec-maven-plugin-java (3.1.0-1) ... Setting up libfontbox2-java (2.0.27-2) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... 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 (3.2.2-2) ... Setting up libasound2-data (1.2.8-1) ... 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) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-2) ... Setting up libjaxen-java (1.1.6-4) ... Setting up libapiguardian-java (1.1.2-1) ... Setting up libmbedcrypto7:amd64 (2.28.3-1) ... Setting up libx11-data (2:1.8.4-2+deb12u2) ... Setting up libnspr4:amd64 (2:4.35-1) ... Setting up gnupg-l10n (2.2.40-1.1) ... Setting up libjtidy-java (7+svn20110807-5) ... Setting up libjansi-java (2.4.0-2) ... Setting up libapache-pom-java (29-2) ... Setting up libavahi-common-data:amd64 (0.8-10) ... Setting up libatinject-jsr330-api-java (1.0+ds1-5) ... Setting up libdbus-1-3:amd64 (1.14.10-1~deb12u1) ... Setting up libwebsocket-api-java (1.1-2) ... Setting up libfribidi0:amd64 (1.0.8-2.1) ... Setting up libproc2-0:amd64 (2:4.0.2-3) ... Setting up libplexus-interpolation-java (1.26-1) ... Setting up libpng16-16:amd64 (1.6.39-2) ... Setting up libitext5-java (5.5.13.3-2) ... Setting up libxml-commons-resolver1.1-java (1.2-11) ... Setting up libxz-java (1.9-1) ... Setting up libitext1-java (1.4-7) ... Setting up libio-html-perl (1.004-3) ... Setting up autopoint (0.21-12) ... Setting up libb-hooks-op-check-perl:amd64 (0.22-2+b1) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up libipc-run-perl (20220807.0-1) ... Setting up libpcsclite1:amd64 (1.9.9-2) ... Setting up libtrove3-java-doc (3.0.3-5) ... Setting up libsensors5:amd64 (1:3.6.0-7.1) ... Setting up libactivation-java (1.2.0-2) ... Setting up libhamcrest-java (2.2-1) ... Setting up libglapi-mesa:amd64 (22.3.6-1+deb12u1) ... Setting up libbsh-java (2.0b4-20) ... Setting up libjsp-api-java (2.3.4-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up autoconf (2.71-3) ... Setting up libapfloat-java (1.10.1-2) ... Setting up libwebp7:amd64 (1.2.4-0.2+deb12u1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libregexp-ipv6-perl (0.03-3) ... Setting up libgif7:amd64 (5.2.1-2.5) ... Setting up libtrove3-java (3.0.3-5) ... Setting up libfreemarker-java (2.3.31-2) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libxshmfence1:amd64 (1.3-1) ... Setting up libjsoup-java (1.15.3-1) ... Setting up at-spi2-common (2.46.0-5) ... Setting up libcommons-math-java (2.2-8) ... Setting up libtiff6:amd64 (4.5.0-6+deb12u1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libxml-commons-external-java (1.4.01-5) ... Setting up procps (2:4.0.2-3) ... Setting up libxbean-reflect-java (4.5-8) ... Setting up libasound2:amd64 (1.2.8-1+b1) ... 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 libjackson2-core-java (2.14.1-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up ncbi-vdb-data (3.0.2+dfsg-2) ... Setting up libthai-data (0.1.29-1) ... 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+b1) ... Setting up libgtk2.0-common (2.24.33-2) ... Setting up libatk1.0-0:amd64 (2.46.0-5) ... Setting up libwagon-http-shaded-java (3.5.3-1) ... Setting up libhttpcore-java (4.4.16-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libxerces2-java (2.12.2-1) ... Setting up libfile-dirlist-perl (0.05-3) ... Setting up libjaxp1.3-java (1.3.05-6) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up librelaxng-datatype-java (1.0+ds1-3.1) ... Setting up openssl (3.0.11-1~deb12u2) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up libdrm-common (2.4.114-1) ... Setting up libcdi-api-java (1.2-3) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libsnappy-jni (1.1.8.3-1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3~deb12u1) ... Setting up liburi-perl (5.17-1) ... Setting up libargs4j-java (2.33-2) ... Setting up libfile-touch-perl (0.12-2) ... Setting up dctrl-tools (2.24-3+b1) ... Setting up libinchi1 (1.03+dfsg-4+b2) ... Setting up libnaga-java (3.0+svn80-5) ... Setting up libnet-ssleay-perl:amd64 (1.92-2+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 (1.2.1-1) ... Setting up libdom4j-java (2.1.3-2) ... 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 libhttp-date-perl (6.05-2) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libjetty9-java (9.4.50-4+deb12u2) ... Setting up libxcb-xfixes0:amd64 (1.15-1) ... Setting up java-wrappers (0.4) ... Setting up libfile-listing-perl (6.15-1) ... Setting up libmbedx509-1:amd64 (2.28.3-1) ... Setting up libplexus-languages-java (1.1.1-2) ... Setting up libmbedtls14:amd64 (2.28.3-1) ... Setting up libtool (2.4.7-5) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libstax-ex-java (1.7.8-3) ... Setting up libxcb-glx0:amd64 (1.15-1) ... Setting up libmaven-parent-java (35-1) ... Setting up libedit2:amd64 (3.1-20221030-2) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-10) ... Setting up libncbi-vdb3:amd64 (3.0.2+dfsg-2) ... Setting up libcommons-logging-java (1.2-3) ... Setting up libnet-http-perl (6.22-1) ... Setting up libsisu-inject-java (0.3.4-2) ... Setting up libnss3:amd64 (2:3.87.1-1) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libciftools-java (4.0.5-1) ... Setting up libdevel-callchecker-perl:amd64 (0.008-2) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up libjackson2-databind-java (2.14.0-1) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... 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 (0.1.29-1) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.4-3) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-5) ... Setting up libxcb-sync1:amd64 (1.15-1) ... Setting up libxalan2-java (2.7.2-4) ... Setting up shared-mime-info (2.2-1) ... Setting up libstreambuffer-java (1.5.4-1.1) ... Setting up libcommons-lang3-java (3.12.0-2) ... 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 librngom-java (2.3.0.1-10.1) ... Setting up libdrm2:amd64 (2.4.114-1+b1) ... Setting up libjni-inchi-jni (0.8+dfsg-7) ... Setting up dwz (0.15-1) ... Setting up libmaven-common-artifact-filters-java (3.3.2-1) ... Setting up libjgraphx-java (2.1.0.7-3) ... Setting up groff-base (1.22.4-10) ... Setting up libxcb-randr0:amd64 (1.15-1) ... Setting up libhtml-parser-perl:amd64 (3.81-1) ... Setting up libllvm15:amd64 (1:15.0.6-4+b1) ... Setting up gpgconf (2.2.40-1.1) ... Setting up openjdk-17-doc (17.0.9+9-1~deb12u1) ... Setting up libcommons-beanutils-java (1.9.4-1) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libx11-6:amd64 (2:1.8.4-2+deb12u2) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-1+b1) ... Setting up libsnappy-java (1.1.8.3-1) ... Setting up libfontconfig1:amd64 (2.14.1-4) ... Setting up libxsom-java (2.3.0.1-10.1) ... Setting up ca-certificates-java (20230710~deb12u1) ... 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~deb12u1) ... Setting up libcommons-codec-java (1.15-1) ... Setting up libxcomposite1:amd64 (1:0.4.5-1) ... Setting up libavahi-client3:amd64 (0.8-10) ... Setting up libio-socket-ssl-perl (2.081-2) ... Setting up gpg (2.2.40-1.1) ... Setting up gnupg-utils (2.2.40-1.1) ... Setting up libhttp-message-perl (6.44-1) ... Setting up libdrm-amdgpu1:amd64 (2.4.114-1+b1) ... Setting up libncbi-ngs3:amd64 (3.0.3+dfsg-6~deb12u1) ... Setting up libxcb-dri3-0:amd64 (1.15-1) ... Setting up gtk-update-icon-cache (3.24.38-2~deb12u1) ... Setting up libx11-xcb1:amd64 (2:1.8.4-2+deb12u2) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up velocity (1.7-6) ... Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libngs-jni:amd64 (3.0.3+dfsg-6~deb12u1) ... Setting up libdrm-nouveau2:amd64 (2.4.114-1+b1) ... Setting up libxdamage1:amd64 (1:1.1.6-1) ... Setting up gpg-agent (2.2.40-1.1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up libcommons-compress-java (1.22-1) ... Setting up libhttp-cookies-perl (6.10-1) ... Setting up libcommons-io-java (2.11.0-2) ... Setting up libdrm-radeon1:amd64 (2.4.114-1+b1) ... Setting up libcommons-digester-java (1.8.1-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up libdistlib-java (1.0-4) ... Setting up libparams-classify-perl:amd64 (0.015-2+b1) ... Setting up gpgsm (2.2.40-1.1) ... Setting up libpango-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libdrm-intel1:amd64 (2.4.114-1+b1) ... Setting up libgl1-mesa-dri:amd64 (22.3.6-1+deb12u1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libxmlgraphics-commons-java (2.8-2) ... Setting up default-jdk-doc (2:1.17-74) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.16.0-7) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up dirmngr (2.2.40-1.1) ... Setting up libmaven-filtering-java (3.3.0-1) ... Setting up libmaven-resolver-java (1.6.3-1) ... Setting up adwaita-icon-theme (43-1) ... 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) ... Setting up libxinerama1:amd64 (2:1.1.4-3) ... Setting up libxrandr2:amd64 (2:1.5.2-2+b1) ... Setting up gpg-wks-server (2.2.40-1.1) ... Setting up libcups2:amd64 (2.4.2-3+deb12u5) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up libwagon-http-java (3.5.3-1) ... Setting up libmaven-shared-utils-java (3.3.4-1) ... Setting up libfastinfoset-java (1.2.12-3) ... Setting up libngs-java:amd64 (3.0.3+dfsg-6~deb12u1) ... Setting up libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libmaven-resources-plugin-java (3.3.0-1) ... Setting up libhtsjdk-java (3.0.4+dfsg-2) ... Setting up libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up libglx-mesa0:amd64 (22.3.6-1+deb12u1) ... Setting up libxi6:amd64 (2:1.8-1+b1) ... Setting up gpg-wks-client (2.2.40-1.1) ... Setting up libglx0:amd64 (1.6.0-1) ... 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) ... Setting up libbatik-java (1.16+dfsg-1+deb12u1) ... Setting up libmoo-perl (2.005005-1) ... Setting up libxcursor1:amd64 (1:1.2.1-1) ... Setting up libmaven-invoker-java (3.2.0-1) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up libbiojava6-java-doc (6.1.0+dfsg-4) ... Setting up libgl1:amd64 (1.6.0-1) ... Setting up libmaven-clean-plugin-java (3.2.0-2) ... Setting up openjdk-17-jre-headless:amd64 (17.0.9+9-1~deb12u1) ... 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 gnupg (2.2.40-1.1) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libfop-java (1:2.8-2) ... Setting up libgtk2.0-0:amd64 (2.24.33-2) ... Setting up libmaven-archiver-java (3.6.0-1) ... Setting up liblwp-protocol-https-perl (6.10-1) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libwww-perl (6.68-1) ... Setting up devscripts (2.23.4+deb12u1) ... Setting up libguava-java (31.1-1) ... Setting up javahelper (0.78) ... 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 (3.8.7-1) ... Setting up libmaven-shared-incremental-java (1.1-3) ... Setting up libmaven-shared-io-java (3.0.0-4) ... Setting up libplexus-bsh-factory-java (1.0~alpha7-5) ... Setting up libplexus-compiler-java (2.12.1-1) ... Setting up libmaven-compiler-plugin-java (3.10.1-2) ... Setting up libjni-inchi-java (0.8+dfsg-7) ... Setting up libmaven-artifact-transfer-java (0.13.1-2) ... Setting up libmaven-file-management-java (3.0.0-1) ... Setting up libjmol-java (14.32.83+dfsg-2) ... 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 (1.10.0-1) ... Setting up libmsgpack-java (0.9.3-1) ... Setting up libmmtf-java (1.0.11-1) ... Setting up libjgrapht-java (1.5.1-3) ... 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 (2.36-9+deb12u3) ... Processing triggers for ca-certificates-java (20230710~deb12u1) ... 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:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068_2.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: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:E-Tugra_Certification_Authority.pem Adding debian:E-Tugra_Global_Root_CA_ECC_v3.pem Adding debian:E-Tugra_Global_Root_CA_RSA_v3.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_1.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:SZAFIR_ROOT_CA2.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:TrustCor_ECA-1.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_RootCert_CA-2.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 (3.8.7-1) ... update-alternatives: using /usr/share/maven/bin/mvn to provide /usr/bin/mvn (mvn) in auto mode Setting up openjdk-17-jdk-headless:amd64 (17.0.9+9-1~deb12u1) ... 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 (1.10.13-1) ... Setting up junit4 (4.13.2-3) ... Setting up default-jre-headless (2:1.17-74) ... Setting up openjdk-17-jre:amd64 (17.0.9+9-1~deb12u1) ... Setting up default-jre (2:1.17-74) ... Setting up openjdk-17-jdk:amd64 (17.0.9+9-1~deb12u1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up libplexus-ant-factory-java (1.0~alpha2.1-4) ... Setting up ant-optional (1.10.13-1) ... Setting up default-jdk-headless (2:1.17-74) ... Setting up junit5 (5.9.2-1) ... Setting up libistack-commons-java (3.0.6-5) ... Setting up default-jdk (2:1.17-74) ... Setting up libcodemodel-java (2.6+jaxb2.3.0.1-10.1) ... Setting up libtxw2-java (2.3.0.1-10.1) ... Setting up libjaxb-java (2.3.0.1-10.1) ... Setting up libbiojava6-java (6.1.0+dfsg-4) ... Processing triggers for sgml-base (1.31) ... Setting up libvelocity-tools-java (2.0-8) ... 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 (3.4.1-2) ... Setting up libmaven-reporting-impl-java (3.2.0-2) ... Setting up libmaven-plugin-tools-java (3.7.1-1) ... Setting up libsurefire-java (2.22.3-2) ... Setting up maven-debian-helper (2.6.3) ... Processing triggers for ca-certificates (20230311) ... 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 (20230710~deb12u1) ... 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/snpeff-5.1+d+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../snpeff_5.1+d+dfsg-3_source.changes dpkg-buildpackage: info: source package snpeff dpkg-buildpackage: info: source version 5.1+d+dfsg-3 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 debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/snpeff-5.1+d+dfsg' 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 -plibsnpeff-java # Removing the unit tests we copied into a subdirectory of src/test. if [ -e src/test/java/org ]; then \ rm -f -rf src/test/java/org; \ fi # Replacing our modified org/snpeff/SnpEff.java with the original one. if [ -e SnpEff.java.old ]; then \ mv SnpEff.java.old src/main/java/org/snpeff/SnpEff.java; \ fi make[1]: Leaving directory '/build/reproducible-path/snpeff-5.1+d+dfsg' jh_clean dh_clean debian/rules binary dh binary --with javahelper dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/snpeff-5.1+d+dfsg' # We replace the compiling timestamp by the one in d/changelog to enhance # build reproducibility. cp src/main/java/org/snpeff/SnpEff.java SnpEff.java.old sed "s/Gpr\.compile.*/\"$(date --utc --date="@1674244532" +"%Y-%m-%d %H:%M" )\";/" SnpEff.java.old > src/main/java/org/snpeff/SnpEff.java dh_auto_configure mh_patchpoms -plibsnpeff-java --debian-build --keep-pom-version --maven-repo=/build/reproducible-path/snpeff-5.1\+d\+dfsg/debian/maven-repo Failed to parse /build/reproducible-path/snpeff-5.1+d+dfsg/debian/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) at org.debian.maven.repo.POMReader.readPom(POMReader.java:82) at org.debian.maven.repo.POMReader.readPom(POMReader.java:57) at org.debian.maven.repo.Repository.scan(Repository.java:397) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:201) at org.debian.maven.repo.Repository.scanOnce(Repository.java:196) at org.debian.maven.repo.POMTransformer.usePluginVersionsFromRepository(POMTransformer.java:107) at org.debian.maven.repo.POMTransformer.main(POMTransformer.java:779) Failed to parse /build/reproducible-path/snpeff-5.1+d+dfsg/debian/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) at org.debian.maven.repo.POMReader.readPom(POMReader.java:82) at org.debian.maven.repo.POMReader.readPom(POMReader.java:57) at org.debian.maven.repo.Repository.scan(Repository.java:397) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:201) at org.debian.maven.repo.Repository.scanOnce(Repository.java:196) at org.debian.maven.repo.POMTransformer.usePluginVersionsFromRepository(POMTransformer.java:107) at org.debian.maven.repo.POMTransformer.main(POMTransformer.java:779) make[1]: Leaving directory '/build/reproducible-path/snpeff-5.1+d+dfsg' 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/snpeff-5.1\+d\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/snpeff-5.1\+d\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/snpeff-5.1\+d\+dfsg/debian/maven-repo --batch-mode package javadoc:jar javadoc:aggregate -DskipTests -Dnotimestamp=true -Dlocale=en_US OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release. [INFO] Scanning for projects... [INFO] [INFO] -------------------------< org.snpeff:snpeff >-------------------------- [INFO] Building SnpEff 5.1 [INFO] --------------------------------[ jar ]--------------------------------- [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 [WARNING] The POM for org.biojava:biojava-structure:jar:6.x is invalid, transitive dependencies (if any) will not be available, enable debug logging for more details [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ snpeff --- [INFO] Copying 5 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ snpeff --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 412 source files to /build/reproducible-path/snpeff-5.1+d+dfsg/target/classes [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/nextProt/NextProtDb.java:[122,28] ReaderInputStream(java.io.Reader) in org.apache.commons.io.input.ReaderInputStream has been deprecated [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdTranslocationsReport.java:[266,45] Configuration() in freemarker.template.Configuration has been deprecated [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdTranslocationsReport.java:[272,46] DefaultObjectWrapper() in freemarker.template.DefaultObjectWrapper has been deprecated [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdEff.java:[973,45] Configuration() in freemarker.template.Configuration has been deprecated [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdEff.java:[979,46] DefaultObjectWrapper() in freemarker.template.DefaultObjectWrapper has been deprecated [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ snpeff --- [INFO] skip non existing resourceDirectory /build/reproducible-path/snpeff-5.1+d+dfsg/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ snpeff --- [INFO] Changes detected - recompiling the module! [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ snpeff --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ snpeff --- [INFO] Building jar: /build/reproducible-path/snpeff-5.1+d+dfsg/target/snpeff-5.1.