Running as unit: rb-build-amd64_23-47642.service ==================================================================================== Fri Feb 21 20:07:19 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_23) on jenkins, called using "ionos11-amd64 ionos15-amd64" as arguments. Fri Feb 21 20:07:19 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-NOqrNVVC" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Feb 21 20:07:19 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Fri Feb 21 20:07:19 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-Jrytg8' Fri Feb 21 20:07:20 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Fri Feb 21 20:07:20 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-sVDApO' ok, let's check if snpeff is building anywhere yet… ok, snpeff is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of snpeff in trixie on amd64 on jenkins now. 1st build will be done on ionos11-amd64.debian.net. 2nd build will be done on ionos15-amd64.debian.net. ============================================================================= Fri Feb 21 20:07:25 UTC 2025 I: starting to build snpeff/trixie/amd64 on jenkins on '2025-02-21 20:07' Fri Feb 21 20:07:25 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_23/47642/console.log 1740168445 amd64 trixie snpeff Fri Feb 21 20:07:25 UTC 2025 I: Downloading source for trixie/snpeff=5.2.f+dfsg-1 --2025-02-21 20:07:25-- http://deb.debian.org/debian/pool/main/s/snpeff/snpeff_5.2.f%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.f+dfsg-1.dsc’ 0K .. 100% 366M=0s 2025-02-21 20:07:25 (366 MB/s) - ‘snpeff_5.2.f+dfsg-1.dsc’ saved [2569/2569] --2025-02-21 20:07:25-- http://deb.debian.org/debian/pool/main/s/snpeff/snpeff_5.2.f%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.f+dfsg-1.dsc’ 0K .. 100% 366M=0s 2025-02-21 20:07:25 (366 MB/s) - ‘snpeff_5.2.f+dfsg-1.dsc’ saved [2569/2569] Fri Feb 21 20:07:25 UTC 2025 I: snpeff_5.2.f+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.f+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: df32f1460a5b7793b5bdfc57cbbeaf416c7533da 154934504 snpeff_5.2.f+dfsg.orig.tar.xz 5b52843808da06b826ef07910dfa88a4c31e5b44 14288 snpeff_5.2.f+dfsg-1.debian.tar.xz Checksums-Sha256: ede30e648f777130b763d27ca150b7514498c91c732a980758a800dc5fd087c6 154934504 snpeff_5.2.f+dfsg.orig.tar.xz a43d295999391815dcb9b1db8ec6ae1d5438e240441f5e356e6a678757b73388 14288 snpeff_5.2.f+dfsg-1.debian.tar.xz Files: 4a630eadf7a8b0d65e8341356a924a02 154934504 snpeff_5.2.f+dfsg.orig.tar.xz e508f98c9ec478a09c4c29bcadfb0e1d 14288 snpeff_5.2.f+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEM8soQxPpC9J9y0UjYAMWptwndHYFAmexyP4ACgkQYAMWptwn dHaNnQ/+LrVoGR0NATAGjrUnG5zrHL3KhPnQVG1WL+52KxA0N3h3bHvTUiqRemcv IRMOaT6hWIhFLT1sVHyEhls94rofjliXiUNzo+vxxq5joOEqoodX9+eOpz2/L8ge Qo48A9JCWEAHwbBLC1Sx8uMTcULLGw/VW9eXD66VSpZspqrqfyBiqBAvx70j/FZ4 6piXCPNiEasLgbkowActMtfUUOYqC06XEfl6cL4qE+mu17XC/wL1UjQEReNI0ptS 6dq5hPa58BzdFGUCoUigLbCzQWvYs16cMiM9HyO/afjippitPG1QSbU1nBr6XkOu QHoV9G3wCG0lR50hjB8BT+o35hXeRqBUrrUjF61zA6Y6S/FbeQYWf1bm/HWHH76E B0srFxZ4b65XFlPsijVs8g68hKgyPuyF78sGpJb0sbIOMGVDibo+QBWtH4lDV06l 5JKrzeL4+NhzrX9dN9Z9vXzrMC1BXmmMgWUaANK9c5KdtO3igB8SQTfnRE+ogY3d n9d3AJGrxJs7nTtsRWjcwZ5QyPgk9pyQWNgmb9DKaUsaa92lrw98E14OSTNUYYbm zDCSqwJH8nB5Dp27959WfSIuAZbghXV2V/8yEwnVyTENXaOR/sR6YUs7XQn9SDxA zsqUpQkYi85m6TqGgq6rBp3+yk2JKZ54VobC5PRbiLvMl6fE4YY= =g6gI -----END PGP SIGNATURE----- Fri Feb 21 20:07:26 UTC 2025 I: Checking whether the package is not for us Fri Feb 21 20:07:26 UTC 2025 I: Starting 1st build on remote node ionos11-amd64.debian.net. Fri Feb 21 20:07:26 UTC 2025 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Fri Feb 21 20:07:26 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Fri Feb 21 20:07:26 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-KszjuZ' ==================================================================================== Fri Feb 21 20:07:27 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos11-amd64, called using "1 snpeff trixie /srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc 5.2.f+dfsg-1" as arguments. Fri Feb 21 20:07:27 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-liiAjWMa" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Feb 21 20:07:27 UTC 2025 I: Downloading source for trixie/snpeff=5.2.f+dfsg-1 Reading package lists... NOTICE: 'snpeff' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/snpeff.git Please use: git clone https://salsa.debian.org/med-team/snpeff.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 155 MB of source archives. Get:1 http://deb.debian.org/debian trixie/main snpeff 5.2.f+dfsg-1 (dsc) [2569 B] Get:2 http://deb.debian.org/debian trixie/main snpeff 5.2.f+dfsg-1 (tar) [155 MB] Get:3 http://deb.debian.org/debian trixie/main snpeff 5.2.f+dfsg-1 (diff) [14.3 kB] Fetched 155 MB in 5s (32.1 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'snpeff' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/snpeff.git Please use: git clone https://salsa.debian.org/med-team/snpeff.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 155 MB of source archives. Get:1 http://deb.debian.org/debian trixie/main snpeff 5.2.f+dfsg-1 (dsc) [2569 B] Get:2 http://deb.debian.org/debian trixie/main snpeff 5.2.f+dfsg-1 (tar) [155 MB] Get:3 http://deb.debian.org/debian trixie/main snpeff 5.2.f+dfsg-1 (diff) [14.3 kB] Fetched 155 MB in 5s (32.1 MB/s) Download complete and in download only mode ============================================================================= Building snpeff in trixie on amd64 on ionos11-amd64 now. Date: Fri Feb 21 20:07:32 UTC 2025 Date UTC: Fri Feb 21 20:07:32 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Fri Feb 21 08:07:33 -12 2025 I: pbuilder-time-stamp: 1740168453 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [snpeff_5.2.f+dfsg-1.dsc] I: copying [./snpeff_5.2.f+dfsg.orig.tar.xz] I: copying [./snpeff_5.2.f+dfsg-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./snpeff_5.2.f+dfsg-1.dsc: unsupported subcommand dpkg-source: info: extracting snpeff in snpeff-5.2.f+dfsg dpkg-source: info: unpacking snpeff_5.2.f+dfsg.orig.tar.xz dpkg-source: info: unpacking snpeff_5.2.f+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/1686575/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='b715f5724f154bf19a933374d9143114' 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='1686575' 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.ssl2lMWc/pbuilderrc_yzVc --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc/b1 --logfile b1/build.log snpeff_5.2.f+dfsg-1.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) 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/1686575/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 ... 19809 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 1301 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libsystemd-shared amd64 257.3-1 [2138 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libapparmor1 amd64 3.1.7-4 [42.0 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 systemd amd64 257.3-1 [3092 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 systemd-sysv amd64 257.3-1 [61.4 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libdbus-1-3 amd64 1.16.0-1 [177 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 dbus-bin amd64 1.16.0-1 [78.