Mon Jan 20 17:45:35 UTC 2025 I: starting to build snpeff/unstable/amd64 on jenkins on '2025-01-20 17:45' Mon Jan 20 17:45:35 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_35/44077/console.log Mon Jan 20 17:45:35 UTC 2025 I: Downloading source for unstable/snpeff=5.2.e+dfsg-1 --2025-01-20 17:45:36-- http://deb.debian.org/debian/pool/main/s/snpeff/snpeff_5.2.e%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2569 (2.5K) [text/prs.lines.tag] Saving to: ‘snpeff_5.2.e+dfsg-1.dsc’ 0K .. 100% 425M=0s 2025-01-20 17:45:36 (425 MB/s) - ‘snpeff_5.2.e+dfsg-1.dsc’ saved [2569/2569] Mon Jan 20 17:45:36 UTC 2025 I: snpeff_5.2.e+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: snpeff Binary: libsnpeff-java, snpeff, libsnpeff-java-doc Architecture: all Version: 5.2.e+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Pierre Gruet Homepage: https://pcingola.github.io/SnpEff/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/snpeff Vcs-Git: https://salsa.debian.org/med-team/snpeff.git Testsuite: autopkgtest Testsuite-Triggers: default-jdk-headless, junit5, quilt Build-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 Package-List: libsnpeff-java deb java optional arch=all libsnpeff-java-doc deb doc optional arch=all snpeff deb java optional arch=all Checksums-Sha1: 6dbcf5b97936bc51cc02aa7a1014a0ec3540c633 154908804 snpeff_5.2.e+dfsg.orig.tar.xz 7a5c9068c417beb66599edc40a3f436c737ea682 14208 snpeff_5.2.e+dfsg-1.debian.tar.xz Checksums-Sha256: 5f8b813711a867fd455fd5019593268cbfdab23268fb8a2c03f4957066bb0df7 154908804 snpeff_5.2.e+dfsg.orig.tar.xz 4103f573f83c604e0ddc132a4531a6eb8ad72f6770fb6fde497066ebd3a5a3d7 14208 snpeff_5.2.e+dfsg-1.debian.tar.xz Files: 5881f26c0692e8fd2b4acdc716f42355 154908804 snpeff_5.2.e+dfsg.orig.tar.xz e4d6f7abf6f67562cc810f03a4ffce2d 14208 snpeff_5.2.e+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEM8soQxPpC9J9y0UjYAMWptwndHYFAmcBtRwACgkQYAMWptwn dHY94Q//XPnEFxlef/2ryMn+rn+DSYb1iOsp2iUtR5nHNJpLT4vFZDE0MJY/QzYt 1cBDwjwvrS8cGHp4PT+p/epVAHqlT3mgHzhIk8j/atOQjRJ8cksGR6tfLHIsQSn9 R4YgT1ykwimHAAI9jLOArmgPkbDyPm0rI7BneUNI/CilZpO1EWjLr/5PV2VaHAp8 prq23GTNoMbN/25xLOpWvBDp0hiElFnGqvsRMyoDMrpvWCpYmUr0AP3XdvGkDAHn 1f51KXlZ7uLcGxFA+V2etu8ZuurON2GtBW4f1vEx0DqLiMpLyH6Z0V0+/wK7Hf/K CInl7cGrt/8bar8jum0Qi1xcGQR7EAnyKuTy9z1RdukxORHWwAtMInfoqRQFK8mM yq0i9MV+Sju/3rRW5ebr62BLeL9X4u0DVfq5PKcKOTFUkPYO6mYlt4vwbLic3f3k IxFMsnnp2yjHD4PezOtTrc78P4Voy1SaXf/CC/dAuN//iDjFYSt6ns68PxBSK4qb hnMI01k6f0iUVY+K0rB+k+NaNHpdhKMYZ4K4opnwDKHX1/re1az3R62zn8hMUlZP DYYvPOglaMx9OqXWCr3QvGUmyU+vfggC35MzTF0nBrxojVjVFGawynjLD3Wm5op+ /509WV/gXtUI0Hkf+SP52flMFgOipoeF0c9jhDQUHdGQHe+8hoQ= =cRVZ -----END PGP SIGNATURE----- Mon Jan 20 17:45:36 UTC 2025 I: Checking whether the package is not for us Mon Jan 20 17:45:36 UTC 2025 I: Starting 1st build on remote node infom01-amd64.debian.net. Mon Jan 20 17:45:36 UTC 2025 I: Preparing to do remote build '1' on infom01-amd64.debian.net. Mon Jan 20 17:57:58 UTC 2025 I: Deleting $TMPDIR on infom01-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Jan 20 05:45:40 -12 2025 I: pbuilder-time-stamp: 1737395140 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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_5.2.e+dfsg-1.dsc] I: copying [./snpeff_5.2.e+dfsg.orig.tar.xz] I: copying [./snpeff_5.2.e+dfsg-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./snpeff_5.2.e+dfsg-1.dsc: unsupported subcommand dpkg-source: info: extracting snpeff in snpeff-5.2.e+dfsg dpkg-source: info: unpacking snpeff_5.2.e+dfsg.orig.tar.xz dpkg-source: info: unpacking snpeff_5.2.e+dfsg-1.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/2895180/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='e8b06ac20d72447e8af5f16bc349075e' 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='2895180' 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.xQEJybCC/pbuilderrc_9uNF --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xQEJybCC/b1 --logfile b1/build.log snpeff_5.2.e+dfsg-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom01-amd64 6.1.0-30-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.124-1 (2025-01-12) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2895180/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 ... 19851 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} binfmt-support{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} dbus{a} dbus-bin{a} dbus-daemon{a} dbus-session-bus-common{a} dbus-system-bus-common{a} dbus-user-session{a} dconf-gsettings-backend{a} dconf-service{a} dctrl-tools{a} debhelper{a} default-jdk{a} default-jdk-doc{a} default-jdk-headless{a} default-jre{a} default-jre-headless{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} dwz{a} fastjar{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gpg{a} gpg-agent{a} gpgconf{a} gpgsm{a} gpgv{a} groff-base{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} intltool-debian{a} jarwrapper{a} java-common{a} javahelper{a} junit4{a} junit5{a} libactivation-java{a} libantlr4-runtime-java{a} libaopalliance-java{a} libapache-pom-java{a} libapfloat-java{a} libapiguardian-java{a} libapparmor1{a} libarchive-zip-perl{a} libargs4j-java{a} libasm-java{a} libasound2-data{a} libasound2t64{a} libassuan9{a} libatinject-jsr330-api-java{a} libatk-bridge2.0-0t64{a} libatk1.0-0t64{a} libatspi2.0-0t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libb-hooks-op-check-perl{a} libbiojava6-java{a} libbiojava6-java-doc{a} libbrotli1{a} libbsh-java{a} libcairo-gobject2{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} libcloudproviders0{a} libcodemodel-java{a} libcolord2{a} libcom-err2{a} libcommons-beanutils-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-collections4-java{a} libcommons-compress-java{a} libcommons-digester-java{a} libcommons-exec-java{a} libcommons-io-java{a} libcommons-jexl2-java{a} libcommons-lang-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-math-java{a} libcommons-math3-java{a} libcommons-parent-java{a} libcommons-text-java{a} libcommons-validator-java{a} libcups2t64{a} libdatrie1{a} libdbus-1-3{a} libdconf1{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdistlib-java{a} libdom4j-java{a} libdoxia-core-java{a} libdoxia-java{a} libdoxia-sitetools-java{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-radeon1{a} libdrm2{a} libdtd-parser-java{a} libdynaloader-functions-perl{a} libedit2{a} libel-api-java{a} libelf1t64{a} libencode-locale-perl{a} libepoxy0{a} liberror-prone-java{a} libexec-maven-plugin-java{a} libexpat1{a} libezmorph-java{a} libfastinfoset-java{a} libfastutil-java{a} libffi8{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} libfontconfig1{a} libfreemarker-java{a} libfreetype6{a} libfribidi0{a} libgbm1{a} libgcrypt20{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libgif7{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0t64{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgnutls30t64{a} libgoogle-gson-java{a} libgpg-error0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgtk-3-0t64{a} libgtk-3-common{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} 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} libidn2-0{a} libimport-into-perl{a} libinchi1.07{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libistack-commons-java{a} libitext5-java{a} libjackson2-annotations-java{a} libjackson2-core-java{a} libjackson2-databind-java{a} libjansi-java{a} libjaxb-api-java{a} libjaxb-java{a} libjaxen-java{a} libjbig0{a} libjetty9-java{a} libjgrapht-java{a} libjgraphx-java{a} libjheaps-java{a} libjmol-java{a} libjni-inchi-java{a} libjni-inchi-jni{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-jquery-ui-theme-base{a} libjson-java{a} libjson-simple-java{a} libjsoup-java{a} libjsp-api-java{a} libjsr305-java{a} libjtidy-java{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libksba8{a} liblcms2-2{a} libldap2{a} liblerc4{a} libllvm19{a} liblog4j1.2-java{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1t64{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-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} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{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} libnpth0t64{a} libnspr4{a} libnss3{a} libopentest4j-java{a} libopentest4j-reporting-java{a} liboro-java{a} libp11-kit0{a} libpam-systemd{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libparams-classify-perl{a} libpciaccess0{a} libpcsclite1{a} libpicocli-java{a} libpipeline1{a} libpixman-1-0{a} libplexus-ant-factory-java{a} libplexus-archiver-java{a} libplexus-bsh-factory-java{a} libplexus-build-api-java{a} libplexus-cipher-java{a} libplexus-classworlds-java{a} libplexus-compiler-java{a} libplexus-component-annotations-java{a} libplexus-container-default-java{a} libplexus-container-default1.5-java{a} libplexus-i18n-java{a} libplexus-interactivity-api-java{a} libplexus-interpolation-java{a} libplexus-io-java{a} libplexus-languages-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libplexus-velocity-java{a} libplexus-xml-java{a} libpng16-16t64{a} libproc2-0{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqdox2-java{a} libreadline8t64{a} librelaxng-datatype-java{a} 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} libsharpyuv0{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libstax-ex-java{a} libstreambuffer-java{a} libsub-quote-perl{a} libsurefire-java{a} libsystemd-shared{a} libtasn1-6{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtool{a} libtrove3-java{a} libtrove3-java-doc{a} libtry-tiny-perl{a} libtxw2-java{a} libuchardet0{a} libunistring5{a} libunivocity-parsers-java{a} liburi-perl{a} libvecmath-java{a} libvelocity-tools-java{a} libvulkan1{a} libwagon-file-java{a} libwagon-http-java{a} libwagon-provider-api-java{a} libwayland-client0{a} libwayland-cursor0{a} libwayland-egl1{a} libwayland-server0{a} libwebp7{a} libwebsocket-api-java{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxbean-reflect-java{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxerces2-java{a} libxext6{a} libxfixes3{a} libxi6{a} libxinerama1{a} libxkbcommon0{a} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxml2-utils{a} libxom-java{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxsom-java{a} libxtst6{a} libxxf86vm1{a} libxz-java{a} libz3-4{a} m4{a} man-db{a} maven{a} maven-debian-helper{a} maven-repo-helper{a} media-types{a} mesa-libgallium{a} ncbi-vdb-data{a} netbase{a} openjdk-21-doc{a} openjdk-21-jdk{a} openjdk-21-jdk-headless{a} openjdk-21-jre{a} openjdk-21-jre-headless{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} procps{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} sopv-gpgv{a} systemd{a} systemd-sysv{a} tzdata{a} unzip{a} velocity{a} wdiff{a} x11-common{a} xkb-data{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf at-spi2-core chrony curl debian-keyring dput dput-ng dupload equivs fonts-dejavu-extra gnupg-utils gpg-wks-client javascript-common krb5-locales libarchive-cpio-perl libatk-wrapper-java-jni libdata-dump-perl libdistro-info-perl