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ snpeff --- [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.snpeff... [WARNING] Loading source files for package org.snpeff.vcf... [WARNING] Loading source files for package org.snpeff.util... [WARNING] Loading source files for package org.snpeff.svg... [WARNING] Loading source files for package org.snpeff.stats.plot... [WARNING] Loading source files for package org.snpeff.stats... [WARNING] Loading source files for package org.snpeff.spliceSites... [WARNING] Loading source files for package org.snpeff.snpEffect... [WARNING] Loading source files for package org.snpeff.snpEffect.testCases.unity... [WARNING] Loading source files for package org.snpeff.snpEffect.testCases.integration... [WARNING] Loading source files for package org.snpeff.snpEffect.testCases... [WARNING] Loading source files for package org.snpeff.snpEffect.factory... [WARNING] Loading source files for package org.snpeff.snpEffect.commandLine... [WARNING] Loading source files for package org.snpeff.serializer... [WARNING] Loading source files for package org.snpeff.sam... [WARNING] Loading source files for package org.snpeff.reactome.events... [WARNING] Loading source files for package org.snpeff.reactome... [WARNING] Loading source files for package org.snpeff.probablility.bootstrap... [WARNING] Loading source files for package org.snpeff.probablility... [WARNING] Loading source files for package org.snpeff.ped... [WARNING] Loading source files for package org.snpeff.pdb... [WARNING] Loading source files for package org.snpeff.overlap... [WARNING] Loading source files for package org.snpeff.outputFormatter... [WARNING] Loading source files for package org.snpeff.osCmd... [WARNING] Loading source files for package org.snpeff.nmer... [WARNING] Loading source files for package org.snpeff.nextProt... [WARNING] Loading source files for package org.snpeff.motif... [WARNING] Loading source files for package org.snpeff.logStatsServer... [WARNING] Loading source files for package org.snpeff.interval.tree... [WARNING] Loading source files for package org.snpeff.interval.codonChange... [WARNING] Loading source files for package org.snpeff.interval... [WARNING] Loading source files for package org.snpeff.gtex... [WARNING] Loading source files for package org.snpeff.gsa... [WARNING] Loading source files for package org.snpeff.genotypes... [WARNING] Loading source files for package org.snpeff.geneSets.algorithm... [WARNING] Loading source files for package org.snpeff.geneSets... [WARNING] Loading source files for package org.snpeff.geneOntology... [WARNING] Loading source files for package org.snpeff.genBank... [WARNING] Loading source files for package org.snpeff.filter... [WARNING] Loading source files for package org.snpeff.fileIterator... [WARNING] Loading source files for package org.snpeff.fileIterator.parser... [WARNING] Loading source files for package org.snpeff.fileIterator.microCosm... [WARNING] Loading source files for package org.snpeff.fastq... [WARNING] Loading source files for package org.snpeff.coverage... [WARNING] Loading source files for package org.snpeff.complexity... [WARNING] Loading source files for package org.snpeff.collections... [WARNING] Loading source files for package org.snpeff.codons... [WARNING] Loading source files for package org.snpeff.binseq... [WARNING] Loading source files for package org.snpeff.binseq.indexer... [WARNING] Loading source files for package org.snpeff.binseq.comparator... [WARNING] Loading source files for package org.snpeff.binseq.coder... [WARNING] Loading source files for package org.snpeff.align... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 [WARNING] Building tree for all the packages and classes... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/spliceSites/AcgtTree.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/AlleleCountStats.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/collections/ArrayUtil.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/collections/AutoHashMap.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/Average.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/AverageInt.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/overlap/BasesChangeCounter.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/outputFormatter/BedAnnotationOutputFormatter.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fileIterator/BedFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/outputFormatter/BedOutputFormatter.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fileIterator/BigBedFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/binseq/BinarySequence.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/probablility/Binomial.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/probablility/Binomial.java:34: warning: invalid input: '<' [WARNING] * P( K <= k ) [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/probablility/Binomial.java:34: warning: invalid input: '<' [WARNING] * P( K <= k ) [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fileIterator/BinSeqFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/BioType.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/collections/BitUtil.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/collections/BitUtil.java:216: warning: invalid input: '&' [WARNING] /** Returns the popcount or cardinality of A & ~B [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/collections/BitUtil.java:216: warning: invalid input: '&' [WARNING] /** Returns the popcount or cardinality of A & ~B [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/reactome/events/BlackBoxEvent.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fileIterator/BlastResultEntry.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fileIterator/BlastResultFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/BooleanMutable.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/reactome/events/CatalystActivity.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/Cds.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/Chromosome.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/ChromosomeSimpleName.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/gsa/ChrPosScoreList.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/gsa/ChrPosScoreList.java:11: warning: invalid input: '<' [WARNING] * A list of [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/ChrPosStats.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/stats/ChrPosStats.java:67: warning: @param argument "num" is not a parameter name. [WARNING] * @param num [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/CircularCorrection.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/probablility/CochranArmitageTest.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/binseq/coder/Coder.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/coder/Coder.java:6: warning: invalid input: '&' [WARNING] * Class used to encode & decode sequences into binary and vice-versa [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/coder/Coder.java:58: warning: @param argument "c" is not a parameter name. [WARNING] * @param c [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/coder/Coder.java:67: warning: @param argument "c" is not a parameter name. [WARNING] * @param c [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/coder/Coder.java:82: warning: @param argument "c" is not a parameter name. [WARNING] * @param c [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/codonChange/CodonChange.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/codonChange/CodonChangeDel.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/codonChange/CodonChangeDup.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/codonChange/CodonChangeIns.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/codonChange/CodonChangeInterval.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/codonChange/CodonChangeInv.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/codonChange/CodonChangeMixed.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/codonChange/CodonChangeMnp.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/codonChange/CodonChangeSnp.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/codonChange/CodonChangeStructural.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/codons/CodonTable.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/codons/CodonTable.java:126: warning: @param argument "Amino" is not a parameter name. [WARNING] * @param Amino acid in three letter code [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/codons/CodonTables.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/codons/CodonTables.java:95: warning: invalid input: '&' [WARNING] * Set a codon table for a given genome & chromosome [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/codons/CodonTables.java:95: warning: invalid input: '&' [WARNING] * Set a codon table for a given genome & chromosome [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/util/CombinatorialIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/CommandLine.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/geneOntology/CompareByValue.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/geneSets/CompareByValue.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/snpEffect/testCases/integration/CompareEffects.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/snpEffect/testCases/integration/CompareToEnsembl.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/snpEffect/testCases/integration/CompareToVep.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/reactome/Compartment.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/reactome/events/Complex.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/snpEffect/Config.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/CountByKey.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/CountByType.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/Counter.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/CounterDouble.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/coverage/CountFragments.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/coverage/CountReads.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/coverage/CountReadsOnMarkers.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/coverage/Coverage.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/CoverageByType.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/coverage/CoverageChr.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/snpEffect/testCases/integration/CreateSpliceSiteTestCase.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/snpEffect/testCases/integration/CreateSpliceSiteTestCase.java:32: warning: @param argument "args" is not a parameter name. [WARNING] * @param args [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/Custom.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/nextProt/CvTerm.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/CytoBands.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/reactome/events/Depolymerisation.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/util/Diff.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/pdb/DistanceResult.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/binseq/DnaAndQualitySequence.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/DnaAndQualitySequence.java:21: warning: invalid input: '<' [WARNING] * - Two bits for the base {a, c, g, t} <=> {0, 1, 2, 3} [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/DnaAndQualitySequence.java:245: warning: @param argument "dataOutStream" is not a parameter name. [WARNING] * @param dataOutStream [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/DnaAndQualitySequence.java:261: warning: @param argument "dataOutStream" is not a parameter name. [WARNING] * @param dataOutStream [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/binseq/DnaAndQualitySequenceWithId.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/DnaAndQualitySequenceWithId.java:42: warning: @param argument "dataOutStream" is not a parameter name. [WARNING] * @param dataOutStream [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/binseq/coder/DnaCoder.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/coder/DnaCoder.java:8: warning: invalid input: '&' [WARNING] * Class used to encode & decode sequences into binary and vice-versa [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/coder/DnaCoder.java:12: warning: invalid input: '<' [WARNING] * It stores DNA bases into 2 bits {a,c,g,t} <-> {0,1,2,3} [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/coder/DnaCoder.java:290: warning: @param argument "linearIndex" is not a parameter name. [WARNING] * @param linearIndex [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/binseq/DnaNSequence.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/binseq/coder/DnaQualityCoder.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/coder/DnaQualityCoder.java:4: warning: invalid input: '&' [WARNING] * Class used to encode & decode sequences into binary and vice-versa [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/coder/DnaQualityCoder.java:9: warning: invalid input: '<' [WARNING] * - Two bits for the base {a, c, g, t} <=> {0, 1, 2, 3} [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/coder/DnaQualityCoder.java:60: warning: @param argument "c" is not a parameter name. [WARNING] * @param c [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/binseq/comparator/DnaQualSubsequenceComparator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fileIterator/DnaSeqFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fileIterator/DnaSeqIdFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fileIterator/DnaSeqPeFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/binseq/DnaSequence.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/DnaSequence.java:16: warning: invalid input: '<' [WARNING] * - Every base is encoded in 2 bits {a, c, g, t} <=> {0, 1, 2, 3} [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/binseq/DnaSequenceByte.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/DnaSequenceByte.java:8: warning: invalid input: '<' [WARNING] * - Every base is encoded in 2 bits {a, c, g, t} <=> {0, 1, 2, 3} [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/binseq/DnaSequenceId.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/DnaSequenceId.java:68: warning: @param argument "dataOutStream" is not a parameter name. [WARNING] * @param dataOutStream [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/DnaSequenceId.java:84: warning: @param argument "dataOutStream" is not a parameter name. [WARNING] * @param dataOutStream [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/binseq/DnaSequencePe.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/DnaSequencePe.java:109: warning: @param argument "dataOutStream" is not a parameter name. [WARNING] * @param dataOutStream [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/DnaSequencePe.java:125: warning: @param argument "dataOutStream" is not a parameter name. [WARNING] * @param dataOutStream [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/binseq/comparator/DnaSubsequenceComparator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/util/Download.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/Downstream.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/snpEffect/EffectType.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/vcf/EffFormatVersion.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/genBank/Embl.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/genBank/Embl.java:19: warning: @param argument "fileName" is not a parameter name. [WARNING] * @param fileName [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/genBank/Embl.java:120: warning: @param argument "fileName" is not a parameter name. [WARNING] * @param fileName [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/genBank/EmblFile.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/geneSets/algorithm/EnrichmentAlgorithm.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/geneSets/algorithm/EnrichmentAlgorithm.EnrichmentAlgorithmType.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/geneSets/algorithm/EnrichmentAlgorithmGreedy.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/geneSets/algorithm/EnrichmentAlgorithmGreedyVariableSize.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/reactome/Entity.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/reactome/Entity.TransferFunction.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/snpEffect/ErrorWarningType.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/reactome/events/Event.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/osCmd/ExecuteOsCommand.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/Exon.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/Exon.ExonSpliceType.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/ExonSpliceCharacterizer.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fileIterator/FastaFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/Fastq2Fastq.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fileIterator/FastqFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fastq/FastqSplit.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fastq/FastqTools.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fastq/FastqTrimmer.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fastq/FastqTrimmerAdrian.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/fastq/FastqTrimmerAdrian.java:29: warning: invalid input: '<' [WARNING] * if v(3)<25 then exit [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fastq/FastqTrimmerMedian.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/genBank/Feature.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/genBank/Feature.Type.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/genBank/FeatureCoordinates.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/genBank/Features.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/genBank/FeaturesFile.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/vcf/FileIndexChrPos.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/vcf/FileIndexChrPos.java:246: warning: invalid input: '<' [WARNING] * @return An array of 'len' bytes. null if either end of file (len > 0) or beginning of file (len < 0) [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/vcf/FileIndexChrPos.FileRegion.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/vcf/FileIndexChrPos.LineAndPos.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fileIterator/FileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/filter/Filter.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/codons/FindRareAaIntervals.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/probablility/FisherExactTest.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/probablility/FisherExactTest.java:170: warning: @param argument "theshold" is not a parameter name. [WARNING] * @param theshold Threshold value [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/probablility/FisherExactTest.java:249: warning: @param argument "theshold" is not a parameter name. [WARNING] * @param theshold Threshold value [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/probablility/FisherExactTest.java:315: warning: @param argument "theshold" is not a parameter name. [WARNING] * @param theshold Threshold value [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/probablility/FisherExactTest.java:336: warning: @param argument "theshold" is not a parameter name. [WARNING] * @param theshold Threshold value [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/geneSets/algorithm/FisherPValueAlgorithm.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/geneSets/algorithm/FisherPValueGreedyAlgorithm.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/FloatStats.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/FrameType.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/genBank/GenBank.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/genBank/GenBankFile.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/Gene.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/Gene.GeneType.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/GeneCountByTypeTable.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/stats/GeneCountByTypeTable.java:114: warning: invalid input: '<' [WARNING] * Sample this tuple to update statistics [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/stats/GeneCountByTypeTable.java:114: warning: invalid input: '<' [WARNING] * Sample this tuple to update statistics [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/reactome/GeneIds.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/GenericMarker.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fileIterator/GenericMarkerFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/Genes.