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 dbus-session-bus-common all 1.16.0-1 [51.1 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 dbus-daemon amd64 1.16.0-1 [157 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 dbus-system-bus-common all 1.16.0-1 [52.2 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 dbus amd64 1.16.0-1 [70.5 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 binfmt-support amd64 2.2.2-7 [64.3 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025a-2 [259 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.2-1 [745 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B] Get: 26 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.1-2 [28.0 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-7 [878 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.4.1-1 [1427 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20241223 [164 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libpam-systemd amd64 257.3-1 [293 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-3 [92.1 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [311 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.83.3-2 [1511 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 shared-mime-info amd64 2.4-5+b2 [760 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.46-4 [284 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-2 [140 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 gtk-update-icon-cache amd64 4.17.4+ds-4 [51.3 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 hicolor-icon-theme all 0.18-2 [11.8 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 adwaita-icon-theme all 47.0-2 [463 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 java-common all 0.76 [6776 B] Get: 61 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libnspr4 amd64 2:4.36-1 [110 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libnss3 amd64 2:3.108-1 [1393 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libpcsclite1 amd64 2.3.1-1 [56.0 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jre-headless amd64 21.0.6+7-1 [41.7 MB] Get: 66 http://deb.debian.org/debian trixie/main amd64 default-jre-headless amd64 2:1.21-76 [3192 B] Get: 67 http://deb.debian.org/debian trixie/main amd64 ant all 1.10.15-1 [2163 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 ant-optional all 1.10.15-1 [456 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 at-spi2-common all 2.55.2-1 [170 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 dbus-user-session amd64 1.16.0-1 [51.0 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libdconf1 amd64 0.40.0-5 [41.8 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 dconf-service amd64 0.40.0-5 [32.4 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 dconf-gsettings-backend amd64 0.40.0-5 [28.6 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 dctrl-tools amd64 2.24-3+b1 [104 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 86 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libatk1.0-0t64 amd64 2.55.2-1 [51.4 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libatspi2.0-0t64 amd64 2.55.2-1 [77.0 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libatk-bridge2.0-0t64 amd64 2.55.2-1 [68.1 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-2 [391 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b4 [27.8 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libcairo-gobject2 amd64 1.18.2-2 [130 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libcloudproviders0 amd64 0.3.6-1+b1 [29.2 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libcolord2 amd64 1.4.7-1+b2 [140 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libavahi-common-data amd64 0.8-16 [112 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libavahi-common3 amd64 0.8-16 [44.2 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libavahi-client3 amd64 0.8-16 [48.4 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 128 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libcups2t64 amd64 2.4.10-2+b1 [251 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libepoxy0 amd64 1.5.10-2 [193 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.2.0-1 [479 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-2 [463 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.56.1-1 [226 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.56.1-1 [55.3 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.56.1-1 [35.8 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libwayland-client0 amd64 1.23.1-1 [26.5 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 libwayland-cursor0 amd64 1.23.1-1 [11.4 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libwayland-egl1 amd64 1.23.1-1 [5452 B] Get: 145 http://deb.debian.org/debian trixie/main amd64 libxcomposite1 amd64 1:0.4.6-1 [16.3 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libxfixes3 amd64 1:6.0.0-2+b4 [20.2 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libxcursor1 amd64 1:1.2.3-1 [39.7 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libxdamage1 amd64 1:1.1.6-1+b2 [15.5 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 libxinerama1 amd64 2:1.1.4-3+b3 [16.0 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 xkb-data all 2.42-1 [790 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 libxkbcommon0 amd64 1.7.0-2 [113 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 libxrandr2 amd64 2:1.5.4-1+b3 [36.3 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libgtk-3-common all 3.24.48-4 [4873 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libgtk-3-0t64 amd64 3.24.48-4 [2767 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.123-1 [8084 B] Get: 157 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 libglapi-mesa amd64 24.3.4-3 [38.5 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 libx11-xcb1 amd64 2:1.8.10-2 [241 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b4 [19.3 kB] Get: 165 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 libdrm-intel1 amd64 2.4.123-1 [63.7 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 libdrm-radeon1 amd64 2.4.123-1 [22.3 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 libllvm19 amd64 1:19.1.7-1+b1 [26.0 MB] Get: 172 http://deb.debian.org/debian trixie/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 libsensors5 amd64 1:3.6.0-10+b1 [35.1 kB] Get: 174 http://deb.debian.org/debian trixie/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 libxshmfence1 amd64 1.3-1+b3 [8852 B] Get: 177 http://deb.debian.org/debian trixie/main amd64 mesa-libgallium amd64 24.3.4-3 [9492 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 libwayland-server0 amd64 1.23.1-1 [34.0 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 libgbm1 amd64 24.3.4-3 [43.7 kB] Get: 180 http://deb.debian.org/debian trixie/main amd64 libvulkan1 amd64 1.4.304.0-1 [129 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 libgl1-mesa-dri amd64 24.3.4-3 [45.2 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 libglx-mesa0 amd64 24.3.4-3 [143 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB] Get: 184 http://deb.debian.org/debian trixie/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 libasound2-data all 1.2.13-1 [21.1 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 libasound2t64 amd64 1.2.13-1+b1 [373 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 libgif7 amd64 5.2.2-1+b1 [44.2 kB] Get: 188 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+24 [217 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 libxtst6 amd64 2:1.2.5-1 [25.8 kB] Get: 190 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jre amd64 21.0.6+7-1 [205 kB] Get: 191 http://deb.debian.org/debian trixie/main amd64 default-jre amd64 2:1.21-76 [1068 B] Get: 192 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jdk-headless amd64 21.0.6+7-1 [82.8 MB] Get: 193 http://deb.debian.org/debian