libgdk-pixbuf2.0-bin libgit-wrapper-perl libgitlab-api-v4-perl libglib2.0-data libgpg-error-l10n libgtk-3-bin libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjline3-java libjson-perl libkmod2 libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl libnss-systemd librsvg2-common libsasl2-modules libsoap-lite-perl libstring-shellquote-perl libxstring-perl libxt-dev licensecheck lintian linux-sysctl-defaults lynx mesa-vulkan-drivers ntpsec openntpd pristine-tar psmisc python3-apt python3-argcomplete python3-debian python3-magic python3-requests python3-unidiff python3-xdg strace systemd-cryptsetup systemd-timesyncd wget xdg-user-dirs 0 packages upgraded, 438 newly installed, 0 to remove and 0 not upgraded. Need to get 361 MB of archives. After unpacking 1304 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libsystemd-shared amd64 257.2-2 [2138 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libapparmor1 amd64 3.1.7-1+b3 [42.1 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 systemd amd64 257.2-2 [3092 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 systemd-sysv amd64 257.2-2 [60.8 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.16.0-1 [177 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 dbus-bin amd64 1.16.0-1 [78.9 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 dbus-session-bus-common all 1.16.0-1 [51.1 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 dbus-daemon amd64 1.16.0-1 [157 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 dbus-system-bus-common all 1.16.0-1 [52.2 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 dbus amd64 1.16.0-1 [70.5 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 binfmt-support amd64 2.2.2-7 [64.3 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.1-3 [858 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.1-3 [2202 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025a-1 [259 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.1-3 [1973 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.1-3 [740 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B] Get: 26 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.1-2 [28.0 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.4.0-2 [1422 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20241223 [164 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libpam-systemd amd64 257.2-2 [293 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-1 [92.2 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [311 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.82.4-2 [1502 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 shared-mime-info amd64 2.4-5+b1 [759 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.45-1 [281 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-1+b1 [141 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 gtk-update-icon-cache amd64 4.16.12+ds-1 [50.6 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 hicolor-icon-theme all 0.18-1 [12.0 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 adwaita-icon-theme all 47.0-2 [463 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 java-common all 0.76 [6776 B] Get: 61 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libnspr4 amd64 2:4.36-1 [110 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libnss3 amd64 2:3.107-1 [1390 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libpcsclite1 amd64 2.3.1-1 [56.0 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 openjdk-21-jre-headless amd64 21.0.6~6ea-1 [41.8 MB] Get: 66 http://deb.debian.org/debian unstable/main amd64 default-jre-headless amd64 2:1.21-76 [3192 B] Get: 67 http://deb.debian.org/debian unstable/main amd64 ant all 1.10.15-1 [2163 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 ant-optional all 1.10.15-1 [456 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 at-spi2-common all 2.55.0.1-1 [170 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 dbus-user-session amd64 1.16.0-1 [51.0 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libdconf1 amd64 0.40.0-5 [41.8 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 dconf-service amd64 0.40.0-5 [32.4 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 dconf-gsettings-backend amd64 0.40.0-5 [28.6 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 dctrl-tools amd64 2.24-3+b1 [104 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-2 [539 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 86 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libatk1.0-0t64 amd64 2.55.0.1-1 [51.5 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libatspi2.0-0t64 amd64 2.55.0.1-1 [77.0 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libatk-bridge2.0-0t64 amd64 2.55.0.1-1 [68.1 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2 [391 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b3 [27.8 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libcairo-gobject2 amd64 1.18.2-2 [130 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libcloudproviders0 amd64 0.3.6-1+b1 [29.2 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libcolord2 amd64 1.4.7-1+b2 [140 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-16 [112 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-16 [44.2 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-16 [48.4 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.19.0-3+b3 [49.5 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.8-2 [1454 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 128 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.10-2+b1 [251 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libepoxy0 amd64 1.5.10-2 [193 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 10.2.0-1 [479 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-2 [463 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.56.1-1 [226 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.56.1-1 [55.3 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.56.1-1 [35.8 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libwayland-client0 amd64 1.23.0-1+b1 [26.6 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libwayland-cursor0 amd64 1.23.0-1+b1 [11.7 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libwayland-egl1 amd64 1.23.0-1+b1 [5664 B] Get: 145 http://deb.debian.org/debian unstable/main amd64 libxcomposite1 amd64 1:0.4.6-1 [16.3 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libxfixes3 amd64 1:6.0.0-2+b3 [20.2 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libxcursor1 amd64 1:1.2.3-1 [39.7 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libxdamage1 amd64 1:1.1.6-1+b2 [15.5 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libxinerama1 amd64 2:1.1.4-3+b3 [16.0 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 xkb-data all 2.42-1 [790 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libxkbcommon0 amd64 1.7.0-2 [113 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libxrandr2 amd64 2:1.5.4-1+b2 [36.4 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 libgtk-3-common all 3.24.43-5 [4655 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libgtk-3-0t64 amd64 3.24.43-5 [2755 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.123-1 [8084 B] Get: 157 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libglapi-mesa amd64 24.3.3-1 [38.0 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libx11-xcb1 amd64 2:1.8.10-2 [241 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b4 [19.3 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libdrm-intel1 amd64 2.4.123-1 [63.7 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libdrm-radeon1 amd64 2.4.123-1 [22.3 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libllvm19 amd64 1:19.1.7-1 [26.0 MB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 libsensors5 amd64 1:3.6.0-10+b1 [35.1 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 libxshmfence1 amd64 1.3-1+b3 [8852 B] Get: 177 http://deb.debian.org/debian unstable/main amd64 mesa-libgallium amd64 24.3.3-1 [9488 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 libvulkan1 amd64 1.4.304.0-1 [129 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 libwayland-server0 amd64 1.23.0-1+b1 [34.2 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 libgbm1 amd64 24.3.3-1 [43.5 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 libgl1-mesa-dri amd64 24.3.3-1 [44.9 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 libglx-mesa0 amd64 24.3.3-1 [142 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 libasound2-data all 1.2.13-1 [21.1 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 libasound2t64 amd64 1.2.13-1+b1 [373 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 libgif7 amd64 5.2.2-1+b1 [44.2 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23.2 [216 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 libxtst6 amd64 2:1.2.3-1.1+b3 [25.9 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 openjdk-21-jre amd64 21.0.6~6ea-1 [204 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 default-jre amd64 2:1.21-76 [1068 B] Get: 192 http://deb.debian.org/debian unstable/main amd64 openjdk-21-jdk-headless amd64 21.0.6~6ea-1 [82.8 MB] Get: 193 http://deb.debian.org/debian unstable/main amd64 default-jdk-headless amd64 2:1.21-76 [1124 B] Get: 194 http://deb.debian.org/debian unstable/main amd64 openjdk-21-jdk amd64 21.0.6~6ea-1 [3938 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 default-jdk amd64 2:1.21-76 [1076 B] Get: 196 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui-theme-base all 1.12.1+dfsg-1.1 [44.3 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 openjdk-21-doc all 21.0.6~6ea-1 [13.2 MB] Get: 200 http://deb.debian.org/debian unstable/main amd64 default-jdk-doc amd64 2:1.21-76 [3264 B] Get: 201 http://deb.debian.org/debian unstable/main amd64 libgpg-error0 amd64 1.51-3 [82.2 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 libassuan9 amd64 3.0.1-2 [60.6 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 libgcrypt20 amd64 1.11.0-7 [843 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 gpgconf amd64 2.2.46-1+b1 [121 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 libksba8 amd64 1.6.7-2+b1 [136 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8+b1 [19.9 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8+b1 [57.6 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 libnpth0t64 amd64 1.8-2 [22.9 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 dirmngr amd64 2.2.46-1+b1 [369 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 gnupg-l10n all 2.2.46-1 [702 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 gpg amd64 2.2.46-1+b1 [532 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 pinentry-curses amd64 1.3.1-2 [86.4 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 gpg-agent amd64 2.2.46-1+b1 [252 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 gpgsm amd64 2.2.46-1+b1 [255 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 gnupg all 2.2.46-1 [376 