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/interval/Genes.java:136: warning: invalid input: '<' [WARNING] * Note: If upDownLength <=0 no interval is created [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/interval/Genes.java:121: warning: @param argument "createIfMissing" is not a parameter name. [WARNING] * @param createIfMissing : If true, create canonical splice sites if they are missing. [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/interval/Genes.java:136: warning: invalid input: '<' [WARNING] * Note: If upDownLength <=0 no interval is created [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/geneSets/GeneSet.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/geneSets/GeneSets.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/geneSets/GeneSets.java:94: warning: @param argument "geneSetName" is not a parameter name. [WARNING] * @param geneSetName [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/geneSets/GeneSets.java:472: warning: @param argument "geneSetType" is not a parameter name. [WARNING] * @param geneSetType [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/geneSets/GeneSetsRanked.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/geneSets/GeneSetsRanked.java:129: warning: invalid input: '<' [WARNING] * Get geneId <-> Rank mapping [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/geneSets/GeneSetsRanked.java:129: warning: invalid input: '<' [WARNING] * Get geneId <-> Rank mapping [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/geneSets/GeneStats.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/Genome.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/interval/Genome.java:442: warning: invalid input: '&' [WARNING] * Show number of genes, transcripts & exons [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/interval/Genome.java:450: warning: invalid input: '&' [WARNING] * Show number of genes, transcripts & exons [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/interval/Genome.java:442: warning: invalid input: '&' [WARNING] * Show number of genes, transcripts & exons [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/interval/Genome.java:450: warning: invalid input: '&' [WARNING] * Show number of genes, transcripts & exons [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/binseq/GenomicSequences.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/genotypes/Genotypes.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/GenotypeStats.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/genotypes/GenotypeVector.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fileIterator/Gff3FileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/GffMarker.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/GffType.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/plot/GoogleBarChart.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/plot/GoogleChartVenn.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/plot/GoogleGenePercentBar.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/plot/GoogleGeneRegionChart.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/plot/GoogleGeneRegionNumExonsChart.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/plot/GoogleHistogram.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/plot/GoogleLineChart.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/plot/GooglePlot.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/plot/GooglePlotInt.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/geneOntology/GoTerm.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/geneOntology/GoTerm.java:95: warning: @param argument "goTermAcc" is not a parameter name. [WARNING] * @param goTermAcc [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/geneOntology/GoTerms.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:103: warning: @param argument "symbolName" is not a parameter name. [WARNING] * @param symbolName : Symbol's name [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:108: warning: @return tag cannot be used in method with void return type. [WARNING] public void addInterestingSymbol(String symbolId, int rank, HashSet noGoTermFound) { [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:117: warning: @param argument "goTermAcc" is not a parameter name. [WARNING] * @param goTermAcc [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:119: warning: @param argument "symbolName" is not a parameter name. [WARNING] * @param symbolName [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:120: warning: @param argument "goTermType" is not a parameter name. [WARNING] * @param goTermType [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:121: warning: @param argument "description" is not a parameter name. [WARNING] * @param description [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:459: warning: @return tag cannot be used in method with void return type. [WARNING] public void readInterestingSymbolIdsFile(String fileName) { [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:500: warning: @param argument "nameSpace" is not a parameter name. [WARNING] * @param nameSpace [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/util/Gpr.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/util/Gpr.java:532: warning: @param argument "showExceptions" is not a parameter name. [WARNING] * @param showExceptions : show exceptions if true [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/util/Gpr.java:543: warning: @param argument "showExceptions" is not a parameter name. [WARNING] * @param showExceptions : show exceptions if true [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/util/Gpr.java:704: warning: @param argument "count" is not a parameter name. [WARNING] * @param count [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/util/GprHtml.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/util/GprSeq.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/gtex/Gtex.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/gtex/GtexExperiment.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/Gtf2Marker.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fileIterator/GuessTableTypes.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/collections/HashLongLongArray.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/collections/HashLongLongArray.java:6: warning: invalid input: '<' [WARNING] * A Hash using primitive types instead or warped object [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/collections/HashLongLongArray.java:9: warning: invalid input: '<' [WARNING] * This could be implemented by simply doing HashMap > (but it [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/collections/HashLongLongArray.java:120: warning: invalid input: '<' [WARNING] * Insert a pair [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/collections/HashLongLongArray.java:120: warning: invalid input: '<' [WARNING] * Insert a pair [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/snpEffect/Hgvs.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/snpEffect/HgvsDna.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/snpEffect/HgvsProtein.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/HomHetStats.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/probablility/Hypergeometric.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/binseq/IdGenerator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/gtex/IdMap.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/gtex/IdMap.java:10: warning: invalid input: '<' [WARNING] * I.e. a mapping id <-> name where neither is unique [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/gtex/IdMap.java:25: warning: invalid input: '<' [WARNING] * Add a mapping id <-> name [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/gtex/IdMap.java:25: warning: invalid input: '<' [WARNING] * Add a mapping id <-> name [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/gtex/IdMap.java:49: warning: @param argument "name" is not a parameter name. [WARNING] * @param name [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/pdb/IdMapper.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/pdb/IdMapperEntry.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/snpEffect/testCases/integration/IntegrationTest.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/Intergenic.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/IntergenicConserved.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/Interval.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/IntervalAndSubIntervals.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/interval/IntervalAndSubIntervals.java:268: warning: invalid input: '<' [WARNING] * by reverse end position (if strand < 0) [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/interval/IntervalAndSubIntervals.java:268: warning: invalid input: '<' [WARNING] * by reverse end position (if strand < 0) [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/IntervalComparatorByEnd.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/IntervalComparatorByStart.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/tree/IntervalForest.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/tree/IntervalNode.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/interval/tree/IntervalNode.java:86: warning: @param argument "queryMarker" is not a parameter name. [WARNING] * @param queryMarker: The interval to intersect [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/tree/IntervalNodeOri.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/IntervalSetIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/tree/IntervalTree.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/tree/IntervalTreeArray.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/tree/IntervalTreeOri.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/snpEffect/IntHisto.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/Intron.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/IntronConserved.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/IntStats.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/util/Iterator2Iterable.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/tree/Itree.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/util/IubString.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/motif/Jaspar.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/util/KeyValue.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/geneSets/algorithm/LeadingEdgeFractionAlgorithm.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/vcf/LineChrPos.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fileIterator/LineClassFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fileIterator/LineFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/osCmd/LineFilter.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fileIterator/LineSeqFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/nextProt/Location.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/nextProt/LocationTargetIsoform.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/nextProt/LocationTargetIsoformInteraction.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/util/Log.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/util/Log.FatalErrorBehabiour.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/logStatsServer/LogStats.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/logStatsServer/LogStats.java:62: warning: invalid input: '<' [WARNING] * @param reportValues : A hash containing pairs to report [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/logStatsServer/LogStats.RequestResult.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/snpEffect/LossOfFunction.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/Marker.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/interval/Marker.java:659: warning: @param argument "variantEndPoint" is not a parameter name. [WARNING] * @param variantEndPoint : Before analyzing results, we have to change markers using variantrRef [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fileIterator/MarkerFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/MarkerParentId.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/Markers.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/MarkerSeq.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/serializer/MarkerSerializer.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/coverage/MarkerTypes.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/MarkerUtil.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/MarkerWithFrame.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fileIterator/MatrixEntry.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fileIterator/MatrixEntryFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fileIterator/microCosm/MicroCosmEntry.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fileIterator/microCosm/MicroCosmFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/MicroRnaBindingSite.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/MineMarkerIntervals.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/MineTwoMarkerIntervals.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/reactome/Monitor.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/Motif.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fileIterator/MotifFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/motif/MotifLogo.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/collections/MultivalueHashMap.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/align/NeedlemanWunsch.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/align/NeedlemanWunschOverlap.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/NextProt.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/nextProt/NextProtDb.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/nextProt/NextProtHandler.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/nextProt/NextProtMarkerFactory.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/nextProt/NextProtSequenceConservation.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/nextProt/NextProtXmlAnnotation.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/nextProt/NextProtXmlEntry.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/nextProt/NextProtXmlIsoform.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/nextProt/NextProtXmlNode.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/nmer/Nmer.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/nmer/Nmer.java:47: warning: @param argument "nmer" is not a parameter name. [WARNING] * @param nmer [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/nmer/Nmer.java:83: warning: @param argument "cq" is not a parameter name. [WARNING] * @param cq [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/nmer/NmerCount.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/nmer/NmerCount.java:34: warning: @param argument "threshold" is not a parameter name. [WARNING] * @param threshold [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/nmer/NmerCount.java:87: warning: @param argument "threshold" is not a parameter name. [WARNING] * @param threshold [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/nmer/NmerCount.java:105: warning: @param argument "threshold" is not a parameter name. [WARNING] * @param threshold [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/nmer/NmerCount.java:177: warning: @param argument "threshold" is not a parameter name. [WARNING] * @param threshold [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/nmer/NmerCountWc.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/geneSets/algorithm/NoneAlgorithm.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/probablility/NormalDistribution.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/probablility/NormalDistribution.java:9: warning: invalid input: '&' [WARNING] * Calculate Normal distribution (PDF & CDF) using more precision if required [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fileIterator/NullReader.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/ObservedOverExpected.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/stats/ObservedOverExpected.java:31: warning: @param argument "t" is not a parameter name. [WARNING] * @param t : Transcript [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/stats/ObservedOverExpected.java:131: warning: @param argument "Exon" is not a parameter name. [WARNING] * @param Exon [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/stats/ObservedOverExpected.java:140: warning: @param argument "Gene" is not a parameter name. [WARNING] * @param Gene [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/stats/ObservedOverExpected.java:160: warning: @param argument "Transcript" is not a parameter name. [WARNING] * @param Transcript [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/ObservedOverExpectedCHG.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/ObservedOverExpectedCHH.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/ObservedOverExpectedCpG.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/collections/OpenBitSet.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/collections/OpenBitSet.java:160: warning: invalid input: '<' [WARNING] * numWords should be <= bits.length, and [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/collections/OpenBitSet.java:161: warning: invalid input: '>' [WARNING] * any existing words in the array at position >= numWords should be zero. [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/osCmd/OsCmdQueue.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/osCmd/OsCmdRunner.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/outputFormatter/OutputFormatter.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/overlap/Overlap.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/overlap/Overlap.java:30: warning: Parameter "seq1" is documented more than once. [WARNING] * @param seq1 [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/overlap/OverlapDnaSeq.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/binseq/indexer/OverlapFilter.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/binseq/indexer/OverlapFilterCompareAllAll.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/binseq/indexer/OverlapFilterDnaId.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/binseq/indexer/OverlapRessult.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/fileIterator/parser/Parser.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/reactome/events/Pathway.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/Pcingola.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/pdb/PdbFile.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/ped/PedEntry.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/ped/PedFamily.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/ped/PedFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/ped/PedGenotype.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/vcf/Pedigree.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/vcf/PedigreeEntry.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/vcf/PedigreeEntry.java:9: warning: invalid input: '<' [WARNING] * ##PEDIGREE= [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/vcf/PedigreeEntry.java:12: warning: invalid input: '<' [WARNING] * ##PEDIGREE= [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/ped/PedPedigree.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/ped/PlinkMap.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/reactome/events/Polymerisation.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/stats/PosStats.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/osCmd/Progress.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/PromoterSequences.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/ProteinInteractionLocus.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/ProteinProteinInteractionLocus.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/apidocs/org/snpeff/interval/ProteinStructuralInteractionLocus.html... 