trixie/main amd64 default-jdk-headless amd64 2:1.21-76 [1124 B] Get: 194 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jdk amd64 21.0.6+7-1 [3434 kB] Get: 195 http://deb.debian.org/debian trixie/main amd64 default-jdk amd64 2:1.21-76 [1076 B] Get: 196 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 197 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 198 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui-theme-base all 1.12.1+dfsg-1.1 [44.3 kB] Get: 199 http://deb.debian.org/debian trixie/main amd64 openjdk-21-doc all 21.0.6+7-1 [13.2 MB] Get: 200 http://deb.debian.org/debian trixie/main amd64 default-jdk-doc amd64 2:1.21-76 [3264 B] Get: 201 http://deb.debian.org/debian trixie/main amd64 libgpg-error0 amd64 1.51-3 [82.2 kB] Get: 202 http://deb.debian.org/debian trixie/main amd64 libassuan9 amd64 3.0.1-2 [60.6 kB] Get: 203 http://deb.debian.org/debian trixie/main amd64 libgcrypt20 amd64 1.11.0-7 [843 kB] Get: 204 http://deb.debian.org/debian trixie/main amd64 gpgconf amd64 2.2.46-1+b1 [121 kB] Get: 205 http://deb.debian.org/debian trixie/main amd64 libksba8 amd64 1.6.7-2+b1 [136 kB] Get: 206 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8+b1 [19.9 kB] Get: 207 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8+b1 [57.6 kB] Get: 208 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB] Get: 209 http://deb.debian.org/debian trixie/main amd64 libnpth0t64 amd64 1.8-2 [22.9 kB] Get: 210 http://deb.debian.org/debian trixie/main amd64 dirmngr amd64 2.2.46-1+b1 [369 kB] Get: 211 http://deb.debian.org/debian trixie/main amd64 gnupg-l10n all 2.2.46-1 [702 kB] Get: 212 http://deb.debian.org/debian trixie/main amd64 gpg amd64 2.2.46-1+b1 [532 kB] Get: 213 http://deb.debian.org/debian trixie/main amd64 pinentry-curses amd64 1.3.1-2 [86.4 kB] Get: 214 http://deb.debian.org/debian trixie/main amd64 gpg-agent amd64 2.2.46-1+b1 [252 kB] Get: 215 http://deb.debian.org/debian trixie/main amd64 gpgsm amd64 2.2.46-1+b1 [255 kB] Get: 216 http://deb.debian.org/debian trixie/main amd64 gnupg all 2.2.46-1 [376 kB] Get: 217 http://deb.debian.org/debian trixie/main amd64 gpgv amd64 2.2.46-1+b1 [219 kB] Get: 218 http://deb.debian.org/debian trixie/main amd64 sopv-gpgv all 0.1.1-1 [10.7 kB] Get: 219 http://deb.debian.org/debian trixie/main amd64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 220 http://deb.debian.org/debian trixie/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 221 http://deb.debian.org/debian trixie/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 222 http://deb.debian.org/debian trixie/main amd64 libfile-touch-perl all 0.12-2 [8816 B] Get: 223 http://deb.debian.org/debian trixie/main amd64 libio-pty-perl amd64 1:1.20-1+b3 [34.3 kB] Get: 224 http://deb.debian.org/debian trixie/main amd64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 225 http://deb.debian.org/debian trixie/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 226 http://deb.debian.org/debian trixie/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b5 [36.1 kB] Get: 227 http://deb.debian.org/debian trixie/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b2 [10.6 kB] Get: 228 http://deb.debian.org/debian trixie/main amd64 libdynaloader-functions-perl all 0.004-1 [12.1 kB] Get: 229 http://deb.debian.org/debian trixie/main amd64 libdevel-callchecker-perl amd64 0.009-1+b1 [16.2 kB] Get: 230 http://deb.debian.org/debian trixie/main amd64 libparams-classify-perl amd64 0.015-2+b4 [22.5 kB] Get: 231 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 232 http://deb.debian.org/debian trixie/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 233 http://deb.debian.org/debian trixie/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 234 http://deb.debian.org/debian trixie/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 235 http://deb.debian.org/debian trixie/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 236 http://deb.debian.org/debian trixie/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 237 http://deb.debian.org/debian trixie/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 238 http://deb.debian.org/debian trixie/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 239 http://deb.debian.org/debian trixie/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 240 http://deb.debian.org/debian trixie/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 241 http://deb.debian.org/debian trixie/main amd64 liburi-perl all 5.30-1 [105 kB] Get: 242 http://deb.debian.org/debian trixie/main amd64 libhtml-parser-perl amd64 3.83-1+b2 [99.7 kB] Get: 243 http://deb.debian.org/debian trixie/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 244 http://deb.debian.org/debian trixie/main amd64 libclone-perl amd64 0.47-1+b1 [13.9 kB] Get: 245 http://deb.debian.org/debian trixie/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 246 http://deb.debian.org/debian trixie/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 247 http://deb.debian.org/debian trixie/main amd64 libhttp-message-perl all 7.00-2 [79.8 kB] Get: 248 http://deb.debian.org/debian trixie/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 249 http://deb.debian.org/debian trixie/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 250 http://deb.debian.org/debian trixie/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get: 251 http://deb.debian.org/debian trixie/main amd64 libnet-ssleay-perl amd64 1.94-3 [339 kB] Get: 252 http://deb.debian.org/debian trixie/main amd64 libio-socket-ssl-perl all 2.089-1 [223 kB] Get: 253 http://deb.debian.org/debian trixie/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 254 http://deb.debian.org/debian trixie/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 255 http://deb.debian.org/debian trixie/main amd64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 256 http://deb.debian.org/debian trixie/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 257 http://deb.debian.org/debian trixie/main amd64 libwww-perl all 6.77-1 [183 kB] Get: 258 http://deb.debian.org/debian trixie/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get: 259 http://deb.debian.org/debian trixie/main amd64 wdiff amd64 1.2.2-7 [122 kB] Get: 260 http://deb.debian.org/debian trixie/main amd64 devscripts all 2.25.2 [1058 kB] Get: 261 http://deb.debian.org/debian trixie/main amd64 fastjar amd64 2:0.98-7 [80.1 kB] Get: 262 http://deb.debian.org/debian trixie/main amd64 jarwrapper all 0.80 [9692 B] Get: 263 http://deb.debian.org/debian trixie/main amd64 javahelper all 0.80 [80.4 kB] Get: 264 http://deb.debian.org/debian trixie/main amd64 libhamcrest-java all 2.2-2 [121 kB] Get: 265 http://deb.debian.org/debian trixie/main amd64 junit4 all 4.13.2-5 [350 kB] Get: 266 http://deb.debian.org/debian trixie/main amd64 libapiguardian-java all 1.1.2-1 [4656 B] Get: 267 http://deb.debian.org/debian trixie/main amd64 libopentest4j-java all 1.2.0-4 [9516 B] Get: 268 http://deb.debian.org/debian trixie/main amd64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 269 http://deb.debian.org/debian trixie/main amd64 libpicocli-java all 4.6.2-2 [390 kB] Get: 270 http://deb.debian.org/debian trixie/main amd64 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 271 http://deb.debian.org/debian trixie/main amd64 junit5 all 5.10.3-1 [2459 kB] Get: 272 http://deb.debian.org/debian trixie/main amd64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 273 http://deb.debian.org/debian trixie/main amd64 libantlr4-runtime-java all 4.9.2-3 [318 kB] Get: 274 http://deb.debian.org/debian trixie/main amd64 libaopalliance-java all 20070526-7 [8572 B] Get: 275 http://deb.debian.org/debian