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 gpgv amd64 2.2.46-1+b1 [219 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 sopv-gpgv all 0.1.1-1 [10.7 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 220 http://deb.debian.org/debian unstable/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 libfile-touch-perl all 0.12-2 [8816 B] Get: 223 http://deb.debian.org/debian unstable/main amd64 libio-pty-perl amd64 1:1.20-1+b2 [34.3 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b4 [36.1 kB] Get: 227 http://deb.debian.org/debian unstable/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b2 [10.6 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 libdynaloader-functions-perl all 0.004-1 [12.1 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 libdevel-callchecker-perl amd64 0.009-1+b1 [16.2 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 libparams-classify-perl amd64 0.015-2+b4 [22.5 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 232 http://deb.debian.org/debian unstable/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 241 http://deb.debian.org/debian unstable/main amd64 liburi-perl all 5.30-1 [105 kB] Get: 242 http://deb.debian.org/debian unstable/main amd64 libhtml-parser-perl amd64 3.83-1+b2 [99.7 kB] Get: 243 http://deb.debian.org/debian unstable/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 libclone-perl amd64 0.47-1+b1 [13.9 kB] Get: 245 http://deb.debian.org/debian unstable/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 247 http://deb.debian.org/debian unstable/main amd64 libhttp-message-perl all 7.00-2 [79.8 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 250 http://deb.debian.org/debian unstable/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get: 251 http://deb.debian.org/debian unstable/main amd64 libnet-ssleay-perl amd64 1.94-2 [339 kB] Get: 252 http://deb.debian.org/debian unstable/main amd64 libio-socket-ssl-perl all 2.089-1 [223 kB] Get: 253 http://deb.debian.org/debian unstable/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 254 http://deb.debian.org/debian unstable/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 255 http://deb.debian.org/debian unstable/main amd64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 256 http://deb.debian.org/debian unstable/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 257 http://deb.debian.org/debian unstable/main amd64 libwww-perl all 6.77-1 [183 kB] Get: 258 http://deb.debian.org/debian unstable/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get: 259 http://deb.debian.org/debian unstable/main amd64 wdiff amd64 1.2.2-7 [122 kB] Get: 260 http://deb.debian.org/debian unstable/main amd64 devscripts all 2.25.1 [1053 kB] Get: 261 http://deb.debian.org/debian unstable/main amd64 fastjar amd64 2:0.98-7 [80.1 kB] Get: 262 http://deb.debian.org/debian unstable/main amd64 jarwrapper all 0.80 [9692 B] Get: 263 http://deb.debian.org/debian unstable/main amd64 javahelper all 0.80 [80.4 kB] Get: 264 http://deb.debian.org/debian unstable/main amd64 libhamcrest-java all 2.2-2 [121 kB] Get: 265 http://deb.debian.org/debian unstable/main amd64 junit4 all 4.13.2-5 [350 kB] Get: 266 http://deb.debian.org/debian unstable/main amd64 libapiguardian-java all 1.1.2-1 [4656 B] Get: 267 http://deb.debian.org/debian unstable/main amd64 libopentest4j-java all 1.2.0-4 [9516 B] Get: 268 http://deb.debian.org/debian unstable/main amd64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 269 http://deb.debian.org/debian unstable/main amd64 libpicocli-java all 4.6.2-2 [390 kB] Get: 270 http://deb.debian.org/debian unstable/main amd64 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 271 http://deb.debian.org/debian unstable/main amd64 junit5 all 5.10.3-1 [2459 kB] Get: 272 http://deb.debian.org/debian unstable/main amd64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 273 http://deb.debian.org/debian unstable/main amd64 libantlr4-runtime-java all 4.9.2-2 [317 kB] Get: 274 http://deb.debian.org/debian unstable/main amd64 libaopalliance-java all 20070526-7 [8572 B] Get: 275 http://deb.debian.org/debian unstable/main amd64 libapache-pom-java all 33-2 [5852 B] Get: 276 http://deb.debian.org/debian unstable/main amd64 libapfloat-java all 1.14.0-2 [725 kB] Get: 277 http://deb.debian.org/debian unstable/main amd64 libargs4j-java all 2.33-2 [138 kB] Get: 278 http://deb.debian.org/debian unstable/main amd64 libasm-java all 9.7.1-1 [391 kB] Get: 279 http://deb.debian.org/debian unstable/main amd64 libatinject-jsr330-api-java all 1.0+ds1-6 [5112 B] Get: 280 http://deb.debian.org/debian unstable/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 281 http://deb.debian.org/debian unstable/main amd64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 282 http://deb.debian.org/debian unstable/main amd64 libciftools-java all 6.0.0-1 [2211 kB] Get: 283 http://deb.debian.org/debian unstable/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 284 http://deb.debian.org/debian unstable/main amd64 libcommons-codec-java all 1.17.1-1 [303 kB] Get: 285 http://deb.debian.org/debian unstable/main amd64 libcommons-math-java all 2.2-9 [933 kB] Get: 286 http://deb.debian.org/debian unstable/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 287 http://deb.debian.org/debian unstable/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 288 http://deb.debian.org/debian unstable/main amd64 libguava-java all 32.0.1-1 [2708 kB] Get: 289 http://deb.debian.org/debian unstable/main amd64 libitext5-java all 5.5.13.3-4 [2667 kB] Get: 290 http://deb.debian.org/debian unstable/main amd64 libjackson2-annotations-java all 2.14.0-1 [68.8 kB] Get: 291 http://deb.debian.org/debian unstable/main amd64 libjackson2-core-java all 2.14.1-1 [447 kB] Get: 292 http://deb.debian.org/debian unstable/main amd64 libjackson2-databind-java all 2.14.0-1 [1584 kB] Get: 293 http://deb.debian.org/debian unstable/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 294 http://deb.debian.org/debian unstable/main amd64 libjaxen-java all 1.1.6-5 [214 kB] Get: 295 http://deb.debian.org/debian unstable/main amd64 libdom4j-java all 2.1.4-1 [312 kB] Get: 296 http://deb.debian.org/debian unstable/main amd64 libcommons-io-java all 2.17.0-1 [488 kB] Get: 297 http://deb.debian.org/debian unstable/main amd64 libslf4j-java all 1.7.32-1 [144 kB] Get: 298 http://deb.debian.org/debian unstable/main amd64 libmaven-shared-utils-java all 3.4.2-1 [137 kB] Get: 299 http://deb.debian.org/debian unstable/main amd64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 300 http://deb.debian.org/debian unstable/main amd64 libguice-java all 5.1.0-1 [932 kB] Get: 301 http://deb.debian.org/debian unstable/main amd64 libmaven-parent-java all 43-2 [6252 B] Get: 302 http://deb.debian.org/debian unstable/main amd64 libcommons-lang3-java all 3.17.0-1 [641 kB] Get: 303 http://deb.debian.org/debian unstable/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 304 http://deb.debian.org/debian unstable/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 305 http://deb.debian.org/debian unstable/main amd64 libmaven-resolver-java all 1.9.22-1 [729 kB] Get: 306 http://deb.debian.org/debian unstable/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 307 http://deb.debian.org/debian unstable/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 308 http://deb.debian.org/debian unstable/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 309 http://deb.debian.org/debian unstable/main amd64 libplexus-interpolation-java all 1.27-1 [76.8 kB] Get: 310 http://deb.debian.org/debian unstable/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 311 http://deb.debian.org/debian unstable/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 312 http://deb.debian.org/debian unstable/main amd64 libcdi-api-java all 1.2-4 [55.3 kB] Get: 313 http://deb.debian.org/debian unstable/main amd64 libsisu-inject-java all 0.3.5-1 [352 kB] Get: 314 http://deb.debian.org/debian unstable/main amd64 libsisu-plexus-java all 0.3.5-1 [183 kB] Get: 315 http://deb.debian.org/debian unstable/main amd64 libmaven3-core-java all 3.9.9-1 [1661 kB] Get: 316 http://deb.debian.org/debian unstable/main amd64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 317 http://deb.debian.org/debian unstable/main amd64 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 318 http://deb.debian.org/debian unstable/main amd64 libcommons-compress-java all 1.27.1-2 [641 kB] Get: 319 http://deb.debian.org/debian unstable/main amd64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 320 http://deb.debian.org/debian unstable/main amd64 libsnappy1v5 amd64 1.2.1-1+b1 [29.6 kB] Get: 321 http://deb.debian.org/debian unstable/main amd64 libsnappy-jni amd64 1.1.10.7-1 [6492 B] Get: 322 http://deb.debian.org/debian unstable/main amd64 libsnappy-java all 1.1.10.7-1 [87.6 kB] Get: 323 http://deb.debian.org/debian unstable/main amd64 libxz-java all 1.9-1 [143 kB] Get: 324 http://deb.debian.org/debian unstable/main amd64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 325 http://deb.debian.org/debian unstable/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 326 http://deb.debian.org/debian unstable/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 327 http://deb.debian.org/debian unstable/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 328 http://deb.debian.org/debian unstable/main amd64 libjsoup-java all 1.15.3-1 [431 kB] Get: 329 http://deb.debian.org/debian unstable/main amd64 libwagon-http-java all 3.5.3-1 [49.5 kB] Get: 330 http://deb.debian.org/debian unstable/main amd64 libistack-commons-java all 3.0.6-5 [145 kB] Get: 331 http://deb.debian.org/debian unstable/main amd64 libcodemodel-java all 2.6+jaxb2.3.0.1-11 [164 kB] Get: 332 http://deb.debian.org/debian unstable/main amd64 librelaxng-datatype-java all 1.0+ds1-3.1 [11.7 kB] Get: 333 http://deb.debian.org/debian unstable/main amd64 librngom-java all 2.3.0.1-11 [292 kB] Get: 334 http://deb.debian.org/debian unstable/main amd64 libxsom-java all 2.3.0.1-11 [401 kB] Get: 335 http://deb.debian.org/debian unstable/main amd64 libtxw2-java all 2.3.0.1-11 [134 kB] Get: 336 http://deb.debian.org/debian unstable/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 337 http://deb.debian.org/debian unstable/main amd64 libdtd-parser-java all 1.2-1 [64.9 kB] Get: 338 http://deb.debian.org/debian unstable/main amd64 libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 339 http://deb.debian.org/debian unstable/main amd64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB] Get: 340 http://deb.debian.org/debian unstable/main amd64 libfastinfoset-java all 1.2.12-3 [343 kB] Get: 341 http://deb.debian.org/debian unstable/main amd64 libjaxb-java all 2.3.0.1-11 [1980 kB] Get: 342 http://deb.debian.org/debian unstable/main amd64 libmaven-archiver-java all 3.6.2-1 [26.1 kB] Get: 343 http://deb.debian.org/debian unstable/main amd64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 344 http://deb.debian.org/debian unstable/main amd64 libcommons-text-java