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[WARNING] 100 warnings [INFO] Building jar: /build/reproducible-path/snpeff-5.1+d+dfsg/target/snpeff-5.1-javadoc.jar [INFO] [INFO] -------------------------< org.snpeff:snpeff >-------------------------- [INFO] Building SnpEff 5.1 [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] >>> maven-javadoc-plugin:3.4.1:aggregate (default-cli) > compile @ snpeff >>> [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ snpeff --- [INFO] Copying 5 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ snpeff --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 412 source files to /build/reproducible-path/snpeff-5.1+d+dfsg/target/classes [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/nextProt/NextProtDb.java:[122,28] ReaderInputStream(java.io.Reader) in org.apache.commons.io.input.ReaderInputStream has been deprecated [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdTranslocationsReport.java:[266,45] Configuration() in freemarker.template.Configuration has been deprecated [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdTranslocationsReport.java:[272,46] DefaultObjectWrapper() in freemarker.template.DefaultObjectWrapper has been deprecated [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdEff.java:[973,45] Configuration() in freemarker.template.Configuration has been deprecated [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdEff.java:[979,46] DefaultObjectWrapper() in freemarker.template.DefaultObjectWrapper has been deprecated [INFO] [INFO] <<< maven-javadoc-plugin:3.4.1:aggregate (default-cli) < compile @ snpeff <<< [INFO] [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:aggregate (default-cli) @ snpeff --- [INFO] Adding the --ignore-source-errors option [INFO] Configuration changed, re-generating javadoc. [WARNING] Javadoc Warnings [WARNING] Loading source files for package org.snpeff... [WARNING] Loading source files for package org.snpeff.vcf... [WARNING] Loading source files for package org.snpeff.util... [WARNING] Loading source files for package org.snpeff.svg... [WARNING] Loading source files for package org.snpeff.stats.plot... [WARNING] Loading source files for package org.snpeff.stats... [WARNING] Loading source files for package org.snpeff.spliceSites... [WARNING] Loading source files for package org.snpeff.snpEffect... [WARNING] Loading source files for package org.snpeff.snpEffect.testCases.unity... [WARNING] Loading source files for package org.snpeff.snpEffect.testCases.integration... [WARNING] Loading source files for package org.snpeff.snpEffect.testCases... [WARNING] Loading source files for package org.snpeff.snpEffect.factory... [WARNING] Loading source files for package org.snpeff.snpEffect.commandLine... 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[WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/probablility/Binomial.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/probablility/Binomial.java:34: warning: invalid input: '<' [WARNING] * P( K <= k ) [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/probablility/Binomial.java:34: warning: invalid input: '<' [WARNING] * P( K <= k ) [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fileIterator/BinSeqFileIterator.html... 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[WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/gsa/ChrPosScoreList.java:11: warning: invalid input: '<' [WARNING] * A list of [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/stats/ChrPosStats.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/stats/ChrPosStats.java:67: warning: @param argument "num" is not a parameter name. [WARNING] * @param num [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/CircularCorrection.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/probablility/CochranArmitageTest.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/binseq/coder/Coder.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/coder/Coder.java:6: warning: invalid input: '&' [WARNING] * Class used to encode & decode sequences into binary and vice-versa [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/coder/Coder.java:58: warning: @param argument "c" is not a parameter name. [WARNING] * @param c [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/coder/Coder.java:67: warning: @param argument "c" is not a parameter name. [WARNING] * @param c [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/coder/Coder.java:82: warning: @param argument "c" is not a parameter name. [WARNING] * @param c [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/CodonChange.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/CodonChangeDel.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/CodonChangeDup.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/CodonChangeIns.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/CodonChangeInterval.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/CodonChangeInv.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/CodonChangeMixed.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/CodonChangeMnp.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/CodonChangeSnp.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/CodonChangeStructural.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/codons/CodonTable.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/codons/CodonTable.java:126: warning: @param argument "Amino" is not a parameter name. [WARNING] * @param Amino acid in three letter code [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/codons/CodonTables.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/codons/CodonTables.java:95: warning: invalid input: '&' [WARNING] * Set a codon table for a given genome & chromosome [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/codons/CodonTables.java:95: warning: invalid input: '&' [WARNING] * Set a codon table for a given genome & chromosome [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/util/CombinatorialIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/CommandLine.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/geneOntology/CompareByValue.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/geneSets/CompareByValue.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/snpEffect/testCases/integration/CompareEffects.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/snpEffect/testCases/integration/CompareToEnsembl.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/snpEffect/testCases/integration/CompareToVep.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/reactome/Compartment.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/reactome/events/Complex.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/snpEffect/Config.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/stats/CountByKey.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/stats/CountByType.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/stats/Counter.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/stats/CounterDouble.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/coverage/CountFragments.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/coverage/CountReads.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/coverage/CountReadsOnMarkers.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/coverage/Coverage.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/stats/CoverageByType.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/coverage/CoverageChr.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/snpEffect/testCases/integration/CreateSpliceSiteTestCase.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/snpEffect/testCases/integration/CreateSpliceSiteTestCase.java:32: warning: @param argument "args" is not a parameter name. [WARNING] * @param args [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/Custom.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/nextProt/CvTerm.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/CytoBands.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/reactome/events/Depolymerisation.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/util/Diff.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/pdb/DistanceResult.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/binseq/DnaAndQualitySequence.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/DnaAndQualitySequence.java:21: warning: invalid input: '<' [WARNING] * - Two bits for the base {a, c, g, t} <=> {0, 1, 2, 3} [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/DnaAndQualitySequence.java:245: warning: @param argument "dataOutStream" is not a parameter name. [WARNING] * @param dataOutStream [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/DnaAndQualitySequence.java:261: warning: @param argument "dataOutStream" is not a parameter name. [WARNING] * @param dataOutStream [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/binseq/DnaAndQualitySequenceWithId.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/DnaAndQualitySequenceWithId.java:42: warning: @param argument "dataOutStream" is not a parameter name. [WARNING] * @param dataOutStream [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/binseq/coder/DnaCoder.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/coder/DnaCoder.java:8: warning: invalid input: '&' [WARNING] * Class used to encode & decode sequences into binary and vice-versa [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/coder/DnaCoder.java:12: warning: invalid input: '<' [WARNING] * It stores DNA bases into 2 bits {a,c,g,t} <-> {0,1,2,3} [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/coder/DnaCoder.java:290: warning: @param argument "linearIndex" is not a parameter name. [WARNING] * @param linearIndex [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/binseq/DnaNSequence.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/binseq/coder/DnaQualityCoder.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/coder/DnaQualityCoder.java:4: warning: invalid input: '&' [WARNING] * Class used to encode & decode sequences into binary and vice-versa [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/coder/DnaQualityCoder.java:9: warning: invalid input: '<' [WARNING] * - Two bits for the base {a, c, g, t} <=> {0, 1, 2, 3} [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/coder/DnaQualityCoder.java:60: warning: @param argument "c" is not a parameter name. [WARNING] * @param c [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/binseq/comparator/DnaQualSubsequenceComparator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fileIterator/DnaSeqFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fileIterator/DnaSeqIdFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fileIterator/DnaSeqPeFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/binseq/DnaSequence.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/DnaSequence.java:16: warning: invalid input: '<' [WARNING] * - Every base is encoded in 2 bits {a, c, g, t} <=> {0, 1, 2, 3} [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/binseq/DnaSequenceByte.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/DnaSequenceByte.java:8: warning: invalid input: '<' [WARNING] * - Every base is encoded in 2 bits {a, c, g, t} <=> {0, 1, 2, 3} [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/binseq/DnaSequenceId.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/DnaSequenceId.java:68: warning: @param argument "dataOutStream" is not a parameter name. [WARNING] * @param dataOutStream [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/DnaSequenceId.java:84: warning: @param argument "dataOutStream" is not a parameter name. [WARNING] * @param dataOutStream [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/binseq/DnaSequencePe.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/DnaSequencePe.java:109: warning: @param argument "dataOutStream" is not a parameter name. [WARNING] * @param dataOutStream [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/binseq/DnaSequencePe.java:125: warning: @param argument "dataOutStream" is not a parameter name. [WARNING] * @param dataOutStream [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/binseq/comparator/DnaSubsequenceComparator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/util/Download.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/Downstream.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/snpEffect/EffectType.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/vcf/EffFormatVersion.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/genBank/Embl.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/genBank/Embl.java:19: warning: @param argument "fileName" is not a parameter name. [WARNING] * @param fileName [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/genBank/Embl.java:120: warning: @param argument "fileName" is not a parameter name. [WARNING] * @param fileName [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/genBank/EmblFile.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/EnrichmentAlgorithm.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/EnrichmentAlgorithm.EnrichmentAlgorithmType.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/EnrichmentAlgorithmGreedy.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/EnrichmentAlgorithmGreedyVariableSize.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/reactome/Entity.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/reactome/Entity.TransferFunction.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/snpEffect/ErrorWarningType.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/reactome/events/Event.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/osCmd/ExecuteOsCommand.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/Exon.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/Exon.ExonSpliceType.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/ExonSpliceCharacterizer.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fileIterator/FastaFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/Fastq2Fastq.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fileIterator/FastqFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fastq/FastqSplit.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fastq/FastqTools.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fastq/FastqTrimmer.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fastq/FastqTrimmerAdrian.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/fastq/FastqTrimmerAdrian.java:29: warning: invalid input: '<' [WARNING] * if v(3)<25 then exit [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fastq/FastqTrimmerMedian.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/genBank/Feature.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/genBank/Feature.Type.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/genBank/FeatureCoordinates.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/genBank/Features.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/genBank/FeaturesFile.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/vcf/FileIndexChrPos.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/vcf/FileIndexChrPos.java:246: warning: invalid input: '<' [WARNING] * @return An array of 'len' bytes. null if either end of file (len > 0) or beginning of file (len < 0) [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/vcf/FileIndexChrPos.FileRegion.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/vcf/FileIndexChrPos.LineAndPos.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fileIterator/FileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/filter/Filter.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/codons/FindRareAaIntervals.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/probablility/FisherExactTest.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/probablility/FisherExactTest.java:170: warning: @param argument "theshold" is not a parameter name. [WARNING] * @param theshold Threshold value [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/probablility/FisherExactTest.java:249: warning: @param argument "theshold" is not a parameter name. [WARNING] * @param theshold Threshold value [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/probablility/FisherExactTest.java:315: warning: @param argument "theshold" is not a parameter name. [WARNING] * @param theshold Threshold value [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/probablility/FisherExactTest.java:336: warning: @param argument "theshold" is not a parameter name. [WARNING] * @param theshold Threshold value [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/FisherPValueAlgorithm.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/FisherPValueGreedyAlgorithm.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/stats/FloatStats.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/FrameType.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/genBank/GenBank.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/genBank/GenBankFile.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/Gene.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/Gene.GeneType.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/stats/GeneCountByTypeTable.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/stats/GeneCountByTypeTable.java:114: warning: invalid input: '<' [WARNING] * Sample this tuple to update statistics [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/stats/GeneCountByTypeTable.java:114: warning: invalid input: '<' [WARNING] * Sample this tuple to update statistics [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/reactome/GeneIds.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/GenericMarker.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fileIterator/GenericMarkerFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/Genes.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/interval/Genes.java:136: warning: invalid input: '<' [WARNING] * Note: If upDownLength <=0 no interval is created [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/interval/Genes.java:121: warning: @param argument "createIfMissing" is not a parameter name. [WARNING] * @param createIfMissing : If true, create canonical splice sites if they are missing. [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/interval/Genes.java:136: warning: invalid input: '<' [WARNING] * Note: If upDownLength <=0 no interval is created [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/geneSets/GeneSet.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/geneSets/GeneSets.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/geneSets/GeneSets.java:94: warning: @param argument "geneSetName" is not a parameter name. [WARNING] * @param geneSetName [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/geneSets/GeneSets.java:472: warning: @param argument "geneSetType" is not a parameter name. [WARNING] * @param geneSetType [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/geneSets/GeneSetsRanked.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/geneSets/GeneSetsRanked.java:129: warning: invalid input: '<' [WARNING] * Get geneId <-> Rank mapping [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/geneSets/GeneSetsRanked.java:129: warning: invalid input: '<' [WARNING] * Get geneId <-> Rank mapping [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/geneSets/GeneStats.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/Genome.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/interval/Genome.java:442: warning: invalid input: '&' [WARNING] * Show number of genes, transcripts & exons [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/interval/Genome.java:450: warning: invalid input: '&' [WARNING] * Show number of genes, transcripts & exons [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/interval/Genome.java:442: warning: invalid input: '&' [WARNING] * Show number of genes, transcripts & exons [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/interval/Genome.java:450: warning: invalid input: '&' [WARNING] * Show number of genes, transcripts & exons [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/binseq/GenomicSequences.