trixie/main amd64 libapache-pom-java all 33-2 [5852 B] Get: 276 http://deb.debian.org/debian trixie/main amd64 libapfloat-java all 1.14.0-2 [725 kB] Get: 277 http://deb.debian.org/debian trixie/main amd64 libargs4j-java all 2.33-2 [138 kB] Get: 278 http://deb.debian.org/debian trixie/main amd64 libasm-java all 9.7.1-1 [391 kB] Get: 279 http://deb.debian.org/debian trixie/main amd64 libatinject-jsr330-api-java all 1.0+ds1-6 [5112 B] Get: 280 http://deb.debian.org/debian trixie/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 281 http://deb.debian.org/debian trixie/main amd64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 282 http://deb.debian.org/debian trixie/main amd64 libciftools-java all 6.0.0-1 [2211 kB] Get: 283 http://deb.debian.org/debian trixie/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 284 http://deb.debian.org/debian trixie/main amd64 libcommons-codec-java all 1.17.1-1 [303 kB] Get: 285 http://deb.debian.org/debian trixie/main amd64 libcommons-math-java all 2.2-9 [933 kB] Get: 286 http://deb.debian.org/debian trixie/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 287 http://deb.debian.org/debian trixie/main amd64 libjsr305-java all 0.1~+svn49-12 [26.6 kB] Get: 288 http://deb.debian.org/debian trixie/main amd64 libguava-java all 32.0.1-1 [2708 kB] Get: 289 http://deb.debian.org/debian trixie/main amd64 libitext5-java all 5.5.13.3-4 [2667 kB] Get: 290 http://deb.debian.org/debian trixie/main amd64 libjackson2-annotations-java all 2.14.0-1 [68.8 kB] Get: 291 http://deb.debian.org/debian trixie/main amd64 libjackson2-core-java all 2.14.1-1 [447 kB] Get: 292 http://deb.debian.org/debian trixie/main amd64 libjackson2-databind-java all 2.14.0+ds-1 [1532 kB] Get: 293 http://deb.debian.org/debian trixie/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 294 http://deb.debian.org/debian trixie/main amd64 libjaxen-java all 1.1.6-5 [214 kB] Get: 295 http://deb.debian.org/debian trixie/main amd64 libdom4j-java all 2.1.4-1 [312 kB] Get: 296 http://deb.debian.org/debian trixie/main amd64 libcommons-io-java all 2.18.0-1 [509 kB] Get: 297 http://deb.debian.org/debian trixie/main amd64 libslf4j-java all 1.7.32-1 [144 kB] Get: 298 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-utils-java all 3.4.2-1 [137 kB] Get: 299 http://deb.debian.org/debian trixie/main amd64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 300 http://deb.debian.org/debian trixie/main amd64 libguice-java all 5.1.0-1 [932 kB] Get: 301 http://deb.debian.org/debian trixie/main amd64 libmaven-parent-java all 43-2 [6252 B] Get: 302 http://deb.debian.org/debian trixie/main amd64 libcommons-lang3-java all 3.17.0-1 [641 kB] Get: 303 http://deb.debian.org/debian trixie/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 304 http://deb.debian.org/debian trixie/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 305 http://deb.debian.org/debian trixie/main amd64 libmaven-resolver-java all 1.9.22-1 [729 kB] Get: 306 http://deb.debian.org/debian trixie/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 307 http://deb.debian.org/debian trixie/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 308 http://deb.debian.org/debian trixie/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 309 http://deb.debian.org/debian trixie/main amd64 libplexus-interpolation-java all 1.27-1 [76.8 kB] Get: 310 http://deb.debian.org/debian trixie/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 311 http://deb.debian.org/debian trixie/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-5 [8444 B] Get: 312 http://deb.debian.org/debian trixie/main amd64 libcdi-api-java all 1.2-4 [55.3 kB] Get: 313 http://deb.debian.org/debian trixie/main amd64 libsisu-inject-java all 0.3.5-1 [352 kB] Get: 314 http://deb.debian.org/debian trixie/main amd64 libsisu-plexus-java all 0.3.5-1 [183 kB] Get: 315 http://deb.debian.org/debian trixie/main amd64 libmaven3-core-java all 3.9.9-1 [1661 kB] Get: 316 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 317 http://deb.debian.org/debian trixie/main amd64 libmaven-file-management-java all 3.0.0-2 [35.1 kB] Get: 318 http://deb.debian.org/debian trixie/main amd64 libcommons-compress-java all 1.27.1-2 [641 kB] Get: 319 http://deb.debian.org/debian trixie/main amd64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 320 http://deb.debian.org/debian trixie/main amd64 libsnappy1v5 amd64 1.2.1-1+b1 [29.6 kB] Get: 321 http://deb.debian.org/debian trixie/main amd64 libsnappy-jni amd64 1.1.10.7-1 [6492 B] Get: 322 http://deb.debian.org/debian trixie/main amd64 libsnappy-java all 1.1.10.7-1 [87.6 kB] Get: 323 http://deb.debian.org/debian trixie/main amd64 libxz-java all 1.9-1 [143 kB] Get: 324 http://deb.debian.org/debian trixie/main amd64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 325 http://deb.debian.org/debian trixie/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 326 http://deb.debian.org/debian trixie/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 327 http://deb.debian.org/debian trixie/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 328 http://deb.debian.org/debian trixie/main amd64 libjsoup-java all 1.15.3-1 [431 kB] Get: 329 http://deb.debian.org/debian trixie/main amd64 libwagon-http-java all 3.5.3-1 [49.5 kB] Get: 330 http://deb.debian.org/debian trixie/main amd64 libistack-commons-java all 3.0.6-5 [145 kB] Get: 331 http://deb.debian.org/debian trixie/main amd64 libcodemodel-java all 2.6+jaxb2.3.0.1-11 [164 kB] Get: 332 http://deb.debian.org/debian trixie/main amd64 librelaxng-datatype-java all 1.0+ds1-4 [11.8 kB] Get: 333 http://deb.debian.org/debian trixie/main amd64 librngom-java all 2.3.0.1-11 [292 kB] Get: 334 http://deb.debian.org/debian trixie/main amd64 libxsom-java all 2.3.0.1-11 [401 kB] Get: 335 http://deb.debian.org/debian trixie/main amd64 libtxw2-java all 2.3.0.1-11 [134 kB] Get: 336 http://deb.debian.org/debian trixie/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 337 http://deb.debian.org/debian trixie/main amd64 libdtd-parser-java all 1.2-1 [64.9 kB] Get: 338 http://deb.debian.org/debian trixie/main amd64 libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 339 http://deb.debian.org/debian trixie/main amd64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB] Get: 340 http://deb.debian.org/debian trixie/main amd64 libfastinfoset-java all 1.2.12-4 [347 kB] Get: 341 http://deb.debian.org/debian trixie/main amd64 libjaxb-java all 2.3.0.1-11 [1980 kB] Get: 342 http://deb.debian.org/debian trixie/main amd64 libmaven-archiver-java all 3.6.2-1 [26.1 kB] Get: 343 http://deb.debian.org/debian trixie/main amd64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 344 http://deb.debian.org/debian trixie/main amd64 libcommons-text-java all 1.12.0-1 [222 kB] Get: 345 http://deb.debian.org/debian trixie/main amd64 libfastutil-java all 8.5.15+dfsg-1 [20.0 MB] Get: 346 http://deb.debian.org/debian trixie/main amd64 libjheaps-java all 0.14-2 [144 kB] Get: 347 http://deb.debian.org/debian trixie/main amd64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 348 http://deb.debian.org/debian trixie/main amd64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 349 http://deb.debian.org/debian trixie/main amd64 libjgraphx-java all 2.1.0.7-5 [809 kB] Get: 350 http://deb.debian.org/debian trixie/main amd64 libjgrapht-java all 1.5.2-1 [1610 kB] Get: 351 http://deb.debian.org/debian trixie/main amd64 libinchi1.07 amd64 1.07.2+dfsg-1 [556 kB] Get: 352 http://deb.debian.org/debian trixie/main amd64 libjni-inchi-jni amd64 0.8+dfsg-8 [9188 B] Get: 353 http://deb.debian.org/debian trixie/main amd64 