all 1.12.0-1 [222 kB] Get: 345 http://deb.debian.org/debian unstable/main amd64 libfastutil-java all 8.5.15+dfsg-1 [20.0 MB] Get: 346 http://deb.debian.org/debian unstable/main amd64 libjheaps-java all 0.14-2 [144 kB] Get: 347 http://deb.debian.org/debian unstable/main amd64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 348 http://deb.debian.org/debian unstable/main amd64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 349 http://deb.debian.org/debian unstable/main amd64 libjgraphx-java all 2.1.0.7-5 [809 kB] Get: 350 http://deb.debian.org/debian unstable/main amd64 libjgrapht-java all 1.5.2-1 [1610 kB] Get: 351 http://deb.debian.org/debian unstable/main amd64 libinchi1.07 amd64 1.07.2+dfsg-1 [556 kB] Get: 352 http://deb.debian.org/debian unstable/main amd64 libjni-inchi-jni amd64 0.8+dfsg-8 [9188 B] Get: 353 http://deb.debian.org/debian unstable/main amd64 libcommons-exec-java all 1.3-2 [48.1 kB] Get: 354 http://deb.debian.org/debian unstable/main amd64 libexec-maven-plugin-java all 3.1.0-2 [66.7 kB] Get: 355 http://deb.debian.org/debian unstable/main amd64 libmaven-shared-incremental-java all 1.1-6 [9916 B] Get: 356 http://deb.debian.org/debian unstable/main amd64 libcommons-lang-java all 2.6-10 [273 kB] Get: 357 http://deb.debian.org/debian unstable/main amd64 libxbean-reflect-java all 4.5-9 [132 kB] Get: 358 http://deb.debian.org/debian unstable/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 359 http://deb.debian.org/debian unstable/main amd64 libplexus-compiler-java all 2.13.0-1 [99.5 kB] Get: 360 http://deb.debian.org/debian unstable/main amd64 libqdox2-java all 2.0.3-1 [296 kB] Get: 361 http://deb.debian.org/debian unstable/main amd64 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 362 http://deb.debian.org/debian unstable/main amd64 libmaven-compiler-plugin-java all 3.13.0-1 [78.8 kB] Get: 363 http://deb.debian.org/debian unstable/main amd64 liblog4j1.2-java all 1.2.17-11 [444 kB] Get: 364 http://deb.debian.org/debian unstable/main amd64 libjni-inchi-java all 0.8+dfsg-8 [33.6 kB] Get: 365 http://deb.debian.org/debian unstable/main amd64 libnaga-java all 3.0+svn80-5 [43.5 kB] Get: 366 http://deb.debian.org/debian unstable/main amd64 libjmol-java all 16.2.33+dfsg-1 [10.4 MB] Get: 367 http://deb.debian.org/debian unstable/main amd64 libjson-simple-java all 2.3.0-1 [63.8 kB] Get: 368 http://deb.debian.org/debian unstable/main amd64 libmsgpack-java all 0.9.6-1 [161 kB] Get: 369 http://deb.debian.org/debian unstable/main amd64 libmmtf-java all 1.0.11-1 [187 kB] Get: 370 http://deb.debian.org/debian unstable/main amd64 libvecmath-java all 1.5.2-7 [97.0 kB] Get: 371 http://deb.debian.org/debian unstable/main amd64 libbiojava6-java all 6.1.0+dfsg-5 [5359 kB] Get: 372 http://deb.debian.org/debian unstable/main amd64 libbiojava6-java-doc all 6.1.0+dfsg-5 [2256 kB] Get: 373 http://deb.debian.org/debian unstable/main amd64 libbsh-java all 2.0b4-20 [291 kB] Get: 374 http://deb.debian.org/debian unstable/main amd64 libcharts4j-java all 1.3-4 [162 kB] Get: 375 http://deb.debian.org/debian unstable/main amd64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 376 http://deb.debian.org/debian unstable/main amd64 libcommons-beanutils-java all 1.9.4-2 [233 kB] Get: 377 http://deb.debian.org/debian unstable/main amd64 libcommons-collections4-java all 4.4-2 [682 kB] Get: 378 http://deb.debian.org/debian unstable/main amd64 libcommons-digester-java all 1.8.1-7 [138 kB] Get: 379 http://deb.debian.org/debian unstable/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get: 380 http://deb.debian.org/debian unstable/main amd64 libcommons-math3-java all 3.6.1-4 [2040 kB] Get: 381 http://deb.debian.org/debian unstable/main amd64 libcommons-validator-java all 1:1.9.0-1 [191 kB] Get: 382 http://deb.debian.org/debian unstable/main amd64 libdistlib-java all 1.0-5 [72.5 kB] Get: 383 http://deb.debian.org/debian unstable/main amd64 libdoxia-core-java all 2.0.0-1 [149 kB] Get: 384 http://deb.debian.org/debian unstable/main amd64 libplexus-xml-java all 3.0.1-2 [93.7 kB] Get: 385 http://deb.debian.org/debian unstable/main amd64 libdoxia-java all 2.0.0-1 [113 kB] Get: 386 http://deb.debian.org/debian unstable/main amd64 libmaven-reporting-api-java all 4.0.0-1 [6724 B] Get: 387 http://deb.debian.org/debian unstable/main amd64 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB] Get: 388 http://deb.debian.org/debian unstable/main amd64 velocity all 1.7-7 [431 kB] Get: 389 http://deb.debian.org/debian unstable/main amd64 libplexus-velocity-java all 1.2-4 [9676 B] Get: 390 http://deb.debian.org/debian unstable/main amd64 liboro-java all 2.0.8a-14 [70.5 kB] Get: 391 http://deb.debian.org/debian unstable/main amd64 libvelocity-tools-java all 2.0-9 [311 kB] Get: 392 http://deb.debian.org/debian unstable/main amd64 libdoxia-sitetools-java all 2.0.0-1 [176 kB] Get: 393 http://deb.debian.org/debian unstable/main amd64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 394 http://deb.debian.org/debian unstable/main amd64 libezmorph-java all 1.0.6-4 [75.9 kB] Get: 395 http://deb.debian.org/debian unstable/main amd64 libfreemarker-java all 2.3.32-2 [1546 kB] Get: 396 http://deb.debian.org/debian unstable/main amd64 libxom-java all 1.3.9-1 [174 kB] Get: 397 http://deb.debian.org/debian unstable/main amd64 libjson-java all 3.1.0+dfsg-2 [142 kB] Get: 398 http://deb.debian.org/debian unstable/main amd64 libmbedcrypto16 amd64 3.6.2-3 [355 kB] Get: 399 http://deb.debian.org/debian unstable/main amd64 libmbedx509-7 amd64 3.6.2-3 [147 kB] Get: 400 http://deb.debian.org/debian unstable/main amd64 libmbedtls21 amd64 3.6.2-3 [234 kB] Get: 401 http://deb.debian.org/debian unstable/main amd64 ncbi-vdb-data all 3.0.9+dfsg-2 [74.0 kB] Get: 402 http://deb.debian.org/debian unstable/main amd64 libncbi-vdb3 amd64 3.0.9+dfsg-2 [1189 kB] Get: 403 http://deb.debian.org/debian unstable/main amd64 libncbi-ngs3 amd64 3.0.9+dfsg-7+b1 [157 kB] Get: 404 http://deb.debian.org/debian unstable/main amd64 libngs-jni amd64 3.0.9+dfsg-7+b1 [25.8 kB] Get: 405 http://deb.debian.org/debian unstable/main amd64 libngs-java amd64 3.0.9+dfsg-7+b1 [112 kB] Get: 406 http://deb.debian.org/debian unstable/main amd64 librhino-java all 1.7.15-1 [1382 kB] Get: 407 http://deb.debian.org/debian unstable/main amd64 libhtsjdk-java all 4.1.3+dfsg-2 [1841 kB] Get: 408 http://deb.debian.org/debian unstable/main amd64 libjansi-java all 2.4.1-2 [100 kB] Get: 409 http://deb.debian.org/debian unstable/main amd64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 410 http://deb.debian.org/debian unstable/main amd64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 411 http://deb.debian.org/debian unstable/main amd64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 412 http://deb.debian.org/debian unstable/main amd64 libjetty9-java all 9.4.56-1 [2964 kB] Get: 413 http://deb.debian.org/debian unstable/main amd64 libjtidy-java all 7+svn20110807-5 [250 kB] Get: 414 http://deb.debian.org/debian unstable/main amd64 libmaven-common-artifact-filters-java all 3.4.0-1 [47.7 kB] Get: 415 http://deb.debian.org/debian unstable/main amd64 libmaven-artifact-transfer-java all 0.13.1-2 [158 kB] Get: 416 http://deb.debian.org/debian unstable/main amd64 libplexus-build-api-java all 0.0.7-4 [10.3 kB] Get: 417 http://deb.debian.org/debian unstable/main amd64 libmaven-filtering-java all 3.4.0-1 [51.4 kB] Get: 418 http://deb.debian.org/debian unstable/main amd64 libmaven-assembly-plugin-java all 3.4.2-2 [242 kB] Get: 419 http://deb.debian.org/debian unstable/main amd64 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB] Get: 420 http://deb.debian.org/debian unstable/main amd64 libmaven-invoker-java all 3.3.0-1 [29.1 kB] Get: 421 http://deb.debian.org/debian unstable/main amd64 libplexus-interactivity-api-java all 1.3-1 [11.6 kB] Get: 422 http://deb.debian.org/debian unstable/main amd64 libmaven-javadoc-plugin-java all 3.10.1-2 [451 kB] Get: 423 http://deb.debian.org/debian unstable/main amd64 libplexus-container-default1.5-java all 2.1.1-1 [4476 B] Get: 424 http://deb.debian.org/debian unstable/main amd64 libplexus-ant-factory-java all 1.0~alpha2.1-4 [11.4 kB] Get: 425 http://deb.debian.org/debian unstable/main amd64 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B] Get: 426 http://deb.debian.org/debian unstable/main amd64 libmaven-plugin-tools-java all 3.10.2-1 [245 kB] Get: 427 http://deb.debian.org/debian unstable/main amd64 libmaven-reporting-exec-java all 2.0.0-1 [23.9 kB] Get: 428 http://deb.debian.org/debian unstable/main amd64 libmaven-resources-plugin-java all 3.3.1-1 [27.5 kB] Get: 429 http://deb.debian.org/debian unstable/main amd64 libmaven-site-plugin-java all 3.21.0-1 [106 kB] Get: 430 http://deb.debian.org/debian unstable/main amd64 libsurefire-java all 2.22.3-3 [1284 kB] Get: 431 http://deb.debian.org/debian unstable/main amd64 libtrove3-java all 3.0.3-5 [2146 kB] Get: 432 http://deb.debian.org/debian unstable/main amd64 libtrove3-java-doc all 3.0.3-5 [823 kB] Get: 433 http://deb.debian.org/debian unstable/main amd64 libwagon-file-java all 3.5.3-1 [8388 B] Get: 434 http://deb.debian.org/debian unstable/main amd64 libxml2-utils amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [99.4 kB] Get: 435 http://deb.debian.org/debian unstable/main amd64 maven all 3.9.9-1 [19.7 kB] Get: 436 http://deb.debian.org/debian unstable/main amd64 maven-repo-helper all 1.11 [142 kB] Get: 437 http://deb.debian.org/debian unstable/main amd64 unzip amd64 6.0-28 [166 kB] Get: 438 http://deb.debian.org/debian unstable/main amd64 maven-debian-helper all 2.6.7 [108 kB] Fetched 361 MB in 15s (24.3 MB/s) Preconfiguring packages ... Selecting previously unselected package libsystemd-shared: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 ... 19851 files and directories currently installed.) Preparing to unpack .../libsystemd-shared_257.2-2_amd64.deb ... Unpacking libsystemd-shared:amd64 (257.2-2) ... Selecting previously unselected package libapparmor1:amd64. Preparing to unpack .../libapparmor1_3.1.7-1+b3_amd64.deb ... Unpacking libapparmor1:amd64 (3.1.7-1+b3) ... Setting up libsystemd-shared:amd64 (257.2-2) ... Selecting previously unselected package systemd. (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 ... 19865 files and directories currently installed.) Preparing to unpack .../systemd_257.2-2_amd64.deb ... Unpacking systemd (257.2-2) ... Setting up libapparmor1:amd64 (3.1.7-1+b3) ... Setting up systemd (257.2-2) ... Created symlink '/etc/systemd/system/getty.target.wants/getty@tty1.service' -> '/usr/lib/systemd/system/getty@.service'. Created symlink '/etc/systemd/system/multi-user.target.wants/remote-fs.target' -> '/usr/lib/systemd/system/remote-fs.target'. Created symlink '/etc/systemd/system/sysinit.target.wants/systemd-pstore.service' -> '/usr/lib/systemd/system/systemd-pstore.service'. Initializing machine ID from random generator. Creating group 'systemd-journal' with GID 999. Creating group 'systemd-network' with GID 998. Creating user 'systemd-network' (systemd Network Management) with UID 998 and GID 998. /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. Selecting previously unselected package systemd-sysv. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20808 files and directories currently installed.) Preparing to unpack .../00-systemd-sysv_257.2-2_amd64.deb ... Unpacking systemd-sysv (257.2-2) ... Selecting previously unselected package libdbus-1-3:amd64. Preparing to unpack .../01-libdbus-1-3_1.16.0-1_amd64.deb ... Unpacking libdbus-1-3:amd64 (1.16.0-1) ... Selecting previously unselected package dbus-bin. Preparing to unpack .../02-dbus-bin_1.16.0-1_amd64.deb ... Unpacking dbus-bin (1.16.0-1) ... Selecting previously unselected package dbus-session-bus-common. Preparing to unpack .../03-dbus-session-bus-common_1.16.0-1_all.deb ... Unpacking dbus-session-bus-common (1.16.0-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../04-libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package dbus-daemon. Preparing to unpack .../05-dbus-daemon_1.16.0-1_amd64.deb ... Unpacking dbus-daemon (1.16.0-1) ... Selecting previously unselected package dbus-system-bus-common. Preparing to unpack .../06-dbus-system-bus-common_1.16.0-1_all.deb ... Unpacking dbus-system-bus-common (1.16.0-1) ... Selecting previously unselected package dbus. Preparing to unpack .../07-dbus_1.16.0-1_amd64.deb ... Unpacking dbus (1.16.0-1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package binfmt-support. Preparing to unpack .../09-binfmt-support_2.2.2-7_amd64.deb ... Unpacking binfmt-support (2.2.2-7) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../10-libpython3.13-minimal_3.13.1-3_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.1-3) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../11-python3.13-minimal_3.13.1-3_amd64.deb ... Unpacking python3.13-minimal (3.13.1-3) ... Setting up libpython3.13-minimal:amd64 (3.13.1-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.1-3) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21256 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.1-2_amd64.deb ... Unpacking python3-minimal (3.13.1-2) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025a-1_all.deb ... Unpacking tzdata (2025a-1) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../4-libffi8_3.4.6-1_amd64.deb ... Unpacking libffi8:amd64 (3.4.6-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../6-libreadline8t64_8.2-6_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.1-3_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.1-3) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.1-3_amd64.deb ... Unpacking python3.13 (3.13.1-3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.1-2_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.1-2) ... Setting up python3-minimal (3.13.1-2) ... 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 ... 22266 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.1-2_amd64.deb ... Unpacking python3 (3.13.1-2) ... Selecting previously unselected package sgml-base. 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Setting up libtimedate-perl (2.3300-2) ... Setting up libgif7:amd64 (5.2.2-1+b1) ... Setting up libffi8:amd64 (3.4.6-1) ... Setting up libtrove3-java (3.0.3-5) ... Setting up dwz (0.15-1+b1) ... Setting up libplexus-interactivity-api-java (1.3-1) ... Setting up libfreemarker-java (2.3.32-2) ... Setting up sensible-utils (0.0.24) ... Setting up libxshmfence1:amd64 (1.3-1+b3) ... Setting up libjsoup-java (1.15.3-1) ... Setting up at-spi2-common (2.55.0.1-1) ... Setting up libcommons-math-java (2.2-9) ... Setting up gpgv (2.2.46-1+b1) ... Setting up libtiff6:amd64 (4.5.1+git230720-5) ... Setting up libxcb-randr0:amd64 (1.17.0-2+b1) ... Setting up dbus-session-bus-common (1.16.0-1) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libassuan9:amd64 (3.0.1-2) ... Setting up libxml-commons-external-java (1.4.01-6) ... Setting up procps (2:4.0.4-6) ... Setting up libxbean-reflect-java (4.5-9) ... Setting up libservlet-api-java (4.0.1-2) ... Setting up libplexus-xml-java (3.0.1-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libopentest4j-java (1.2.0-4) ... Setting up libtasn1-6:amd64 (4.19.0-3+b3) ... Setting up libjackson2-core-java (2.14.1-1) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up ncbi-vdb-data (3.0.9+dfsg-2) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up libcommons-math3-java (3.6.1-4) ... Setting up sgml-base (1.31) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b4) ... Setting up libkrb5-3:amd64 (1.21.3-4) ... Setting up libwayland-egl1:amd64 (1.23.0-1+b1) ... Setting up libmbedcrypto16:amd64 (3.6.2-3) ... 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 dbus-system-bus-common (1.16.0-1) ... useradd: Warning: missing or non-executable shell '/usr/sbin/nologin' Setting up libfile-homedir-perl (1.006-2) ... Setting up librelaxng-datatype-java (1.0+ds1-3.1) ... Setting up openssl (3.4.0-2) ... Setting up libinchi1.07 (1.07.2+dfsg-1) ... Setting up libdrm-common (2.4.123-1) ... Setting up libcdi-api-java (1.2-4) ... Setting up libsnappy-jni (1.1.10.7-1) ... Setting up libezmorph-java (1.0.6-4) ... Setting up libxcomposite1:amd64 (1:0.4.6-1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libldap2:amd64 (2.6.9+dfsg-1) ... Setting up liburi-perl (5.30-1) ... Setting up dbus-bin (1.16.0-1) ... Setting up libargs4j-java (2.33-2) ... Setting up libfile-touch-perl (0.12-2) ... Setting up dctrl-tools (2.24-3+b1) ... Setting up libxkbcommon0:amd64 (1.7.0-2) ... Setting up libnaga-java (3.0+svn80-5) ... Setting up libwayland-client0:amd64 (1.23.0-1+b1) ... Setting up libnet-ssleay-perl:amd64 (1.94-2) ... 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 libksba8:amd64 (1.6.7-2+b1) ... Setting up pinentry-curses (1.3.1-2) ... Setting up libdom4j-java (2.1.4-1) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libxcb-dri3-0:amd64 (1.17.0-2+b1) ... Setting up libwagon-provider-api-java (3.5.3-1) ... Setting up libllvm19:amd64 (1:19.1.7-1) ... Setting up libwayland-server0:amd64 (1.23.0-1+b1) ... Setting up libx11-xcb1:amd64 (2:1.8.10-2) ... Setting up libhttp-date-perl (6.06-1) ... Setting up gettext (0.23.1-1) ... Setting up libjetty9-java (9.4.56-1) ... Setting up libxdamage1:amd64 (1:1.1.6-1+b2) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libplexus-languages-java (1.1.1-2) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b3) ... Setting up jarwrapper (0.80) ... Setting up libtool (2.5.4-2) ... Setting up fontconfig-config (2.15.0-2) ... Setting up libstax-ex-java (1.7.8-3) ... Setting up libmaven-parent-java (43-2) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-16) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up libnet-http-perl (6.23-1) ... Setting up libsisu-inject-java (0.3.5-1) ... Setting up libidn2-0:amd64 (2.3.7-2+b1) ... Setting up libnss3:amd64 (2:3.107-1) ... Setting up libciftools-java (6.0.0-1) ... Setting up dbus-daemon (1.16.0-1) ... Setting up libxom-java (1.3.9-1) ... Setting up libdevel-callchecker-perl:amd64 (0.009-1+b1) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libjackson2-databind-java (2.14.0-1) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up patchutils (0.4.2-1) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up libthai0:amd64 (0.1.29-2+b1) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.5-1) ... Setting up libglib2.0-0t64:amd64 (2.82.4-2) ... Setting up libmbedx509-7:amd64 (3.6.2-3) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libxfixes3:amd64 (1:6.0.0-2+b3) ... Setting up dbus (1.16.0-1) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up shared-mime-info (2.4-5+b1) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libxinerama1:amd64 (2:1.1.4-3+b3) ... Setting up libstreambuffer-java (1.5.4-1.1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-4) ... Setting up libxrandr2:amd64 (2:1.5.4-1+b2) ... Setting up libcommons-collections4-java (4.4-2) ... Setting up libcommons-lang3-java (3.17.0-1) ... Setting up libmbedtls21:amd64 (3.6.2-3) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up librngom-java (2.3.0.1-11) ... Setting up libdrm2:amd64 (2.4.123-1) ... Setting up libjni-inchi-jni (0.8+dfsg-8) ... Setting up libjgraphx-java (2.1.0.7-5) ... Setting up groff-base (1.23.0-7) ... Setting up libwayland-cursor0:amd64 (1.23.0-1+b1) ... Setting up libhtml-parser-perl:amd64 (3.83-1+b2) ... Setting up gpgconf (2.2.46-1+b1) ... Setting up libpam-systemd:amd64 (257.2-2) ... Setting up libcommons-beanutils-java (1.9.4-2) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libharfbuzz0b:amd64 (10.2.0-1) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-1+b1) ... Setting up libsnappy-java (1.1.10.7-1) ... Setting up libfontconfig1:amd64 (2.15.0-2) ... Setting up libxsom-java (2.3.0.1-11) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libwagon-file-java (3.5.3-1) ... Setting up libxml2-utils (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libcommons-codec-java (1.17.1-1) ... Setting up libpython3.13-stdlib:amd64 (3.13.1-3) ... Setting up libavahi-client3:amd64 (0.8-16) ... Setting up libio-socket-ssl-perl (2.089-1) ... Setting up gpg (2.2.46-1+b1) ... Setting up libpython3-stdlib:amd64 (3.13.1-2) ... Setting up libhttp-message-perl (7.00-2) ... Setting up libdrm-amdgpu1:amd64 (2.4.123-1) ... Setting up libgnutls30t64:amd64 (3.8.8-2) ... Setting up gtk-update-icon-cache (4.16.12+ds-1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up velocity (1.7-7) ... Setting up fontconfig (2.15.0-2) ... Regenerating fonts cache... done. Setting up gpg-agent (2.2.46-1+b1) ... Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent-browser.socket' -> '/usr/lib/systemd/user/gpg-agent-browser.socket'. Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent-extra.socket' -> '/usr/lib/systemd/user/gpg-agent-extra.socket'. Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent-ssh.socket' -> '/usr/lib/systemd/user/gpg-agent-ssh.socket'. Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent.socket' -> '/usr/lib/systemd/user/gpg-agent.socket'. Setting up libatk1.0-0t64:amd64 (2.55.0.1-1) ... Setting up openjdk-21-jre-headless:amd64 (21.0.6~6ea-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libxi6:amd64 (2:1.8.2-1) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up python3.13 (3.13.1-3) ... Setting up libcommons-io-java (2.17.0-1) ... Setting up libdrm-radeon1:amd64 (2.4.123-1) ... Setting up libcommons-digester-java (1.8.1-7) ... Setting up libxtst6:amd64 (2:1.2.3-1.1+b3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libdistlib-java (1.0-5) ... Setting up libxcursor1:amd64 (1:1.2.3-1) ... Setting up libparams-classify-perl:amd64 (0.015-2+b4) ... Setting up gpgsm (2.2.46-1+b1) ... Setting up libpango-1.0-0:amd64 (1.56.1-1) ... Setting up libdrm-intel1:amd64 (2.4.123-1) ... Setting up libncbi-vdb3:amd64 (3.0.9+dfsg-2) ... Setting up libcloudproviders0:amd64 (0.3.6-1+b1) ... Setting up python3 (3.13.1-2) ... Setting up sopv-gpgv (0.1.1-1) ... update-alternatives: using /usr/bin/sopv-gpgv to provide /usr/bin/sopv (sopv) in auto mode Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink '/etc/systemd/system/timers.target.wants/man-db.timer' -> '/usr/lib/systemd/system/man-db.timer'. Setting up libcairo2:amd64 (1.18.2-2) ... Setting up libcolord2:amd64 (1.4.7-1+b2) ... Setting up libdconf1:amd64 (0.40.0-5) ... Setting up dirmngr (2.2.46-1+b1) ... Created symlink '/etc/systemd/user/sockets.target.wants/dirmngr.socket' -> '/usr/lib/systemd/user/dirmngr.socket'. Setting up libmaven-filtering-java (3.4.0-1) ... Setting up openjdk-21-doc (21.0.6~6ea-1) ... Setting up dbus-user-session (1.16.0-1) ... Setting up libmaven-resolver-java (1.9.22-1) ... Setting up adwaita-icon-theme (47.0-2) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up libmodule-runtime-perl (0.016-2) ... Setting up libatspi2.0-0t64:amd64 (2.55.0.1-1) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up libmaven-common-artifact-filters-java (3.4.0-1) ... Setting up gnupg (2.2.46-1) ... Setting up libwagon-http-java (3.5.3-1) ... Setting up libcairo-gobject2:amd64 (1.18.2-2) ... Setting up libmaven-shared-utils-java (3.4.2-1) ... Setting up libfastinfoset-java (1.2.12-3) ... Setting up libpangoft2-1.0-0:amd64 (1.56.1-1) ... Setting up libmaven-resources-plugin-java (3.3.1-1) ... Setting up libcups2t64:amd64 (2.4.10-2+b1) ... Setting up libpangocairo-1.0-0:amd64 (1.56.1-1) ... Setting up libncbi-ngs3:amd64 (3.0.9+dfsg-7+b1) ... Setting up libatk-bridge2.0-0t64:amd64 (2.55.0.1-1) ... Setting up mesa-libgallium:amd64 (24.3.3-1) ... Setting up libngs-jni:amd64 (3.0.9+dfsg-7+b1) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up libcommons-compress-java (1.27.1-2) ... Setting up libcommons-validator-java (1:1.9.0-1) ... Setting up libgbm1:amd64 (24.3.3-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up libgl1-mesa-dri:amd64 (24.3.3-1) ... Setting up libmaven-invoker-java (3.3.0-1) ... Setting up debhelper (13.24.1) ... Setting up dconf-service (0.40.0-5) ... Setting up default-jdk-doc (2:1.21-76) ... Setting up libmaven-clean-plugin-java (3.2.0-2) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libngs-java:amd64 (3.0.9+dfsg-7+b1) ... Setting up libglx-mesa0:amd64 (24.3.3-1) ... Setting up libglx0:amd64 (1.7.0-1+b2) ... Setting up dconf-gsettings-backend:amd64 (0.40.0-5) ... Setting up libmaven-archiver-java (3.6.2-1) ... Setting up libbiojava6-java-doc (6.1.0+dfsg-5) ... Setting up libgl1:amd64 (1.7.0-1+b2) ... Setting up libgtk-3-common (3.24.43-5) ... Setting up libgtk-3-0t64:amd64 (3.24.43-5) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libwww-perl (6.77-1) ... Setting up devscripts (2.25.1) ... Setting up libguava-java (32.0.1-1) ... Setting up javahelper (0.80) ... Setting up libplexus-container-default-java (2.1.1-1) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libguice-java (5.1.0-1) ... Setting up libplexus-i18n-java (1.0-beta-10-6) ... Setting up libplexus-container-default1.5-java (2.1.1-1) ... Setting up libplexus-velocity-java (1.2-4) ... Setting up libmaven3-core-java (3.9.9-1) ... Setting up libmaven-shared-incremental-java (1.1-6) ... Setting up libmaven-shared-io-java (3.0.0-4) ... Setting up libplexus-bsh-factory-java (1.0~alpha7-5) ... Setting up libplexus-compiler-java (2.13.0-1) ... Setting up libmaven-compiler-plugin-java (3.13.0-1) ... Setting up libjni-inchi-java (0.8+dfsg-8) ... Setting up libmaven-artifact-transfer-java (0.13.1-2) ... Setting up libmaven-file-management-java (3.0.0-1) ... Setting up libjmol-java (16.2.33+dfsg-1) ... Setting up libmaven-jar-plugin-java (3.3.0-2) ... Setting up libmaven-assembly-plugin-java (3.4.2-2) ... Setting up libcommons-text-java (1.12.0-1) ... Setting up libmsgpack-java (0.9.6-1) ... Setting up libmmtf-java (1.0.11-1) ... Setting up libjgrapht-java (1.5.2-1) ... Setting up libdoxia-core-java (2.0.0-1) ... Setting up libdoxia-java (2.0.0-1) ... Setting up libmaven-reporting-api-java (4.0.0-1) ... Setting up libmaven-reporting-exec-java (2.0.0-1) ... Processing triggers for libc-bin (2.40-5) ... Processing triggers for systemd (257.2-2) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureSign_Root_CA12.pem Adding debian:SecureSign_Root_CA14.pem Adding debian:SecureSign_Root_CA15.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_CYBER_Root_CA.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up maven (3.9.9-1) ... update-alternatives: using /usr/share/maven/bin/mvn to provide /usr/bin/mvn (mvn) in auto mode Setting up openjdk-21-jre:amd64 (21.0.6~6ea-1) ... Setting up ant (1.10.15-1) ... Setting up junit4 (4.13.2-5) ... Setting up openjdk-21-jdk-headless:amd64 (21.0.6~6ea-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jwebserver to provide /usr/bin/jwebserver (jwebserver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jre-headless (2:1.21-76) ... Setting up maven-repo-helper (1.11) ... Setting up default-jre (2:1.21-76) ... Setting up libplexus-ant-factory-java (1.0~alpha2.1-4) ... Setting up ant-optional (1.10.15-1) ... Setting up openjdk-21-jdk:amd64 (21.0.6~6ea-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up default-jdk-headless (2:1.21-76) ... Setting up junit5 (5.10.3-1) ... Setting up libjson-java (3.1.0+dfsg-2) ... Setting up libhtsjdk-java (4.1.3+dfsg-2) ... Setting up libmaven-plugin-tools-java (3.10.2-1) ... Setting up libistack-commons-java (3.0.6-5) ... Setting up default-jdk (2:1.21-76) ... Setting up libsurefire-java (2.22.3-3) ... Setting up libcodemodel-java (2.6+jaxb2.3.0.1-11) ... Setting up libtxw2-java (2.3.0.1-11) ... Setting up libjaxb-java (2.3.0.1-11) ... Setting up libbiojava6-java (6.1.0+dfsg-5) ... Processing triggers for sgml-base (1.31) ... Setting up libvelocity-tools-java (2.0-9) ... Setting up libdoxia-sitetools-java (2.0.0-1) ... Setting up libmaven-site-plugin-java (3.21.0-1) ... Setting up maven-debian-helper (2.6.7) ... Setting up libmaven-javadoc-plugin-java (3.10.1-2) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/snpeff-5.2.e+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_5.2.e+dfsg-1_source.changes dpkg-buildpackage: info: source package snpeff dpkg-buildpackage: info: source version 5.2.e+dfsg-1 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-5.2.e+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 # 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-5.2.e+dfsg' jh_clean Duplicate specification "unlink|u" for option "u" 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-5.2.e+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="@1728161934" +"%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-5.2.e\+dfsg/debian/maven-repo Failed to parse /build/reproducible-path/snpeff-5.2.e+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-5.2.e+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-5.2.e+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-5.2.e\+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-5.2.e\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/snpeff-5.2.e\+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 5.2 [INFO] from pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The artifact org.apache.maven.plugins:maven-jar-plugin:jar:3.1.2 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: 1 problem was encountered while building the effective model [FATAL] Non-parseable POM /build/reproducible-path/snpeff-5.2.e+dfsg/debian/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom: start tag unexpected character $ (position: TEXT seen ...org.jgrapht.jgrapht-core.originalVersion>\n\t\t\n\t\t\t [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/stats/ChrPosStats.java:67: warning: @param argument "num" is not a parameter name. [WARNING] * @param num [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/binseq/coder/Coder.java:57: warning: @param argument "c" is not a parameter name. [WARNING] * @param c [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/binseq/coder/Coder.java:66: warning: @param argument "c" is not a parameter name. [WARNING] * @param c [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/binseq/coder/Coder.java:81: warning: @param argument "c" is not a parameter name. [WARNING] * @param c [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+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-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/binseq/DnaAndQualitySequence.java:261: warning: @param argument "dataOutStream" is not a parameter name. [WARNING] * @param dataOutStream [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/binseq/DnaAndQualitySequenceWithId.java:42: warning: @param argument "dataOutStream" is not a parameter name. [WARNING] * @param dataOutStream [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+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-5.2.e+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] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/binseq/coder/DnaQualityCoder.java:59: warning: @param argument "c" is not a parameter name. [WARNING] * @param c [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/binseq/DnaSequenceId.java:84: warning: @param argument "dataOutStream" is not a parameter name. [WARNING] * @param dataOutStream [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/binseq/DnaSequencePe.java:125: warning: @param argument "dataOutStream" is not a parameter name. [WARNING] * @param dataOutStream [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/genBank/Embl.java:120: warning: @param argument "fileName" is not a parameter name. [WARNING] * @param fileName [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/fastq/FastqTrimmerAdrian.java:29: warning: invalid input: '<' [WARNING] * if v(3)<25 then exit [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+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-5.2.e+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-5.2.e+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] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+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-5.2.e+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-5.2.e+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-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/geneSets/GeneSets.java:89: warning: @param argument "geneSetName" is not a parameter name. [WARNING] * @param geneSetName [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/geneSets/GeneSets.java:466: warning: @param argument "geneSetType" is not a parameter name. [WARNING] * @param geneSetType [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/geneSets/GeneSetsRanked.java:128: warning: invalid input: '<' [WARNING] * Get geneId <-> Rank mapping [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/geneSets/GeneSetsRanked.java:128: warning: invalid input: '<' [WARNING] * Get geneId <-> Rank mapping [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/interval/Genome.java:420: warning: invalid input: '&' [WARNING] * Show number