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/genotypes/Genotypes.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/stats/GenotypeStats.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/genotypes/GenotypeVector.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fileIterator/Gff3FileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/GffMarker.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/GffType.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/stats/plot/GoogleBarChart.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/stats/plot/GoogleChartVenn.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/stats/plot/GoogleGenePercentBar.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/stats/plot/GoogleGeneRegionChart.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/stats/plot/GoogleGeneRegionNumExonsChart.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/stats/plot/GoogleHistogram.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/stats/plot/GoogleLineChart.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/stats/plot/GooglePlot.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/stats/plot/GooglePlotInt.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/geneOntology/GoTerm.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/geneOntology/GoTerm.java:95: warning: @param argument "goTermAcc" is not a parameter name. [WARNING] * @param goTermAcc [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/geneOntology/GoTerms.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:103: warning: @param argument "symbolName" is not a parameter name. [WARNING] * @param symbolName : Symbol's name [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:108: warning: @return tag cannot be used in method with void return type. [WARNING] public void addInterestingSymbol(String symbolId, int rank, HashSet noGoTermFound) { [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:117: warning: @param argument "goTermAcc" is not a parameter name. [WARNING] * @param goTermAcc [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:119: warning: @param argument "symbolName" is not a parameter name. [WARNING] * @param symbolName [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:120: warning: @param argument "goTermType" is not a parameter name. [WARNING] * @param goTermType [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:121: warning: @param argument "description" is not a parameter name. [WARNING] * @param description [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:459: warning: @return tag cannot be used in method with void return type. [WARNING] public void readInterestingSymbolIdsFile(String fileName) { [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:500: warning: @param argument "nameSpace" is not a parameter name. [WARNING] * @param nameSpace [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/util/Gpr.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/util/Gpr.java:532: warning: @param argument "showExceptions" is not a parameter name. [WARNING] * @param showExceptions : show exceptions if true [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/util/Gpr.java:543: warning: @param argument "showExceptions" is not a parameter name. [WARNING] * @param showExceptions : show exceptions if true [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/util/Gpr.java:704: warning: @param argument "count" is not a parameter name. [WARNING] * @param count [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/util/GprHtml.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/util/GprSeq.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/gtex/Gtex.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/gtex/GtexExperiment.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/Gtf2Marker.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fileIterator/GuessTableTypes.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/collections/HashLongLongArray.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/collections/HashLongLongArray.java:6: warning: invalid input: '<' [WARNING] * A Hash using primitive types instead or warped object [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/collections/HashLongLongArray.java:9: warning: invalid input: '<' [WARNING] * This could be implemented by simply doing HashMap > (but it [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/collections/HashLongLongArray.java:120: warning: invalid input: '<' [WARNING] * Insert a pair [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/collections/HashLongLongArray.java:120: warning: invalid input: '<' [WARNING] * Insert a pair [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/snpEffect/Hgvs.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/snpEffect/HgvsDna.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/snpEffect/HgvsProtein.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/stats/HomHetStats.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/probablility/Hypergeometric.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/binseq/IdGenerator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/gtex/IdMap.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/gtex/IdMap.java:10: warning: invalid input: '<' [WARNING] * I.e. a mapping id <-> name where neither is unique [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/gtex/IdMap.java:25: warning: invalid input: '<' [WARNING] * Add a mapping id <-> name [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/gtex/IdMap.java:25: warning: invalid input: '<' [WARNING] * Add a mapping id <-> name [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/gtex/IdMap.java:49: warning: @param argument "name" is not a parameter name. [WARNING] * @param name [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/pdb/IdMapper.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/pdb/IdMapperEntry.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/snpEffect/testCases/integration/IntegrationTest.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/Intergenic.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/IntergenicConserved.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/Interval.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/IntervalAndSubIntervals.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/interval/IntervalAndSubIntervals.java:268: warning: invalid input: '<' [WARNING] * by reverse end position (if strand < 0) [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/interval/IntervalAndSubIntervals.java:268: warning: invalid input: '<' [WARNING] * by reverse end position (if strand < 0) [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/IntervalComparatorByEnd.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/IntervalComparatorByStart.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/tree/IntervalForest.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/tree/IntervalNode.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/interval/tree/IntervalNode.java:86: warning: @param argument "queryMarker" is not a parameter name. [WARNING] * @param queryMarker: The interval to intersect [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/tree/IntervalNodeOri.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/IntervalSetIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/tree/IntervalTree.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/tree/IntervalTreeArray.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/tree/IntervalTreeOri.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/snpEffect/IntHisto.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/Intron.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/IntronConserved.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/stats/IntStats.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/util/Iterator2Iterable.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/tree/Itree.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/util/IubString.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/motif/Jaspar.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/util/KeyValue.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/LeadingEdgeFractionAlgorithm.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/vcf/LineChrPos.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fileIterator/LineClassFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fileIterator/LineFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/osCmd/LineFilter.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fileIterator/LineSeqFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/nextProt/Location.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/nextProt/LocationTargetIsoform.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/nextProt/LocationTargetIsoformInteraction.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/util/Log.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/util/Log.FatalErrorBehabiour.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/logStatsServer/LogStats.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/logStatsServer/LogStats.java:62: warning: invalid input: '<' [WARNING] * @param reportValues : A hash containing pairs to report [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/logStatsServer/LogStats.RequestResult.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/snpEffect/LossOfFunction.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/Marker.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/interval/Marker.java:659: warning: @param argument "variantEndPoint" is not a parameter name. [WARNING] * @param variantEndPoint : Before analyzing results, we have to change markers using variantrRef [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fileIterator/MarkerFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/MarkerParentId.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/Markers.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/MarkerSeq.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/serializer/MarkerSerializer.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/coverage/MarkerTypes.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/MarkerUtil.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/MarkerWithFrame.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fileIterator/MatrixEntry.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fileIterator/MatrixEntryFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fileIterator/microCosm/MicroCosmEntry.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fileIterator/microCosm/MicroCosmFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/MicroRnaBindingSite.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/stats/MineMarkerIntervals.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/stats/MineTwoMarkerIntervals.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/reactome/Monitor.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/Motif.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fileIterator/MotifFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/motif/MotifLogo.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/collections/MultivalueHashMap.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/align/NeedlemanWunsch.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/align/NeedlemanWunschOverlap.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/NextProt.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/nextProt/NextProtDb.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/nextProt/NextProtHandler.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/nextProt/NextProtMarkerFactory.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/nextProt/NextProtSequenceConservation.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/nextProt/NextProtXmlAnnotation.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/nextProt/NextProtXmlEntry.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/nextProt/NextProtXmlIsoform.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/nextProt/NextProtXmlNode.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/nmer/Nmer.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/nmer/Nmer.java:47: warning: @param argument "nmer" is not a parameter name. [WARNING] * @param nmer [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/nmer/Nmer.java:83: warning: @param argument "cq" is not a parameter name. [WARNING] * @param cq [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/nmer/NmerCount.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/nmer/NmerCount.java:34: warning: @param argument "threshold" is not a parameter name. [WARNING] * @param threshold [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/nmer/NmerCount.java:87: warning: @param argument "threshold" is not a parameter name. [WARNING] * @param threshold [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/nmer/NmerCount.java:105: warning: @param argument "threshold" is not a parameter name. [WARNING] * @param threshold [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/nmer/NmerCount.java:177: warning: @param argument "threshold" is not a parameter name. [WARNING] * @param threshold [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/nmer/NmerCountWc.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/NoneAlgorithm.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/probablility/NormalDistribution.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/probablility/NormalDistribution.java:9: warning: invalid input: '&' [WARNING] * Calculate Normal distribution (PDF & CDF) using more precision if required [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fileIterator/NullReader.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/stats/ObservedOverExpected.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/stats/ObservedOverExpected.java:31: warning: @param argument "t" is not a parameter name. [WARNING] * @param t : Transcript [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/stats/ObservedOverExpected.java:131: warning: @param argument "Exon" is not a parameter name. [WARNING] * @param Exon [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/stats/ObservedOverExpected.java:140: warning: @param argument "Gene" is not a parameter name. [WARNING] * @param Gene [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/stats/ObservedOverExpected.java:160: warning: @param argument "Transcript" is not a parameter name. [WARNING] * @param Transcript [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/stats/ObservedOverExpectedCHG.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/stats/ObservedOverExpectedCHH.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/stats/ObservedOverExpectedCpG.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/collections/OpenBitSet.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/collections/OpenBitSet.java:160: warning: invalid input: '<' [WARNING] * numWords should be <= bits.length, and [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/collections/OpenBitSet.java:161: warning: invalid input: '>' [WARNING] * any existing words in the array at position >= numWords should be zero. [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/osCmd/OsCmdQueue.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/osCmd/OsCmdRunner.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/outputFormatter/OutputFormatter.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/overlap/Overlap.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/overlap/Overlap.java:30: warning: Parameter "seq1" is documented more than once. [WARNING] * @param seq1 [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/overlap/OverlapDnaSeq.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/binseq/indexer/OverlapFilter.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/binseq/indexer/OverlapFilterCompareAllAll.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/binseq/indexer/OverlapFilterDnaId.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/binseq/indexer/OverlapRessult.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fileIterator/parser/Parser.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/reactome/events/Pathway.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/Pcingola.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/pdb/PdbFile.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/ped/PedEntry.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/ped/PedFamily.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/ped/PedFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/ped/PedGenotype.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/vcf/Pedigree.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/vcf/PedigreeEntry.html... [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/vcf/PedigreeEntry.java:9: warning: invalid input: '<' [WARNING] * ##PEDIGREE= [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.1+d+dfsg/src/main/java/org/snpeff/vcf/PedigreeEntry.java:12: warning: invalid input: '<' [WARNING] * ##PEDIGREE= [WARNING] ^ [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/ped/PedPedigree.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/ped/PlinkMap.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/reactome/events/Polymerisation.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/stats/PosStats.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/osCmd/Progress.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/PromoterSequences.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/ProteinInteractionLocus.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/ProteinProteinInteractionLocus.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/ProteinStructuralInteractionLocus.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/snpEffect/PurityChange.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/gsa/PvaluesList.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/motif/Pwm.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/motif/PwmAndSeqs.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/Qseq2Fastq.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/probablility/RandMarker.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/probablility/RankSumNoReplacementPdf.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/probablility/RankSumNoReplacementSimulate.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/probablility/RankSumPdf.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/RankSumPValueAlgorithm.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/RankSumPValueGreedyAlgorithm.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/RareAminoAcid.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/reactome/events/Reaction.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/reactome/events/Reaction.RegulationType.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/reactome/Reactome.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/stats/ReadsOnMarkersModel.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/interval/Regulation.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fileIterator/RegulationBedFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/RegulationConsensusMultipleBed.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/RegulationFileConsensus.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fileIterator/RegulationFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/RegulationFileSplitBytType.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/fileIterator/RegulationGffFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/probablility/bootstrap/ReSampleInt.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/probablility/bootstrap/ReSampleMap.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/probablility/bootstrap/ReSampleMapRank.html... [WARNING] Generating /build/reproducible-path/snpeff-5.1+d+dfsg/target/site/apidocs/org/snpeff/geneSets/Result.html... 