libcommons-exec-java all 1.3-2 [48.1 kB] Get: 354 http://deb.debian.org/debian trixie/main amd64 libexec-maven-plugin-java all 3.1.0-2 [66.7 kB] Get: 355 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-incremental-java all 1.1-6 [9916 B] Get: 356 http://deb.debian.org/debian trixie/main amd64 libcommons-lang-java all 2.6-10 [273 kB] Get: 357 http://deb.debian.org/debian trixie/main amd64 libxbean-reflect-java all 4.5-9 [132 kB] Get: 358 http://deb.debian.org/debian trixie/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 359 http://deb.debian.org/debian trixie/main amd64 libplexus-compiler-java all 2.13.0-1 [99.5 kB] Get: 360 http://deb.debian.org/debian trixie/main amd64 libqdox2-java all 2.0.3-1 [296 kB] Get: 361 http://deb.debian.org/debian trixie/main amd64 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 362 http://deb.debian.org/debian trixie/main amd64 libmaven-compiler-plugin-java all 3.13.0-1 [78.8 kB] Get: 363 http://deb.debian.org/debian trixie/main amd64 liblog4j1.2-java all 1.2.17-11 [444 kB] Get: 364 http://deb.debian.org/debian trixie/main amd64 libjni-inchi-java all 0.8+dfsg-8 [33.6 kB] Get: 365 http://deb.debian.org/debian trixie/main amd64 libnaga-java all 3.0+svn80-5 [43.5 kB] Get: 366 http://deb.debian.org/debian trixie/main amd64 libjmol-java all 16.2.33+dfsg-1 [10.4 MB] Get: 367 http://deb.debian.org/debian trixie/main amd64 libjson-simple-java all 2.3.0-2 [61.7 kB] Get: 368 http://deb.debian.org/debian trixie/main amd64 libmsgpack-java all 0.9.6-1 [161 kB] Get: 369 http://deb.debian.org/debian trixie/main amd64 libmmtf-java all 1.0.11-1 [187 kB] Get: 370 http://deb.debian.org/debian trixie/main amd64 libvecmath-java all 1.5.2-7 [97.0 kB] Get: 371 http://deb.debian.org/debian trixie/main amd64 libbiojava6-java all 6.1.0+dfsg-5 [5359 kB] Get: 372 http://deb.debian.org/debian trixie/main amd64 libbiojava6-java-doc all 6.1.0+dfsg-5 [2256 kB] Get: 373 http://deb.debian.org/debian trixie/main amd64 libbsh-java all 2.0b4-20 [291 kB] Get: 374 http://deb.debian.org/debian trixie/main amd64 libcharts4j-java all 1.3-4 [162 kB] Get: 375 http://deb.debian.org/debian trixie/main amd64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 376 http://deb.debian.org/debian trixie/main amd64 libcommons-beanutils-java all 1.9.4-2 [233 kB] Get: 377 http://deb.debian.org/debian trixie/main amd64 libcommons-collections4-java all 4.4-2 [682 kB] Get: 378 http://deb.debian.org/debian trixie/main amd64 libcommons-digester-java all 1.8.1-7 [138 kB] Get: 379 http://deb.debian.org/debian trixie/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get: 380 http://deb.debian.org/debian trixie/main amd64 libcommons-math3-java all 3.6.1-4 [2040 kB] Get: 381 http://deb.debian.org/debian trixie/main amd64 libcommons-validator-java all 1:1.9.0-1 [191 kB] Get: 382 http://deb.debian.org/debian trixie/main amd64 libdistlib-java all 1.0-5 [72.5 kB] Get: 383 http://deb.debian.org/debian trixie/main amd64 libdoxia-core-java all 2.0.0-1 [149 kB] Get: 384 http://deb.debian.org/debian trixie/main amd64 libplexus-xml-java all 3.0.1-2 [93.7 kB] Get: 385 http://deb.debian.org/debian trixie/main amd64 libdoxia-java all 2.0.0-1 [113 kB] Get: 386 http://deb.debian.org/debian trixie/main amd64 libmaven-reporting-api-java all 4.0.0-1 [6724 B] Get: 387 http://deb.debian.org/debian trixie/main amd64 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB] Get: 388 http://deb.debian.org/debian trixie/main amd64 velocity all 1.7-7 [431 kB] Get: 389 http://deb.debian.org/debian trixie/main amd64 libplexus-velocity-java all 1.2-4 [9676 B] Get: 390 http://deb.debian.org/debian trixie/main amd64 liboro-java all 2.0.8a-14 [70.5 kB] Get: 391 http://deb.debian.org/debian trixie/main amd64 libvelocity-tools-java all 2.0-9 [311 kB] Get: 392 http://deb.debian.org/debian trixie/main amd64 libdoxia-sitetools-java all 2.0.0-1 [176 kB] Get: 393 http://deb.debian.org/debian trixie/main amd64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 394 http://deb.debian.org/debian trixie/main amd64 libezmorph-java all 1.0.6-4 [75.9 kB] Get: 395 http://deb.debian.org/debian trixie/main amd64 libfreemarker-java all 2.3.32-2 [1546 kB] Get: 396 http://deb.debian.org/debian trixie/main amd64 libxom-java all 1.3.9-1 [174 kB] Get: 397 http://deb.debian.org/debian trixie/main amd64 libjson-java all 3.1.0+dfsg-2 [142 kB] Get: 398 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto16 amd64 3.6.2-3 [355 kB] Get: 399 http://deb.debian.org/debian trixie/main amd64 libmbedx509-7 amd64 3.6.2-3 [147 kB] Get: 400 http://deb.debian.org/debian trixie/main amd64 libmbedtls21 amd64 3.6.2-3 [234 kB] Get: 401 http://deb.debian.org/debian trixie/main amd64 ncbi-vdb-data all 3.0.9+dfsg-2 [74.0 kB] Get: 402 http://deb.debian.org/debian trixie/main amd64 libncbi-vdb3 amd64 3.0.9+dfsg-2 [1189 kB] Get: 403 http://deb.debian.org/debian trixie/main amd64 libncbi-ngs3 amd64 3.0.9+dfsg-7+b2 [156 kB] Get: 404 http://deb.debian.org/debian trixie/main amd64 libngs-jni amd64 3.0.9+dfsg-7+b2 [25.9 kB] Get: 405 http://deb.debian.org/debian trixie/main amd64 libngs-java amd64 3.0.9+dfsg-7+b2 [112 kB] Get: 406 http://deb.debian.org/debian trixie/main amd64 librhino-java all 1.7.15-1 [1382 kB] Get: 407 http://deb.debian.org/debian trixie/main amd64 libhtsjdk-java all 4.1.3+dfsg-2 [1841 kB] Get: 408 http://deb.debian.org/debian trixie/main amd64 libjansi-java all 2.4.1-2 [100 kB] Get: 409 http://deb.debian.org/debian trixie/main amd64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 410 http://deb.debian.org/debian trixie/main amd64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 411 http://deb.debian.org/debian trixie/main amd64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 412 http://deb.debian.org/debian trixie/main amd64 libjetty9-java all 9.4.56-1 [2964 kB] Get: 413 http://deb.debian.org/debian trixie/main amd64 libjtidy-java all 7+svn20110807-6 [251 kB] Get: 414 http://deb.debian.org/debian trixie/main amd64 libmaven-common-artifact-filters-java all 3.4.0-1 [47.7 kB] Get: 415 http://deb.debian.org/debian trixie/main amd64 libmaven-artifact-transfer-java all 0.13.1-2 [158 kB] Get: 416 http://deb.debian.org/debian trixie/main amd64 libplexus-build-api-java all 0.0.7-4 [10.3 kB] Get: 417 http://deb.debian.org/debian trixie/main amd64 libmaven-filtering-java all 3.4.0-1 [51.4 kB] Get: 418 http://deb.debian.org/debian trixie/main amd64 libmaven-assembly-plugin-java all 3.4.2-2 [242 kB] Get: 419 http://deb.debian.org/debian trixie/main amd64 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB] Get: 420 http://deb.debian.org/debian trixie/main amd64 libmaven-invoker-java all 3.3.0-1 [29.1 kB] Get: 421 http://deb.debian.org/debian trixie/main amd64 libplexus-interactivity-api-java all 1.3-1 [11.6 kB] Get: 422 http://deb.debian.org/debian trixie/main amd64 libmaven-javadoc-plugin-java all 3.10.1-2 [451 kB] Get: 423 http://deb.debian.org/debian trixie/main amd64 libplexus-container-default1.5-java all 2.1.1-1 [4476 B] Get: 424 http://deb.debian.org/debian trixie/main amd64 libplexus-ant-factory-java all 1.0~alpha2.1-4 [11.4 kB] Get: 425 http://deb.debian.org/debian trixie/main amd64 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B] Get: 426 http://deb.debian.org/debian trixie/main amd64 libmaven-plugin-tools-java all 3.10.2-1 [245 kB] Get: 427 http://deb.debian.org/debian trixie/main amd64 libmaven-reporting-exec-java all 2.0.0-1 [23.9 kB] Get: 428 http://deb.debian.org/debian trixie/main amd64 libmaven-resources-plugin-java all 3.3.1-1 [27.5 kB] Get: 429 http://deb.debian.org/debian trixie/main amd64 libmaven-site-plugin-java all 3.21.0-1 [106 kB] Get: 430 http://deb.debian.org/debian trixie/main amd64 libsurefire-java all 2.22.3-3 [1284 kB] Get: 431 http://deb.debian.org/debian trixie/main amd64 libtrove3-java all 3.0.3-5 [2146 kB] Get: 432 http://deb.debian.org/debian trixie/main amd64 libtrove3-java-doc all 3.0.3-5 [823 kB] Get: 433 http://deb.debian.org/debian trixie/main amd64 libwagon-file-java all 3.5.3-1 [8388 B] Get: 434 http://deb.debian.org/debian trixie/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 trixie/main amd64 maven all 3.9.9-1 [19.7 kB] Get: 436 http://deb.debian.org/debian trixie/main amd64 maven-repo-helper all 1.11 [142 kB] Get: 437 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get: 438 http://deb.debian.org/debian trixie/main amd64 maven-debian-helper all 2.6.7 [108 kB] Fetched 361 MB in 19s (19.2 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 ... 