of genes, transcripts & exons [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/interval/Genome.java:428: warning: invalid input: '&' [WARNING] * Show number of genes, transcripts & exons [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/interval/Genome.java:420: warning: invalid input: '&' [WARNING] * Show number of genes, transcripts & exons [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/interval/Genome.java:428: warning: invalid input: '&' [WARNING] * Show number of genes, transcripts & exons [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/geneOntology/GoTerm.java:95: warning: @param argument "goTermAcc" is not a parameter name. [WARNING] * @param goTermAcc [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:102: warning: @param argument "symbolName" is not a parameter name. [WARNING] * @param symbolName : Symbol's name [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:107: 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-5.2.e+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:116: warning: @param argument "goTermAcc" is not a parameter name. [WARNING] * @param goTermAcc [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:118: warning: @param argument "symbolName" is not a parameter name. [WARNING] * @param symbolName [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:119: warning: @param argument "goTermType" is not a parameter name. [WARNING] * @param goTermType [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:120: warning: @param argument "description" is not a parameter name. [WARNING] * @param description [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:458: warning: @return tag cannot be used in method with void return type. [WARNING] public void readInterestingSymbolIdsFile(String fileName) { [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:501: warning: @param argument "nameSpace" is not a parameter name. [WARNING] * @param nameSpace [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/util/Gpr.java:704: warning: @param argument "count" is not a parameter name. [WARNING] * @param count [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/collections/HashLongLongArray.java:120: warning: invalid input: '<' [WARNING] * Insert a pair [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/collections/HashLongLongArray.java:120: warning: invalid input: '<' [WARNING] * Insert a pair [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+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-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/gtex/IdMap.java:49: warning: @param argument "name" is not a parameter name. [WARNING] * @param name [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/interval/tree/IntervalNode.java:85: warning: @param argument "queryMarker" is not a parameter name. [WARNING] * @param queryMarker: The interval to intersect [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/logStatsServer/LogStats.java:61: warning: invalid input: '<' [WARNING] * @param reportValues : A hash containing pairs to report [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/interval/Marker.java:660: warning: @param argument "variantEndPoint" is not a parameter name. [WARNING] * @param variantEndPoint : Before analyzing results, we have to change markers using variantrRef [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/nmer/Nmer.java:83: warning: @param argument "cq" is not a parameter name. [WARNING] * @param cq [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+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-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/nmer/NmerCount.java:177: warning: @param argument "threshold" is not a parameter name. [WARNING] * @param threshold [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+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-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/stats/ObservedOverExpected.java:160: warning: @param argument "Transcript" is not a parameter name. [WARNING] * @param Transcript [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/collections/OpenBitSet.java:159: warning: invalid input: '<' [WARNING] * numWords should be <= bits.length, and [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/collections/OpenBitSet.java:160: warning: invalid input: '>' [WARNING] * any existing words in the array at position >= numWords should be zero. [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/overlap/Overlap.java:30: warning: Parameter "seq1" is documented more than once. [WARNING] * @param seq1 [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/vcf/PedigreeEntry.java:9: warning: invalid input: '<' [WARNING] * ##PEDIGREE= [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/vcf/PedigreeEntry.java:12: warning: invalid input: '<' [WARNING] * ##PEDIGREE= [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/ped/PlinkMap.java:65: warning: @param argument "dataFileName" is not a parameter name. [WARNING] * @param dataFileName [WARNING] ^ [WARNING] 100 warnings [INFO] Building jar: /build/reproducible-path/snpeff-5.2.e+dfsg/target/snpeff-5.2-javadoc.jar [INFO] [INFO] -------------------------< org.snpeff:snpeff >-------------------------- [INFO] Building SnpEff 5.2 [INFO] from pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] >>> javadoc:3.10.1:aggregate (default-cli) > compile @ snpeff >>> [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ snpeff --- [INFO] Copying 5 resources from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.13.0:compile (default-compile) @ snpeff --- [INFO] Nothing to compile - all classes are up to date. [WARNING] Overwriting artifact's file from /build/reproducible-path/snpeff-5.2.e+dfsg/target/snpeff-5.2.jar to /build/reproducible-path/snpeff-5.2.e+dfsg/target/classes [INFO] [INFO] <<< javadoc:3.10.1:aggregate (default-cli) < compile @ snpeff <<< [INFO] [INFO] [INFO] --- javadoc:3.10.1:aggregate (default-cli) @ snpeff --- [INFO] Adding the --ignore-source-errors option [INFO] Configuration changed, re-generating javadoc. [WARNING] Javadoc Warnings [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/probablility/Binomial.java:34: warning: invalid input: '<' [WARNING] * P( K <= k ) [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/probablility/Binomial.java:34: warning: invalid input: '<' [WARNING] * P( K <= k ) [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/gsa/ChrPosScoreList.java:11: warning: invalid input: '<' [WARNING] * A list of [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/stats/ChrPosStats.java:67: warning: @param argument "num" is not a parameter name. [WARNING] * @param num [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/binseq/coder/Coder.java:57: warning: @param argument "c" is not a parameter name. [WARNING] * @param c [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/binseq/coder/Coder.java:66: warning: @param argument "c" is not a parameter name. [WARNING] * @param c [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/binseq/coder/Coder.java:81: warning: @param argument "c" is not a parameter name. [WARNING] * @param c [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+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-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/binseq/DnaAndQualitySequence.java:261: warning: @param argument "dataOutStream" is not a parameter name. [WARNING] * @param dataOutStream [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/binseq/DnaAndQualitySequenceWithId.java:42: warning: @param argument "dataOutStream" is not a parameter name. [WARNING] * @param dataOutStream [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+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-5.2.e+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] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/binseq/coder/DnaQualityCoder.java:59: warning: @param argument "c" is not a parameter name. [WARNING] * @param c [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/binseq/DnaSequenceId.java:84: warning: @param argument "dataOutStream" is not a parameter name. [WARNING] * @param dataOutStream [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/binseq/BinarySequence.java:43: warning: invalid input: '&' [WARNING] * Get sequence encoder & decoder [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/binseq/DnaSequencePe.java:125: warning: @param argument "dataOutStream" is not a parameter name. [WARNING] * @param dataOutStream [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/genBank/Embl.java:120: warning: @param argument "fileName" is not a parameter name. [WARNING] * @param fileName [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/fastq/FastqTrimmerAdrian.java:29: warning: invalid input: '<' [WARNING] * if v(3)<25 then exit [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+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-5.2.e+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-5.2.e+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] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+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-5.2.e+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-5.2.e+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-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/geneSets/GeneSets.java:89: warning: @param argument "geneSetName" is not a parameter name. [WARNING] * @param geneSetName [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/geneSets/GeneSets.java:466: warning: @param argument "geneSetType" is not a parameter name. [WARNING] * @param geneSetType [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/geneSets/GeneSetsRanked.java:128: warning: invalid input: '<' [WARNING] * Get geneId <-> Rank mapping [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/geneSets/GeneSetsRanked.java:128: warning: invalid input: '<' [WARNING] * Get geneId <-> Rank mapping [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/interval/Genome.java:420: warning: invalid input: '&' [WARNING] * Show number of genes, transcripts & exons [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/interval/Genome.java:428: warning: invalid input: '&' [WARNING] * Show number of genes, transcripts & exons [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/interval/Genome.java:420: warning: invalid input: '&' [WARNING] * Show number of genes, transcripts & exons [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/interval/Genome.java:428: warning: invalid input: '&' [WARNING] * Show number of genes, transcripts & exons [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/geneOntology/GoTerm.java:95: warning: @param argument "goTermAcc" is not a parameter name. [WARNING] * @param goTermAcc [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:102: warning: @param argument "symbolName" is not a parameter name. [WARNING] * @param symbolName : Symbol's name [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:107: 