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[WARNING] 100 warnings [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:44 min [INFO] Finished at: 2025-02-14T05:12:14Z [INFO] ------------------------------------------------------------------------  debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/snpeff-5.1+d+dfsg' # Moving the unit tests into a subdir of src/test so that Maven sees them. mkdir -p src/test/java/org/snpeff/snpEffect/testCases cp -a src/main/java/org/snpeff/snpEffect/testCases/integration src/test/java/org/snpeff/snpEffect/testCases cp -a src/main/java/org/snpeff/snpEffect/testCases/unity src/test/java/org/snpeff/snpEffect/testCases dh_auto_test /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/snpeff-5.1\+d\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/snpeff-5.1\+d\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/snpeff-5.1\+d\+dfsg/debian/maven-repo --batch-mode test OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release. [INFO] Scanning for projects... [INFO] [INFO] -------------------------< org.snpeff:snpeff >-------------------------- [INFO] Building SnpEff 5.1 [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The POM for org.biojava:biojava-structure:jar:6.x is invalid, transitive dependencies (if any) will not be available, enable debug logging for more details [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ snpeff --- [INFO] Copying 5 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ snpeff --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ snpeff --- [INFO] skip non existing resourceDirectory /build/reproducible-path/snpeff-5.1+d+dfsg/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ snpeff --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 135 source files to /build/reproducible-path/snpeff-5.1+d+dfsg/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ snpeff --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesProteinInteraction TestCasesProteinInteraction.test_02_split_codon_base(58): Test TestCasesProteinInteraction.test_01_split_codon_base(26): Test [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.986 s - in org.snpeff.snpEffect.testCases.unity.TestCasesProteinInteraction [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesNmers TestCasesNmers.test_03_Nmers(33): Test [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.019 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNmers [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage TestCasesCochranArmitage.test_01(18): Test TestCasesCochranArmitage.test_02(28): Test TestCasesCochranArmitage.test_03(37): Test TestCasesCochranArmitage.test_04(46): Test TestCasesCochranArmitage.test_05(57): Test [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.064 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCytoBands [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.006 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCytoBands [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesAlign TestCasesAlign.test_01(22): Test TestCasesAlign.test_02(45): Test [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAlign [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDels TestCasesDels.test_01(138): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... 300 .................................................................................................... 400 .................................................................................................... 500 .................................................................................................... 600 .................................................................................................... 700 .................................................................................................... 800 .................................................................................................... 900 .................................................................................................... 1000 [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 16.99 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDels [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSpliceRegion TestCasesSpliceRegion.test_01(33): Test ..................[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.609 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceRegion [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHypergeometric TestCasesHypergeometric.test_0(77): Test TestCasesHypergeometric.test_01_hyper(83): Test TestCasesHypergeometric.test_02_hyper(202): Test [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHypergeometric [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesMnps TestCasesMnps.test_01(187): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... 300 .................................................................................................... 400 .................................................................................................... 500 .................................................................................................... 600 .................................................................................................... 700 .................................................................................................... 800 .................................................................................................... 900 .................................................................................................... 1000 [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 57.622 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMnps [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite TestCasesSpliceSite.test_01(34): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... 300 .................................................................................................... 400 .................................................................................................... 500 .................................................................................................... 600 .................................................................................................... 700 .................................................................................................... 800 .................................................................................................... 900 .................................................................................................... 1000 [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.573 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron TestCasesHgvsIntron.test_01_intron(23): Test ............................................................... 100 ............................................................ 200 ................................................................ 300 ......................................................... 400 ......................................................................................................................... 600 ......................................................................................................... 800 ....................................................... 900 .................................................................. 1000 ............................................................. 1100 .................................................................. 1200 ......................................................... 1300 ........................................................................................................... 1500 ....................................................... 1600 ............................................................... [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.608 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntergenic TestCasesIntergenic.test_01(30): Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.345 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntergenic [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns TestCasesApplyIns.test_apply_variant_01(21): Test TestCasesApplyIns.test_apply_variant_02(32): Test TestCasesApplyIns.test_apply_variant_03(43): Test TestCasesApplyIns.test_apply_variant_04(54): Test TestCasesApplyIns.test_apply_variant_05(72): Test TestCasesApplyIns.test_apply_variant_06(90): Test TestCasesApplyIns.test_apply_variant_07(108): Test TestCasesApplyIns.test_apply_variant_08(126): Test TestCasesApplyIns.test_apply_variant_09(137): Test TestCasesApplyIns.test_apply_variant_10(148): Test TestCasesApplyIns.test_apply_variant_11(159): Test TestCasesApplyIns.test_apply_variant_12(178): Test TestCasesApplyIns.test_apply_variant_13(192): Test [INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 28.132 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp TestCasesApplyMnp.test_apply_variant_01(22): Test TestCasesApplyMnp.test_apply_variant_02(33): Test TestCasesApplyMnp.test_apply_variant_03(44): Test TestCasesApplyMnp.test_apply_variant_04(61): Test TestCasesApplyMnp.test_apply_variant_05(79): Test TestCasesApplyMnp.test_apply_variant_06(97): Test TestCasesApplyMnp.test_apply_variant_07(115): Test TestCasesApplyMnp.test_apply_variant_08(133): Test TestCasesApplyMnp.test_apply_variant_09(144): Test TestCasesApplyMnp.test_apply_variant_10(155): Test TestCasesApplyMnp.test_apply_variant_11(176): Test TestCasesApplyMnp.test_apply_variant_12(197): Test TestCasesApplyMnp.test_apply_variant_13(219): Test [INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 27.264 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCds TestCasesCds.test_CdsPos(35): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... 300 .................................................................................................... 400 .................................................................................................... 500 .................................................................................................... 600 .................................................................................................... 700 .................................................................................................... 800 .................................................................................................... 900 .................................................................................................... 1000 TestCasesCds.test_cdsStartEnd_1(73): Test TestCasesCds.test_cdsStartEnd_2(96): Test WARNING_EXON_NOT_FOUND: WARNING: Cannot find first exonic position after 101 for transcript 'tr1' [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.446 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCds [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence TestCasesDnaSequence.test_02_long_replaceBase(277): Test TestCasesDnaSequence.test_05_fastqReader(320): Test TestCasesDnaSequence.test_06_quality_long(349): Test TestCasesDnaSequence.test_02_long_getBases(267): Test TestCasesDnaSequence.test_01_short_getBases(228): Test TestCasesDnaSequence.test_01_short(209): Test TestCasesDnaSequence.test_02_long(248): Test TestCasesDnaSequence.test_05_quality_short(340): Test TestCasesDnaSequence.test_02_long_getBase(257): Test TestCasesDnaSequence.test_01_short_getBase(218): Test TestCasesDnaSequence.test_04_Pe(287): Test TestCasesDnaSequence.test_01_short_replaceBase(238): Test [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 22.613 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesBinomial TestCasesBinomial.test_01(86): Test TestCasesBinomial.test_02(191): Test TestCasesBinomial.test_03(299): Test [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBinomial [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp TestCasesApplySnp.test_apply_variant_01(21): Test TestCasesApplySnp.test_apply_variant_02(31): Test TestCasesApplySnp.test_apply_variant_04(41): Test TestCasesApplySnp.test_apply_variant_05(59): Test TestCasesApplySnp.test_apply_variant_06(77): Test TestCasesApplySnp.test_apply_variant_08(95): Test TestCasesApplySnp.test_apply_variant_09(106): Test [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.728 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon TestCasesHgvsExon.test_01_coding(27): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... 300 .................................................................................................... 400 .................................................................................................... 500 .................................................................................................... 600 .................................................................................................... 700 .................................................................................................... 800 .................................................................................................... 900 .................................................................................................... 1000 [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.503 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList TestCasesGenePvalueList.test_01(28): Test TestCasesGenePvalueList.test_02(46): Test TestCasesGenePvalueList.test_03(64): Test TestCasesGenePvalueList.test_04(82): Test TestCasesGenePvalueList.test_05(111): Test TestCasesGenePvalueList.test_06(129): Test TestCasesGenePvalueList.test_07(155): Test TestCasesGenePvalueList.test_08(187): Test TestCasesGenePvalueList.test_09(209): Test [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.088 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment TestCasesVariantRealignment.test_07_savant(203): Test TestCasesVariantRealignment.test_01(56): Test TestCasesVariantRealignment.test_02(82): Test TestCasesVariantRealignment.test_03(105): Test TestCasesVariantRealignment.test_05_savant(157): Test TestCasesVariantRealignment.test_04_Intron(131): Test TestCasesVariantRealignment.test_06_savant(194): Test TestCasesVariantRealignment.test_09_reallyLongRealign(224): Test TestCasesVariantRealignment.test_05_savant_opposite(174): Test TestCasesVariantRealignment.test_08_reallyLongRealign(213): Test [INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 14.268 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap TestCasesDnaOverlap.test_10_overlap(332): Test TestCasesDnaOverlap.test_07_overlap(297): Test TestCasesDnaOverlap.test_12_overlap(356): Test TestCasesDnaOverlap.test_09_overlap(320): Test TestCasesDnaOverlap.test_17_overlap_rand(462): Test Overlap random test: .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... 300 .................................................................................................... 400 .................................................................................................... 500 .................................................................................................... 600 .................................................................................................... 700 .................................................................................................... 800 .................................................................................................... 900 ................................................................................................... Done. TestCasesDnaOverlap.test_15_DnaCoder_copy_1(380): Test .........TestCasesDnaOverlap.test_11_overlap(344): Test TestCasesDnaOverlap.test_08_overlap(308): Test TestCasesDnaOverlap.test_18_DnaCoder_score_rand(477): Test DnaCoder.score test: .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... 300 .................................................................................................... 400 .................................................................................................... 500 .................................................................................................... 600 .................................................................................................... 700 .................................................................................................... 800 .................................................................................................... 900 ...................................................................................................Done. TestCasesDnaOverlap.test_13_overlap(368): Test TestCasesDnaOverlap.test_19_score_threshold_rand(496): Test Score (threshold) random test: .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... 300 .................................................................................................... 400 .................................................................................................... 500 .................................................................................................... 600 .................................................................................................... 700 .................................................................................................... 800 .................................................................................................... 