19809 files and directories currently installed.) Preparing to unpack .../libsystemd-shared_257.3-1_amd64.deb ... Unpacking libsystemd-shared:amd64 (257.3-1) ... Selecting previously unselected package libapparmor1:amd64. Preparing to unpack .../libapparmor1_3.1.7-4_amd64.deb ... Unpacking libapparmor1:amd64 (3.1.7-4) ... Setting up libsystemd-shared:amd64 (257.3-1) ... 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 ... 19822 files and directories currently installed.) Preparing to unpack .../systemd_257.3-1_amd64.deb ... Unpacking systemd (257.3-1) ... Setting up libapparmor1:amd64 (3.1.7-4) ... Setting up systemd (257.3-1) ... Created symlink '/etc/systemd/system/getty.target.wants/getty@tty1.service' -> '/usr/lib/systemd/system/getty@.service'. Created symlink '/etc/systemd/system/multi-user.target.wants/remote-fs.target' -> '/usr/lib/systemd/system/remote-fs.target'. Created symlink '/etc/systemd/system/sysinit.target.wants/systemd-pstore.service' -> '/usr/lib/systemd/system/systemd-pstore.service'. Initializing machine ID from random generator. Creating group 'systemd-journal' with GID 999. Creating group 'systemd-network' with GID 998. Creating user 'systemd-network' (systemd Network Management) with UID 998 and GID 998. /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. Selecting previously unselected package systemd-sysv. (Reading database ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_amd64.deb ... Unpacking python3.13 (3.13.2-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up libopentest4j-reporting-java (0.1.0-M1-2) ... Setting up libicu72:amd64 (72.1-6) ... Setting up libplexus-build-api-java (0.0.7-4) ... Setting up libxcb-xfixes0:amd64 (1.17.0-2+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-5) ... Setting up libjsr305-java (0.1~+svn49-12) ... Setting up bsdextrautils (2.40.4-3) ... Setting up hicolor-icon-theme (0.18-2) ... Setting up libgpg-error0:amd64 (1.51-3) ... Setting up java-common (0.76) ... Setting up libdynaloader-functions-perl (0.004-1) ... Setting up libdatrie1:amd64 (0.2.13-3+b1) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up libqdox2-java (2.0.3-1) ... Setting up libaopalliance-java (20070526-7) ... Setting up libcommons-cli-java (1.6.0-1) ... Setting up libjheaps-java (0.14-2) ... Setting up libio-pty-perl (1:1.20-1+b3) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libcommons-exec-java (1.3-2) ... Setting up libvecmath-java (1.5.2-7) ... Setting up libxcb-render0:amd64 (1.17.0-2+b1) ... Setting up libclone-perl:amd64 (0.47-1+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglvnd0:amd64 (1.7.0-1+b2) ... Setting up libgoogle-gson-java (2.10.1-1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libxcb-glx0:amd64 (1.17.0-2+b1) ... Setting up unzip (6.0-28) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libedit2:amd64 (3.1-20250104-1) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up libpicocli-java (4.6.2-2) ... Setting up libasm-java (9.7.1-1) ... Setting up libjs-jquery-ui-theme-base (1.12.1+dfsg-1.1) ... Setting up x11-common (1:7.7+24) ... Running in chroot, ignoring request. Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libtry-tiny-perl (0.32-1) ... Setting up libsensors-config (1:3.6.0-10) ... Setting up libdeflate0:amd64 (1.23-1+b1) ... Setting up perl-openssl-defaults:amd64 (7+b2) ... Setting up liblog4j1.2-java (1.2.17-11) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up libel-api-java (3.0.0-3) ... Setting up libgcrypt20:amd64 (1.11.0-7) ... Setting up xkb-data (2.42-1) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libplexus-component-annotations-java (2.1.1-1) ... Setting up libantlr4-runtime-java (4.9.2-3) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up libcom-err2:amd64 (1.47.2-1) ... Setting up file (1:5.45-3+b1) ... Setting up libjson-simple-java (2.3.0-2) ... Setting up libunivocity-parsers-java (2.9.1-1) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up liboro-java (2.0.8a-14) ... Setting up libsnappy1v5:amd64 (1.2.1-1+b1) ... Setting up libcharts4j-java (1.3-4) ... Setting up libkrb5support0:amd64 (1.21.3-4) ... Setting up libexec-maven-plugin-java (3.1.0-2) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8+b1) ... Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Feb 21 20:15:19 UTC 2025. Universal Time is now: Fri Feb 21 20:15:19 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:amd64 (1.17.0-2+b1) ... Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... Setting up libgeronimo-interceptor-3.0-spec-java (1.0.1-5) ... Setting up libcommons-collections3-java (3.2.2-3) ... Setting up libasound2-data (1.2.13-1) ... Setting up librhino-java (1.7.15-1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.13.3-1) ... Setting up libasound2t64:amd64 (1.2.13-1+b1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Setting up libjaxen-java (1.1.6-5) ... Setting up libapiguardian-java (1.1.2-1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libepoxy0:amd64 (1.5.10-2) ... Setting up libnspr4:amd64 (2:4.36-1) ... Setting up gnupg-l10n (2.2.46-1) ... Setting up libxcb-sync1:amd64 (1.17.0-2+b1) ... Setting up libjtidy-java (7+svn20110807-6) ... Setting up libjansi-java (2.4.1-2) ... Setting up libapache-pom-java (33-2) ... Setting up libavahi-common-data:amd64 (0.8-16) ... Setting up libatinject-jsr330-api-java (1.0+ds1-6) ... Setting up libdbus-1-3:amd64 (1.16.0-1) ... Setting up libwebsocket-api-java (1.1-2) ... Setting up libfribidi0:amd64 (1.0.16-1) ... Setting up libproc2-0:amd64 (2:4.0.4-7) ... Setting up libplexus-interpolation-java (1.27-1) ... Setting up libunistring5:amd64 (1.3-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libitext5-java (5.5.13.3-4) ... Setting up libpng16-16t64:amd64 (1.6.46-4) ... Setting up libxml-commons-resolver1.1-java (1.2-11) ... Setting up libxz-java (1.9-1) ... Setting up libio-html-perl (1.004-3) ... Setting up autopoint (0.23.1-1) ... Setting up binfmt-support (2.2.2-7) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Created symlink '/etc/systemd/system/multi-user.target.wants/binfmt-support.service' -> '/usr/lib/systemd/system/binfmt-support.service'. Setting up libb-hooks-op-check-perl:amd64 (0.22-3+b2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up libpcsclite1:amd64 (2.3.1-1) ... Setting up libtrove3-java-doc (3.0.3-5) ... Setting up libsensors5:amd64 (1:3.6.0-10+b1) ... Setting up libk5crypto3:amd64 (1.21.3-4) ... Setting up libactivation-java (1.2.0-2) ... Setting up libhamcrest-java (2.2-2) ... Setting up libglapi-mesa:amd64 (24.3.4-3) ... Setting up libbsh-java (2.0b4-20) ... Setting up libjsp-api-java (2.3.4-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8+b1) ... Setting up libvulkan1:amd64 (1.4.304.0-1) ... Setting up autoconf (2.72-3) ... Setting up libapfloat-java (1.14.0-2) ... Setting up libwebp7:amd64 (1.5.0-0.1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libgif7:amd64 (5.2.2-1+b1) ... Setting up libffi8:amd64 (3.4.7-1) ... 