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-5.2.e+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:116: warning: @param argument "goTermAcc" is not a parameter name. [WARNING] * @param goTermAcc [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:118: warning: @param argument "symbolName" is not a parameter name. [WARNING] * @param symbolName [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:119: warning: @param argument "goTermType" is not a parameter name. [WARNING] * @param goTermType [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:120: warning: @param argument "description" is not a parameter name. [WARNING] * @param description [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:458: warning: @return tag cannot be used in method with void return type. [WARNING] public void readInterestingSymbolIdsFile(String fileName) { [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/geneOntology/GoTerms.java:501: warning: @param argument "nameSpace" is not a parameter name. [WARNING] * @param nameSpace [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/util/Gpr.java:704: warning: @param argument "count" is not a parameter name. [WARNING] * @param count [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/collections/HashLongLongArray.java:120: warning: invalid input: '<' [WARNING] * Insert a pair [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/collections/HashLongLongArray.java:120: warning: invalid input: '<' [WARNING] * Insert a pair [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+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-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/gtex/IdMap.java:49: warning: @param argument "name" is not a parameter name. [WARNING] * @param name [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/interval/tree/IntervalNode.java:85: warning: @param argument "queryMarker" is not a parameter name. [WARNING] * @param queryMarker: The interval to intersect [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/logStatsServer/LogStats.java:61: warning: invalid input: '<' [WARNING] * @param reportValues : A hash containing pairs to report [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/interval/Marker.java:660: warning: @param argument "variantEndPoint" is not a parameter name. [WARNING] * @param variantEndPoint : Before analyzing results, we have to change markers using variantrRef [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/nmer/Nmer.java:83: warning: @param argument "cq" is not a parameter name. [WARNING] * @param cq [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+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-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/nmer/NmerCount.java:177: warning: @param argument "threshold" is not a parameter name. [WARNING] * @param threshold [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+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] /build/reproducible-path/snpeff-5.2.e+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-5.2.e+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-5.2.e+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-5.2.e+dfsg/src/main/java/org/snpeff/stats/ObservedOverExpected.java:160: warning: @param argument "Transcript" is not a parameter name. [WARNING] * @param Transcript [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/collections/OpenBitSet.java:159: warning: invalid input: '<' [WARNING] * numWords should be <= bits.length, and [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/collections/OpenBitSet.java:160: warning: invalid input: '>' [WARNING] * any existing words in the array at position >= numWords should be zero. [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/overlap/Overlap.java:30: warning: Parameter "seq1" is documented more than once. [WARNING] * @param seq1 [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/vcf/PedigreeEntry.java:9: warning: invalid input: '<' [WARNING] * ##PEDIGREE= [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/vcf/PedigreeEntry.java:12: warning: invalid input: '<' [WARNING] * ##PEDIGREE= [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.e+dfsg/src/main/java/org/snpeff/ped/PlinkMap.java:65: warning: @param argument "dataFileName" is not a parameter name. [WARNING] * @param dataFileName [WARNING] ^ [WARNING] 100 warnings [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 13.026 s [INFO] Finished at: 2025-01-20T05:51:07-12:00 [INFO] ------------------------------------------------------------------------ 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-5.2.e\+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-5.2.e\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/snpeff-5.2.e\+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 5.2 [INFO] from pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The POM for org.biojava:biojava-structure:jar:6.x is invalid, transitive dependencies (if any) will not be available: 1 problem was encountered while building the effective model [FATAL] Non-parseable POM /build/reproducible-path/snpeff-5.2.e+dfsg/debian/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom: start tag unexpected character $ (position: TEXT seen ...org.jgrapht.jgrapht-core.originalVersion>\n\t\t\n\t\t\t-------------------------- [INFO] Building SnpEff 5.2 [INFO] from pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian:2.6:install (default-cli) @ snpeff --- [INFO] Cleaning pom file: /build/reproducible-path/snpeff-5.2.e+dfsg/pom.xml.save with options: [INFO] --keep-pom-version --package=libsnpeff-java [INFO] --rules=/build/reproducible-path/snpeff-5.2.e+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/snpeff-5.2.e+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/snpeff-5.2.e+dfsg/debian/maven.publishedRules [INFO] Install jar for snpeff into /usr/share/java [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.317 s [INFO] Finished at: 2025-01-20T05:54:31-12:00 [INFO] ------------------------------------------------------------------------ mh_resolve_dependencies --non-interactive --offline --build -plibsnpeff-java --javadoc --base-directory=/build/reproducible-path/snpeff-5.2.e\+dfsg --non-explore 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.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.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.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) 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. Jan 20, 2025 5:54:41 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve SEVERE: Cannot resolve dependencies in /build/reproducible-path/snpeff-5.2.e+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 'libsnpeff-java' in '../libsnpeff-java_5.2.e+dfsg-1_all.deb'. dpkg-deb: building package 'libsnpeff-java-doc' in '../libsnpeff-java-doc_5.2.e+dfsg-1_all.deb'. dpkg-deb: building package 'snpeff' in '../snpeff_5.2.e+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../snpeff_5.2.e+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../snpeff_5.2.e+dfsg-1_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: including full 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/2895180 and its subdirectories I: Current time: Mon Jan 20 05:57:56 -12 2025 I: pbuilder-time-stamp: 1737395876 Mon Jan 20 17:57:59 UTC 2025 I: 1st build successful. Starting 2nd build on remote node infom02-amd64.debian.net. Mon Jan 20 17:57:59 UTC 2025 I: Preparing to do remote build '2' on infom02-amd64.debian.net. Mon Jan 20 18:08:39 UTC 2025 I: Deleting $TMPDIR on infom02-amd64.debian.net. Mon Jan 20 18:08:40 UTC 2025 I: snpeff_5.2.e+dfsg-1_amd64.changes: Format: 1.8 Date: Sat, 05 Oct 2024 22:58:54 +0200 Source: snpeff Binary: libsnpeff-java libsnpeff-java-doc snpeff Architecture: all Version: 5.2.e+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Pierre Gruet Description: libsnpeff-java - genetic variant annotation and effect prediction toolbox - lib libsnpeff-java-doc - Documentation for Snp Effect snpeff - genetic variant annotation and effect prediction toolbox - tool Changes: snpeff (5.2.e+dfsg-1) unstable; urgency=medium . * New upstream version 5.2.e+dfsg * Refreshing patches * Raising Standards version to 4.7.0 (no change) * Updating the list of files to remove when repacking Checksums-Sha1: f01882968cca521fac878f8912e949b0d2ad86cb 1296412 libsnpeff-java-doc_5.2.e+dfsg-1_all.deb 8230bb03613181b3637ff42d2127d6d015a867fa 2156680 libsnpeff-java_5.2.e+dfsg-1_all.deb bbee30fdef9ded36d4645b0afca4cdb886c79eb5 7200 snpeff_5.2.e+dfsg-1_all.deb 05e31a592751e01dad19b4c0f8404d2fcf846111 18805 snpeff_5.2.e+dfsg-1_amd64.buildinfo Checksums-Sha256: b9a3b769c2a9dab614992bba108bda9bb5b0d08b4b24519c50fa2c580dc9433f 1296412 libsnpeff-java-doc_5.2.e+dfsg-1_all.deb 61068d33e06639047e383aa1355675fbf81c1064b72dd3a5ea7d7cbfd2f37aac 2156680 libsnpeff-java_5.2.e+dfsg-1_all.deb b8db14e0b4becc31bbb9d81de8e45f63c0f836a24bc2b5cfcda6efeb88d71ea5 7200 snpeff_5.2.e+dfsg-1_all.deb cb3be0213f1e659be777a641f9de3faa044ae49a7257af3d349a28e0b08759f6 18805 snpeff_5.2.e+dfsg-1_amd64.buildinfo Files: fabdd7c641b48f1bd4f6b79f7081d6b6 1296412 doc optional libsnpeff-java-doc_5.2.e+dfsg-1_all.deb 0247bccd47090011850aa5091fbaf788 2156680 java optional libsnpeff-java_5.2.e+dfsg-1_all.deb fafc1461e175421c7515c220ab6f3a44 7200 java optional snpeff_5.2.e+dfsg-1_all.deb 1461a12940ac6655844bbeb09259c641 18805 java optional snpeff_5.2.e+dfsg-1_amd64.buildinfo Mon Jan 20 18:08:42 UTC 2025 I: diffoscope 285 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_35-44077.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.xQEJybCC/snpeff_5.2.e+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.xQEJybCC/snpeff_5.2.e+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.xQEJybCC/snpeff_5.2.e+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.xQEJybCC/b1/snpeff_5.2.e+dfsg-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.xQEJybCC/b2/snpeff_5.2.e+dfsg-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.351s) 0.351s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.044s) 0.044s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 683ms CPU time consumed: 685ms Mon Jan 20 18:25:48 UTC 2025 I: diffoscope 285 found no differences in the changes files, and a .buildinfo file also exists. Mon Jan 20 18:25:48 UTC 2025 I: snpeff from unstable built successfully and reproducibly on amd64. Mon Jan 20 18:25:50 UTC 2025 I: Submitting .buildinfo files to external archives: Mon Jan 20 18:25:50 UTC 2025 I: Submitting 20K b1/snpeff_5.2.e+dfsg-1_amd64.buildinfo.asc Mon Jan 20 18:26:12 UTC 2025 I: Submitting 20K b2/snpeff_5.2.e+dfsg-1_amd64.buildinfo.asc Mon Jan 20 18:26:40 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Jan 20 18:26:40 UTC 2025 I: Done submitting .buildinfo files. Mon Jan 20 18:26:40 UTC 2025 I: Removing signed snpeff_5.2.e+dfsg-1_amd64.buildinfo.asc files: removed './b1/snpeff_5.2.e+dfsg-1_amd64.buildinfo.asc' removed './b2/snpeff_5.2.e+dfsg-1_amd64.buildinfo.asc'