900 ................................................................................................... Done. TestCasesDnaOverlap.test_16_DnaCoder_copy_2(438): Test DnaCoder.copyBases test: Max words: 1 ......... Max words: 2 ......... Max words: 3 ......... Max words: 4 ......... Max words: 5 ......... Max words: 6 ......... Max words: 7 ......... Max words: 8 ......... Max words: 9 ......... Done. [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 29.343 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesReactome TestCasesReactome.test_01(32): Test TestCasesReactome.test_01(48): Out: 0.9051482536448667 TestCasesReactome.test_02(57): Test TestCasesReactome.test_02(75): Out: -0.8192933610763514 TestCasesReactome.test_02(80): Out: 2.1152011710898737 TestCasesReactome.test_03(89): Test TestCasesReactome.test_03(105): Out: 0.86631007995171 TestCasesReactome.test_03(110): Out: 2.1219547901144384 TestCasesReactome.test_04(119): Test TestCasesReactome.test_04(135): Out: 0.6973026352658382 TestCasesReactome.test_04(140): Out: -0.5583420748968899 TestCasesReactome.test_05(149): Test TestCasesReactome.test_05(165): Out: -0.9154962776570641 TestCasesReactome.test_05(170): Out: 0.34014843250566407 [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.snpeff.snpEffect.testCases.unity.TestCasesReactome [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesChiSquare TestCasesChiSquare.test_1(26): Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesChiSquare [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesJaspar TestCasesJaspar.test_01(22): Test TestCasesJaspar.test_02(56): Test [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.342 s - in org.snpeff.snpEffect.testCases.unity.TestCasesJaspar [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse2 TestCasesEffectCollapse2.test_01(40): Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.137 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse2 [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDel [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.094 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDel [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup TestCasesStructuralDup.test01_dupGene(157): Test TestCasesStructuralDup.test02(194): Test TestCasesStructuralDup.test03(212): Test TestCasesStructuralDup.test04(229): Test TestCasesStructuralDup.test05(247): Test TestCasesStructuralDup.test06(265): Test TestCasesStructuralDup.test07(286): Test TestCasesStructuralDup.test08(303): Test TestCasesStructuralDup.test09(324): Test TestCasesStructuralDup.test10(345): Test TestCasesStructuralDup.test01_dupTr(175): Test [INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 21.702 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv TestCasesStructuralInv.test01_invGene(214): Test TestCasesStructuralInv.test02(249): Test TestCasesStructuralInv.test03(266): Test TestCasesStructuralInv.test04(283): Test TestCasesStructuralInv.test05(300): Test TestCasesStructuralInv.test06(317): Test TestCasesStructuralInv.test07(334): Test TestCasesStructuralInv.test08(352): Test TestCasesStructuralInv.test09(370): Test TestCasesStructuralInv.test10(387): Test TestCasesStructuralInv.test01_invTr(231): Test [INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 21.588 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesBuild TestCasesBuild.test_01_chromoNamesDoNotMatch_Gff(18): Test TestCasesBuild.test_02_chromoNamesDoNotMatch_GffFasta(54): Test [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.41 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBuild [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDupNegative TestCasesHgvsDnaDupNegative.test_01(34): Test TestCasesHgvsDnaDupNegative.test_02(61): Test TestCasesHgvsDnaDupNegative.test_03(91): Test TestCasesHgvsDnaDupNegative.test_04(122): Test [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.47 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDupNegative [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSeekableReader TestCasesSeekableReader.test_00(60): Test ffffffff232744e0 ffffffff232744e0 tests/unity/seekableReader/testLukas.vcf TestCasesSeekableReader.test_01(74): Test ffffffff232744e0 ffffffff232744e0 tests/unity/seekableReader/testLukas.vcf [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.857 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSeekableReader [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence TestCasesDnaNSequence.test_02_long_replaceBase(243): Test TestCasesDnaNSequence.test_13_reverseWc(253): Test TestCasesDnaNSequence.test_02_long_getBases(233): Test TestCasesDnaNSequence.test_01_short_getBases(194): Test TestCasesDnaNSequence.test_01_short(175): Test TestCasesDnaNSequence.test_02_long(214): Test TestCasesDnaNSequence.test_02_long_getBase(223): Test TestCasesDnaNSequence.test_01_short_getBase(184): Test TestCasesDnaNSequence.test_01_short_replaceBase(204): Test [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.796 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer TestCasesSequenceIndexer.test_01(69): Test TestCasesSequenceIndexer.test_02(100): Test TestCasesSequenceIndexer.test_03(125): Test TestCasesSequenceIndexer.test_04(152): Test TestCasesSequenceIndexer.test_05(182): Test TestCasesSequenceIndexer.test_06(207): Test TestCasesSequenceIndexer.test_07(225): Test TestCasesSequenceIndexer.test_08(247): Test TestCasesSequenceIndexer.test_09(267): Test TestCasesSequenceIndexer.test_10(287): Test [INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 17.019 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIubString TestCasesIubString.test_01(29): Test TestCasesIubString.test_02(39): Test TestCasesIubString.test_03(49): Test TestCasesIubString.test_04(68): Test [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIubString [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed TestCasesApplyMixed.test_apply_variant_04_shorter(116): Test TestCasesApplyMixed.test_apply_variant_06_longer(169): Test TestCasesApplyMixed.test_apply_variant_06_shorter(186): Test TestCasesApplyMixed.test_apply_variant_04_longer(98): Test TestCasesApplyMixed.test_apply_variant_09_longer(259): Test TestCasesApplyMixed.test_apply_variant_01_shorter(32): Test TestCasesApplyMixed.test_apply_variant_08_shorter(248): Test TestCasesApplyMixed.test_apply_variant_02_longer(42): Test TestCasesApplyMixed.test_apply_variant_07_longer(203): Test TestCasesApplyMixed.test_apply_variant_03_shorter(81): Test TestCasesApplyMixed.test_apply_variant_05_shorter(152): Test TestCasesApplyMixed.test_apply_variant_05_longer(134): Test TestCasesApplyMixed.test_apply_variant_07_shorter(220): Test TestCasesApplyMixed.test_apply_variant_03_longer(64): Test TestCasesApplyMixed.test_apply_variant_08_longer(237): Test TestCasesApplyMixed.test_apply_variant_02_shorter(53): Test TestCasesApplyMixed.test_apply_variant_09_shorter(270): Test TestCasesApplyMixed.test_apply_variant_01_longer(22): Test [INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 34.062 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest TestCasesFisherExactTest.test_05_fisher(313): Test TestCasesFisherExactTest.test_0(97): Test TestCasesFisherExactTest.test_03_fisher(103): Test TestCasesFisherExactTest.test_06_fisher_vs_chi2(352): Test TestCasesFisherExactTest.test_04_fisher(208): Test [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequenceByte TestCasesDnaSequenceByte.test_01(18): Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.404 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequenceByte [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable TestCasesCodonTable.test_01(28): Test TestCasesCodonTable.test_02(59): Test [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.088 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVcf TestCasesVcf.test_22_huge_headers(363): Test TestCasesVcf.test_12_readHeader_NL(257): Test TestCasesVcf.test_36_cleanupUnderscores(703): Test TestCasesVcf.test_23_VcfUnsorted(379): Test TestCasesVcf.test_00(40): Test TestCasesVcf.test_01(54): Test TestCasesVcf.test_29(568): Test TestCasesVcf.test_16_indels(321): Test TestCasesVcf.test_09_empty_ALT(195): Test TestCasesVcf.test_27_vcfInfoHeaderReplace(489): Test TestCasesVcf.test_18_vcf_tabix(348): Test TestCasesVcf.test_26_vcfInfoHeaderAdd(456): Test TestCasesVcf.test_14_VcfInfoKey(283): Test TestCasesVcf.test_10_empty_QUAL(210): Test TestCasesVcf.test_06_mixed_change(121): Test TestCasesVcf.test_12_readHeader(237): Test TestCasesVcf.test_15_Eff_format_version_guess(309): Test TestCasesVcf.test_28_vcfInfoReplace(533): Test TestCasesVcf.test_30_gVCF_NON_REF(590): Test TestCasesVcf.test_05_choking_on_dot_slash_dot(89): Test TestCasesVcf.test_08_alt_del(169): Test TestCasesVcf.test_07_long_lines(143): Test TestCasesVcf.test_11_empty(225): Test TestCasesVcf.test_33_translocations(652): Test TestCasesVcf.test_35_translocations_parsing(680): Test TestCasesVcf.test_13_chrOri(268): Test TestCasesVcf.test_04_del(72): Test TestCasesVcf.test_14_VcfInfoValue(296): Test [INFO] Tests run: 33, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 50.728 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVcf [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCircular TestCasesCircular.test_circular_01(26): Test TestCasesCircular.test_circular_02(54): Test TestCasesCircular.test_circular_03(83): Test TestCasesCircular.test_circular_04(103): Test [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCircular [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesNextProt TestCasesNextProt.test_10_nextprotFactory(205): Test TestCasesNextProt.test_09_nextprotFactory(182): Test TestCasesNextProt.test_06_nextprotFactory(116): Test TestCasesNextProt.test_14(304): Test TestCasesNextProt.test_15(322): Test TestCasesNextProt.test_16(340): Test TestCasesNextProt.test_17(358): Test TestCasesNextProt.test_18(376): Test TestCasesNextProt.test_19(394): Test TestCasesNextProt.test_03_nextprotFactory(60): Test TestCasesNextProt.test_11_nextprotFactory(228): Test TestCasesNextProt.test_07_nextprotFactory(136): Test TestCasesNextProt.test_04_nextprotFactory(80): Test TestCasesNextProt.test_01_nextprotFactory(24): Test TestCasesNextProt.test_12_nextprotFactory(251): Test TestCasesNextProt.test_08_nextprotFactory(159): Test TestCasesNextProt.test_05_nextprotFactory(98): Test TestCasesNextProt.test_02_nextprotFactory(42): Test TestCasesNextProt.test_13_nextprotFactory(277): Test [INFO] Tests run: 19, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNextProt [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations TestCasesStructuralTranslocations.test02_2_nonFs(532): Test TestCasesStructuralTranslocations.test01_0_nonFs(286): Test TestCasesStructuralTranslocations.test01_0(260): Test TestCasesStructuralTranslocations.test01_1(314): Test TestCasesStructuralTranslocations.test01_2(341): Test TestCasesStructuralTranslocations.test01_3(368): Test TestCasesStructuralTranslocations.test02_0(423): Test TestCasesStructuralTranslocations.test02_1(450): Test TestCasesStructuralTranslocations.test02_2(505): Test TestCasesStructuralTranslocations.test02_3(560): Test TestCasesStructuralTranslocations.test03_0(587): Test TestCasesStructuralTranslocations.test03_1(614): Test TestCasesStructuralTranslocations.test03_2(669): Test TestCasesStructuralTranslocations.test03_3(724): Test TestCasesStructuralTranslocations.test04_0(751): Test TestCasesStructuralTranslocations.test04_1(806): Test TestCasesStructuralTranslocations.test04_2(833): Test TestCasesStructuralTranslocations.test04_3(860): Test TestCasesStructuralTranslocations.test05_2_one_gene(951): Test TestCasesStructuralTranslocations.test04_3_nonFs(887): Test TestCasesStructuralTranslocations.test03_1_nonFs(641): Test TestCasesStructuralTranslocations.test05_1_one_gene(919): Test TestCasesStructuralTranslocations.test03_2_nonFs(696): Test TestCasesStructuralTranslocations.test01_3_noFs(395): Test TestCasesStructuralTranslocations.test04_0_nonFs(778): Test TestCasesStructuralTranslocations.test02_1_nonFs(477): Test TestCasesStructuralTranslocations.test06_no_gene(981): Test [INFO] Tests run: 27, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 67.079 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup TestCasesHgvsDnaDup.test_01(31): Test TestCasesHgvsDnaDup.test_02(54): Test TestCasesHgvsDnaDup.test_03(81): Test TestCasesHgvsDnaDup.test_04(111): Test TestCasesHgvsDnaDup.test_05(141): Test TestCasesHgvsDnaDup.test_06(167): Test TestCasesHgvsDnaDup.test_07(195): Test TestCasesHgvsDnaDup.test_08(221): Test TestCasesHgvsDnaDup.test_09(247): Test TestCasesHgvsDnaDup.test_10(277): Test TestCasesHgvsDnaDup.test_11(308): Test [INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 28.024 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSnps TestCasesSnps.test_01(43): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... 300 .................................................................................................... 400 .................................................................................................... 500 .................................................................................................... 600 .................................................................................................... 700 .................................................................................................... 800 .................................................................................................... 900 .................................................................................................... 1000 [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.416 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSnps [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel TestCasesStructuralDel.test02(249): Test TestCasesStructuralDel.test03(266): Test TestCasesStructuralDel.test04(283): Test TestCasesStructuralDel.test05(302): Test TestCasesStructuralDel.test06(321): Test TestCasesStructuralDel.test07(342): Test TestCasesStructuralDel.test08(360): Test TestCasesStructuralDel.test09(379): Test TestCasesStructuralDel.test10(398): Test TestCasesStructuralDel.test01_delTr(230): Test TestCasesStructuralDel.test01_delGene(212): Test [INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 19.622 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray TestCasesIntervalTree.test_01(141): Test . 0 .................................................................................................... 10000 .................................................................................................... 20000 .................................................................................................... 30000 .................................................................................................... 40000 .................................................................................................... 50000 .................................................................................................... 60000 .................................................................................................... 70000 .................................................................................................... 80000 .................................................................................................... 90000 ................................................................................................... TestCasesIntervalTree.test_02(164): Test . 0 .................................................................................................... 1000 .................................................................................................... 2000 .................................................................................................... 3000 .................................................................................................... 4000 .................................................................................................... 5000 .................................................................................................... 6000 .................................................................................................... 7000 .................................................................................................... 8000 .................................................................................................... 9000 ................................................................................................... [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 15.124 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesGenomicSequences [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.002 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenomicSequences [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse TestCasesEffectCollapse.test_01(68): Test TestCasesEffectCollapse.test_02(74): Test TestCasesEffectCollapse.test_03(80): Test TestCasesEffectCollapse.test_04(86): Test TestCasesEffectCollapse.test_05(92): Test [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.583 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvs TestCasesHgvs.test_01(56): Test TestCasesHgvs.test_02(69): Test TestCasesHgvs.test_03(83): Test [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.461 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvs [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntStats TestCasesIntStats.test_01(31): Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.129 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntStats [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsProtDup TestCasesHgvsProtDup.test_01(31): Test TestCasesHgvsProtDup.test_02(70): Test [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.244 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsProtDup [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIns TestCasesIns.test_01(38): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... 300 .................................................................................................... 400 .................................................................................................... 500 .................................................................................................... 600 .................................................................................................... 700 .................................................................................................... 800 .................................................................................................... 900 .................................................................................................... 1000 [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.761 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIns [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant TestCasesIntervalVariant.test_01(36): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... 300 .................................................................................................... 400 .................................................................................................... 500 .................................................................................................... 600 .................................................................................................... 700 .................................................................................................... 800 .................................................................................................... 900 .................................................................................................... 1000 [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.658 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree TestCasesIntervalTree.test_01(141): Test . 0 .................................................................................................... 10000 .................................................................................................... 20000 .................................................................................................... 30000 .................................................................................................... 40000 .................................................................................................... 50000 .................................................................................................... 60000 .................................................................................................... 70000 .................................................................................................... 80000 .................................................................................................... 90000 ................................................................................................... TestCasesIntervalTree.test_02(164): Test . 0 .................................................................................................... 1000 .................................................................................................... 2000 .................................................................................................... 3000 .................................................................................................... 4000 .................................................................................................... 5000 .................................................................................................... 6000 .................................................................................................... 7000 .................................................................................................... 8000 .................................................................................................... 9000 ................................................................................................... [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 13.549 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeOri TestCasesIntervalTree.test_01(141): Test . 0 .................................................................................................... 10000 .................................................................................................... 