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 (2.55.2-1) ... 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 (2:4.0.4-7) ... 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 (4.20.0-2) ... 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+b5) ... Setting up libkrb5-3:amd64 (1.21.3-4) ... Setting up libwayland-egl1:amd64 (1.23.1-1) ... 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+ds1-4) ... Setting up openssl (3.4.1-1) ... 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 (1.23.1-1) ... Setting up libnet-ssleay-perl:amd64 (1.94-3) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 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 (1.14.1-2) ... 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+b1) ... Setting up libwayland-server0:amd64 (1.23.1-1) ... 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+b4) ... Setting up jarwrapper (0.80) ... Setting up libtool (2.5.4-3) ... 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 (2:3.108-1) ... 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+ds-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 (2.83.3-2) ... 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+b4) ... 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+b2) ... 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+b3) ... 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 (1.14.1-2) ... 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 (1.23.1-1) ... Setting up libhtml-parser-perl:amd64 (3.83-1+b2) ... Setting up gpgconf (2.2.46-1+b1) ... Setting up libpam-systemd:amd64 (257.3-1) ... 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-2) ... 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 (3.13.2-1) ... 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 (3.8.9-2) ... Setting up gtk-update-icon-cache (4.17.4+ds-4) ... 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 (2.55.2-1) ... Setting up openjdk-21-jre-headless:amd64 (21.0.6+7-1) ... 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 (3.13.2-1) ... Setting up libcommons-io-java (2.18.0-1) ... Setting up libdrm-radeon1:amd64 (2.4.123-1) ... Setting up libcommons-digester-java (1.8.1-7) ... Setting up libxtst6:amd64 (2:1.2.5-1) ... 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+7-1) ... 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 (2.55.2-1) ... 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 (1.2.12-4) ... 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+b2) ... Setting up libatk-bridge2.0-0t64:amd64 (2.55.2-1) ... Setting up mesa-libgallium:amd64 (24.3.4-3) ... Setting up libngs-jni:amd64 (3.0.9+dfsg-7+b2) ... 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 (24.3.4-3) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up libgl1-mesa-dri:amd64 (24.3.4-3) ... 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+b2) ... Setting up libglx-mesa0:amd64 (24.3.4-3) ... 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 (3.24.48-4) ... Setting up libgtk-3-0t64:amd64 (3.24.48-4) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libwww-perl (6.77-1) ... Setting up devscripts (2.25.2) ... 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 (3.0.0-2) ... 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 (2.40-6) ... Processing triggers for systemd (257.3-1) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian: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+7-1) ... Setting up ant (1.10.15-1) ... Setting up junit4 (4.13.2-5) ... Setting up openjdk-21-jdk-headless:amd64 (21.0.6+7-1) ... 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+7-1) ... 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.f+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.f+dfsg-1_source.changes dpkg-buildpackage: info: source package snpeff dpkg-buildpackage: info: source version 5.2.f+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.f+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.f+dfsg' jh_clean Duplicate specification "u=s" 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.f+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="@1739702387" +"%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.f\+dfsg/debian/maven-repo Failed to parse /build/reproducible-path/snpeff-5.2.f+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) Failed to parse /build/reproducible-path/snpeff-5.2.f+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) make[1]: Leaving directory '/build/reproducible-path/snpeff-5.2.f+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.f\+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.f\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/snpeff-5.2.f\+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+dfsg/src/main/java/org/snpeff/vcf/PedigreeEntry.java:9: warning: invalid input: '<' [WARNING] * ##PEDIGREE= [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.f+dfsg/src/main/java/org/snpeff/vcf/PedigreeEntry.java:12: warning: invalid input: '<' [WARNING] * ##PEDIGREE= [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.f+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.f+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.f+dfsg/target/snpeff-5.2.jar to /build/reproducible-path/snpeff-5.2.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+dfsg/src/main/java/org/snpeff/vcf/PedigreeEntry.java:9: warning: invalid input: '<' [WARNING] * ##PEDIGREE= [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.f+dfsg/src/main/java/org/snpeff/vcf/PedigreeEntry.java:12: warning: invalid input: '<' [WARNING] * ##PEDIGREE= [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.f+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: 02:19 min [INFO] Finished at: 2025-02-21T08:21:17-12:00 [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.f\+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.f\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/snpeff-5.2.f\+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.f+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.f+dfsg/pom.xml.save with options: [INFO] --keep-pom-version --package=libsnpeff-java [INFO] --rules=/build/reproducible-path/snpeff-5.2.f+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/snpeff-5.2.f+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/snpeff-5.2.f+dfsg/debian/maven.publishedRules [INFO] Install jar for snpeff into /usr/share/java [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 5.696 s [INFO] Finished at: 2025-02-21T08:51:17-12:00 [INFO] ------------------------------------------------------------------------ mh_resolve_dependencies --non-interactive --offline --build -plibsnpeff-java --javadoc --base-directory=/build/reproducible-path/snpeff-5.2.f\+dfsg --non-explore Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) at org.debian.maven.repo.POMReader.readPom(POMReader.java:82) at org.debian.maven.repo.POMReader.readPom(POMReader.java:57) at org.debian.maven.repo.Repository.scan(Repository.java:397) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:201) at org.debian.maven.repo.Repository.scanOnce(Repository.java:196) at org.debian.maven.repo.POMTransformer.usePluginVersionsFromRepository(POMTransformer.java:107) at org.debian.maven.packager.DependenciesSolver.main(DependenciesSolver.java:907) Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) at org.debian.maven.repo.POMReader.readPom(POMReader.java:82) at