20000 .................................................................................................... 30000 .................................................................................................... 40000 .................................................................................................... 50000 .................................................................................................... 60000 .................................................................................................... 70000 .................................................................................................... 80000 .................................................................................................... 90000 ................................................................................................... TestCasesIntervalTree.test_02(164): Test . 0 .................................................................................................... 1000 .................................................................................................... 2000 .................................................................................................... 3000 .................................................................................................... 4000 .................................................................................................... 5000 .................................................................................................... 6000 .................................................................................................... 7000 .................................................................................................... 8000 .................................................................................................... 9000 ................................................................................................... [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 13.569 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeOri [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos TestCasesFileIndexChrPos.test_00_short_file(79): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... 300 .................................................................................................... 400 .................................................................................................... 500 .................................................................................................... 600 .................................................................................................... 700 .................................................................................................... 800 .................................................................................................... 900 ................................................................................................... TestCasesFileIndexChrPos.test_01(88): Test TestCasesFileIndexChrPos.test_02(109): Test TestCasesFileIndexChrPos.test_03(131): Test TestCasesFileIndexChrPos.test_04(158): Test TestCasesFileIndexChrPos.test_05(186): Test TestCasesFileIndexChrPos.test_06(214): Test TestCasesFileIndexChrPos.test_07(242): Test TestCasesFileIndexChrPos.test_10(267): Test TestCasesFileIndexChrPos.test_11(300): Test TestCasesFileIndexChrPos.test_20(347): Test TestCasesFileIndexChrPos.test_21(369): Test TestCasesFileIndexChrPos.test_22(391): Test TestCasesFileIndexChrPos.test_23(413): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... 300 .................................................................................................... 400 .................................................................................................... 500 .................................................................................................... 600 .................................................................................................... 700 .................................................................................................... 800 .................................................................................................... 900 ................................................................................................... TestCasesFileIndexChrPos.test_24(477): Test .................................................................................................... 100 TestCasesFileIndexChrPos.test_00_long_file(70): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... 300 .................................................................................................... 400 .................................................................................................... 500 .................................................................................................... 600 .................................................................................................... 700 .................................................................................................... 800 .................................................................................................... 900 ................................................................................................... [INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 52.211 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesFasta TestCasesFasta.test_01(23): Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.11 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFasta [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesGenotypeVector TestCasesGenotypeVector.test_01(23): Test TestCasesGenotypeVector.test_02(48): Test [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenotypeVector [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervals TestCasesIntervals.test_00(140): Test TestCasesIntervals.test_01(152): Test TestCasesIntervals.test_02(163): Test TestCasesIntervals.test_03(175): Test TestCasesIntervals.test_04(187): Test TestCasesIntervals.test_05(200): Test TestCasesIntervals.test_06(231): Test TestCasesIntervals.test_08(392): Test TestCasesIntervals.test_10_chrOrder(475): Test TestCasesIntervals.test_09_chrOrder(460): Test TestCasesIntervals.test_07_01(271): Test TestCasesIntervals.test_07_02(292): Test TestCasesIntervals.test_07_03(313): Test TestCasesIntervals.test_07_04(337): Test TestCasesIntervals.test_07_05(362): Test TestCasesIntervals.test_08_02(413): Test TestCasesIntervals.test_08_03(438): Test [INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 18.124 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervals [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesOverlap TestCasesOverlap.test_binSeq_01(26): Test TestCasesOverlap.test_binSeq_02(32): Test TestCasesOverlap.test_binSeq_03(38): Test TestCasesOverlap.test_binSeq_04(44): Test TestCasesOverlap.test_binSeq_05(50): Test TestCasesOverlap.test_binSeq_06(56): Test TestCasesOverlap.test_binSeq_07(62): Test TestCasesOverlap.test_binSeq_08(68): Test TestCasesOverlap.test_binSeq_09(74): Test TestCasesOverlap.test_binSeq_10(80): Test TestCasesOverlap.test_binSeq_11(87): Test TestCasesOverlap.test_binSeq_12(94): Test TestCasesOverlap.test_binSeq_13(100): Test [INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.snpeff.snpEffect.testCases.unity.TestCasesOverlap [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel TestCasesApplyDel.test_apply_variant_01(21): Test TestCasesApplyDel.test_apply_variant_02(31): Test TestCasesApplyDel.test_apply_variant_03(42): Test TestCasesApplyDel.test_apply_variant_04(59): Test TestCasesApplyDel.test_apply_variant_05(77): Test TestCasesApplyDel.test_apply_variant_06(95): Test TestCasesApplyDel.test_apply_variant_07(113): Test TestCasesApplyDel.test_apply_variant_08(131): Test TestCasesApplyDel.test_apply_variant_09(142): Test TestCasesApplyDel.test_apply_variant_10(153): Test TestCasesApplyDel.test_apply_variant_11(176): Test TestCasesApplyDel.test_apply_variant_12(199): Test TestCasesApplyDel.test_apply_variant_13(223): Test [INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 11.192 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesMarkerUtils TestCasesMarkerUtils.test_collapseZeroGap(107): Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.168 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMarkerUtils [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse TestCasesAnnParse.test_EffectType(29): Test TestCasesAnnParse.test_old_SO(45): Test TestCasesAnnParse.test_old_SO_vcf(53): Test TestCasesAnnParse.testCase_tfbs_ablation(71): Test [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.972 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVariantDecompose TestCasesVariantDecompose.test_00_decomposeVariant_01(35): Test TestCasesVariantDecompose.test_00_decomposeVariant_02(45): Test [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantDecompose [INFO] [INFO] Results: [INFO] [WARNING] Tests run: 391, Failures: 0, Errors: 0, Skipped: 5 [INFO] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 12:06 min [INFO] Finished at: 2025-02-14T05:24:28Z [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/reproducible-path/snpeff-5.1+d+dfsg' 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/snpeff-5.1\+d\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/snpeff-5.1\+d\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/snpeff-5.1\+d\+dfsg/debian/maven-repo --batch-mode -Ddebian.dir=/build/reproducible-path/snpeff-5.1\+d\+dfsg/debian -Ddebian.package=libsnpeff-java -Dmaven.repo.local=/build/reproducible-path/snpeff-5.1\+d\+dfsg/debian/maven-repo -Dinstall.to.usj=true org.debian.maven:debian-maven-plugin:2.6:install OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release. [INFO] Scanning for projects... [INFO] [INFO] -------------------------< org.snpeff:snpeff >-------------------------- [INFO] Building SnpEff 5.1 [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ snpeff --- [INFO] Cleaning pom file: /build/reproducible-path/snpeff-5.1+d+dfsg/pom.xml.save with options: [INFO] --keep-pom-version --package=libsnpeff-java [INFO] --rules=/build/reproducible-path/snpeff-5.1+d+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/snpeff-5.1+d+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/snpeff-5.1+d+dfsg/debian/maven.publishedRules [INFO] Install jar for snpeff into /usr/share/java [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.956 s [INFO] Finished at: 2025-02-14T05:24:31Z [INFO] ------------------------------------------------------------------------  mh_resolve_dependencies --non-interactive --offline --build -plibsnpeff-java --javadoc --base-directory=/build/reproducible-path/snpeff-5.1\+d\+dfsg --non-explore Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) at org.debian.maven.repo.POMReader.readPom(POMReader.java:82) at org.debian.maven.repo.POMReader.readPom(POMReader.java:57) at org.debian.maven.repo.Repository.scan(Repository.java:397) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:201) at org.debian.maven.repo.Repository.scanOnce(Repository.java:196) at org.debian.maven.repo.POMTransformer.usePluginVersionsFromRepository(POMTransformer.java:107) at org.debian.maven.packager.DependenciesSolver.main(DependenciesSolver.java:907) Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) at org.debian.maven.repo.POMReader.readPom(POMReader.java:82) at org.debian.maven.repo.POMReader.readPom(POMReader.java:57) at org.debian.maven.repo.Repository.scan(Repository.java:397) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:201) at org.debian.maven.repo.Repository.scanOnce(Repository.java:196) at org.debian.maven.repo.POMTransformer.usePluginVersionsFromRepository(POMTransformer.java:107) at org.debian.maven.packager.DependenciesSolver.main(DependenciesSolver.java:907) Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) at org.debian.maven.repo.POMReader.readPom(POMReader.java:82) at org.debian.maven.repo.POMReader.readPom(POMReader.java:57) at org.debian.maven.repo.Repository.scan(Repository.java:397) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:201) at org.debian.maven.packager.DependenciesSolver.getRepository(DependenciesSolver.java:231) at org.debian.maven.packager.DependenciesSolver.solveDependencies(DependenciesSolver.java:237) at org.debian.maven.packager.DependenciesSolver.main(DependenciesSolver.java:922) Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) at org.debian.maven.repo.POMReader.readPom(POMReader.java:82) at org.debian.maven.repo.POMReader.readPom(POMReader.java:57) at org.debian.maven.repo.Repository.scan(Repository.java:397) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:201) at org.debian.maven.packager.DependenciesSolver.getRepository(DependenciesSolver.java:231) at org.debian.maven.packager.DependenciesSolver.solveDependencies(DependenciesSolver.java:237) at org.debian.maven.packager.DependenciesSolver.main(DependenciesSolver.java:922) Analysing pom.xml... > dpkg --search /usr/share/maven-repo/org/biojava/biojava-structure/*/* Found /usr/share/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom in libbiojava6-java Found /usr/share/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom in libbiojava6-java > dpkg --status libbiojava6-java [error] Package libbiojava6-java (6.1.0+dfsg) is already installed and contains a possible match, but I cannot resolve library org.biojava:biojava-structure:jar:6.x in it. [error] Please check manually that the library is up to date, otherwise it may be necessary to package version 6.x in Debian. Feb 14, 2025 5:24:43 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve SEVERE: Cannot resolve dependencies in /build/reproducible-path/snpeff-5.1+d+dfsg/pom.xml: Dependency not found org.biojava:biojava-structure:jar:6.x ERROR: pom.xml: dependency is not packaged in the Maven repository for Debian: org.biojava:biojava-structure:6.x -------- Checking dependencies for documentation packages... > dpkg --search /usr/share/doc/libapfloat-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libapfloat-java/api/index.html > dpkg --search /usr/share/doc/libapfloat-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libapfloat-java-doc/api/index.html > dpkg --search /usr/share/doc/libapfloat-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libapfloat-java/apidocs/index.html > dpkg --search /usr/share/doc/libapfloat-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libapfloat-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libbiojava6-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libbiojava6-java/api/index.html > dpkg --search /usr/share/doc/libbiojava6-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libbiojava6-java-doc/api/index.html > dpkg --search /usr/share/doc/libbiojava6-java/apidocs/index.html Found libbiojava6-java-doc > dpkg --search /usr/share/doc/libcharts4j-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcharts4j-java/api/index.html > dpkg --search /usr/share/doc/libcharts4j-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcharts4j-java-doc/api/index.html > dpkg --search /usr/share/doc/libcharts4j-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcharts4j-java/apidocs/index.html > dpkg --search /usr/share/doc/libcharts4j-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcharts4j-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libcommons-cli-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-cli-java/api/index.html > dpkg --search /usr/share/doc/libcommons-cli-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-cli-java-doc/api/index.html > dpkg --search /usr/share/doc/libcommons-cli-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-cli-java/apidocs/index.html > dpkg --search /usr/share/doc/libcommons-cli-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-cli-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libcommons-codec-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-codec-java/api/index.html > dpkg --search /usr/share/doc/libcommons-codec-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-codec-java-doc/api/index.html > dpkg --search /usr/share/doc/libcommons-codec-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-codec-java/apidocs/index.html > dpkg --search /usr/share/doc/libcommons-codec-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-codec-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libcommons-io-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-io-java/api/index.html > dpkg --search /usr/share/doc/libcommons-io-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-io-java-doc/api/index.html > dpkg --search /usr/share/doc/libcommons-io-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-io-java/apidocs/index.html > dpkg --search /usr/share/doc/libcommons-io-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-io-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libcommons-math3-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-math3-java/api/index.html > dpkg --search /usr/share/doc/libcommons-math3-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-math3-java-doc/api/index.html > dpkg --search /usr/share/doc/libcommons-math3-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-math3-java/apidocs/index.html > dpkg --search /usr/share/doc/libcommons-math3-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-math3-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libdistlib-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libdistlib-java/api/index.html > dpkg --search /usr/share/doc/libdistlib-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libdistlib-java-doc/api/index.html > dpkg --search /usr/share/doc/libdistlib-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libdistlib-java/apidocs/index.html > dpkg --search /usr/share/doc/libdistlib-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libdistlib-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libfreemarker-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libfreemarker-java/api/index.html > dpkg --search /usr/share/doc/libfreemarker-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libfreemarker-java-doc/api/index.html > dpkg --search /usr/share/doc/libfreemarker-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libfreemarker-java/apidocs/index.html > dpkg --search /usr/share/doc/libfreemarker-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libfreemarker-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libtrove3-java/api/index.html Found libtrove3-java-doc Some problems were found in this project, exiting... bash -c "rm -f target/apidocs/*.sh target/apidocs/options" mh_unpatchpoms -plibsnpeff-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: package libsnpeff-java: substitution variable ${java:Depends} unused, but is defined dpkg-gencontrol: warning: package libsnpeff-java: substitution variable ${maven:CompileDepends} unused, but is defined dpkg-gencontrol: warning: package libsnpeff-java: substitution variable ${maven:DocDepends} unused, but is defined dpkg-gencontrol: warning: package libsnpeff-java-doc: substitution variable ${maven:CompileDepends} unused, but is defined dpkg-gencontrol: warning: package libsnpeff-java-doc: substitution variable ${maven:Depends} unused, but is defined dpkg-gencontrol: warning: package libsnpeff-java-doc: substitution variable ${maven:DocDepends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'snpeff' in '../snpeff_5.1+d+dfsg-3_all.deb'. dpkg-deb: building package 'libsnpeff-java-doc' in '../libsnpeff-java-doc_5.1+d+dfsg-3_all.deb'. dpkg-deb: building package 'libsnpeff-java' in '../libsnpeff-java_5.1+d+dfsg-3_all.deb'. dpkg-genbuildinfo --build=binary -O../snpeff_5.1+d+dfsg-3_amd64.buildinfo dpkg-genchanges --build=binary -O../snpeff_5.1+d+dfsg-3_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/976963 and its subdirectories I: Current time: Thu Feb 13 17:28:11 -12 2025 I: pbuilder-time-stamp: 1739510891