org.debian.maven.repo.POMReader.readPom(POMReader.java:57) at org.debian.maven.repo.Repository.scan(Repository.java:397) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:201) at org.debian.maven.repo.Repository.scanOnce(Repository.java:196) at org.debian.maven.repo.POMTransformer.usePluginVersionsFromRepository(POMTransformer.java:107) at org.debian.maven.packager.DependenciesSolver.main(DependenciesSolver.java:907) Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) at org.debian.maven.repo.POMReader.readPom(POMReader.java:82) at org.debian.maven.repo.POMReader.readPom(POMReader.java:57) at org.debian.maven.repo.Repository.scan(Repository.java:397) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:201) at org.debian.maven.packager.DependenciesSolver.getRepository(DependenciesSolver.java:231) at org.debian.maven.packager.DependenciesSolver.solveDependencies(DependenciesSolver.java:237) at org.debian.maven.packager.DependenciesSolver.main(DependenciesSolver.java:922) Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) at org.debian.maven.repo.POMReader.readPom(POMReader.java:82) at org.debian.maven.repo.POMReader.readPom(POMReader.java:57) at org.debian.maven.repo.Repository.scan(Repository.java:397) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:201) at org.debian.maven.packager.DependenciesSolver.getRepository(DependenciesSolver.java:231) at org.debian.maven.packager.DependenciesSolver.solveDependencies(DependenciesSolver.java:237) at org.debian.maven.packager.DependenciesSolver.main(DependenciesSolver.java:922) Analysing pom.xml... > dpkg --search /usr/share/maven-repo/org/biojava/biojava-structure/*/* Found /usr/share/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom in libbiojava6-java Found /usr/share/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom in libbiojava6-java > dpkg --status libbiojava6-java [error] Package libbiojava6-java (6.1.0+dfsg) is already installed and contains a possible match, but I cannot resolve library org.biojava:biojava-structure:jar:6.x in it. [error] Please check manually that the library is up to date, otherwise it may be necessary to package version 6.x in Debian. Feb 21, 2025 8:51:45 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve SEVERE: Cannot resolve dependencies in /build/reproducible-path/snpeff-5.2.f+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-doc' in '../libsnpeff-java-doc_5.2.f+dfsg-1_all.deb'. dpkg-deb: building package 'libsnpeff-java' in '../libsnpeff-java_5.2.f+dfsg-1_all.deb'. dpkg-deb: building package 'snpeff' in '../snpeff_5.2.f+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../snpeff_5.2.f+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../snpeff_5.2.f+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/1686575 and its subdirectories I: Current time: Fri Feb 21 08:56:07 -12 2025 I: pbuilder-time-stamp: 1740171367 Fri Feb 21 20:56:07 UTC 2025 I: Signing ./b1/snpeff_5.2.f+dfsg-1_amd64.buildinfo as snpeff_5.2.f+dfsg-1_amd64.buildinfo.asc Fri Feb 21 20:56:07 UTC 2025 I: Signed ./b1/snpeff_5.2.f+dfsg-1_amd64.buildinfo as ./b1/snpeff_5.2.f+dfsg-1_amd64.buildinfo.asc Fri Feb 21 20:56:07 UTC 2025 - build #1 for snpeff/trixie/amd64 on ionos11-amd64 done. Starting cleanup. All cleanup done. Fri Feb 21 20:56:07 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-liiAjWMa, removing. /srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Feb 21 20:56 b1 drwxr-xr-x 2 jenkins jenkins 4096 Feb 21 20:07 b2 -rw------- 1 jenkins jenkins 3687 Feb 21 20:07 rbuildlog.UsLFtmK -rw-r--r-- 1 jenkins jenkins 2569 Feb 16 11:26 snpeff_5.2.f+dfsg-1.dsc /srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc/b1: total 155152 -rw-r--r-- 1 jenkins jenkins 301616 Feb 21 20:56 build.log -rw-r--r-- 1 jenkins jenkins 1295308 Feb 21 20:56 libsnpeff-java-doc_5.2.f+dfsg-1_all.deb -rw-r--r-- 1 jenkins jenkins 2155868 Feb 21 20:56 libsnpeff-java_5.2.f+dfsg-1_all.deb -rw-r--r-- 1 jenkins jenkins 14288 Feb 21 20:56 snpeff_5.2.f+dfsg-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2569 Feb 21 20:56 snpeff_5.2.f+dfsg-1.dsc -rw-r--r-- 1 jenkins jenkins 7244 Feb 21 20:56 snpeff_5.2.f+dfsg-1_all.deb -rw-r--r-- 1 jenkins jenkins 18677 Feb 21 20:56 snpeff_5.2.f+dfsg-1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 19559 Feb 21 20:56 snpeff_5.2.f+dfsg-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1848 Feb 21 20:56 snpeff_5.2.f+dfsg-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 1532 Feb 21 20:56 snpeff_5.2.f+dfsg-1_source.changes -rw-r--r-- 1 jenkins jenkins 154934504 Feb 21 20:56 snpeff_5.2.f+dfsg.orig.tar.xz /srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc/b2: total 0 Fri Feb 21 20:56:10 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Feb 21 08:07:33 -12 2025 I: pbuilder-time-stamp: 1740168453 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [snpeff_5.2.f+dfsg-1.dsc] I: copying [./snpeff_5.2.f+dfsg.orig.tar.xz] I: copying [./snpeff_5.2.f+dfsg-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./snpeff_5.2.f+dfsg-1.dsc: unsupported subcommand dpkg-source: info: extracting snpeff in snpeff-5.2.f+dfsg dpkg-source: info: unpacking snpeff_5.2.f+dfsg.orig.tar.xz dpkg-source: info: unpacking snpeff_5.2.f+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/1686575/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='b715f5724f154bf19a933374d9143114' 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='1686575' 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.ssl2lMWc/pbuilderrc_yzVc --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc/b1 --logfile b1/build.log snpeff_5.2.f+dfsg-1.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) 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/1686575/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 ... 19809 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 1301 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libsystemd-shared amd64 257.3-1 [2138 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libapparmor1 amd64 3.1.7-4 [42.0 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 systemd amd64 257.3-1 [3092 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 systemd-sysv amd64 257.3-1 [61.4 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libdbus-1-3 amd64 1.16.0-1 [177 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 dbus-bin amd64 1.16.0-1 [78.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 dbus-session-bus-common all 1.16.0-1 [51.1 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 dbus-daemon amd64 1.16.0-1 [157 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 dbus-system-bus-common all 1.16.0-1 [52.2 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 dbus amd64 1.16.0-1 [70.5 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 binfmt-support amd64 2.2.2-7 [64.3 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025a-2 [259 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.2-1 [745 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B] Get: 26 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.1-2 [28.0 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-7 [878 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.4.1-1 [1427 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20241223 [164 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libpam-systemd amd64 257.3-1 [293 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-3 [92.1 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [311 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.83.3-2 [1511 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 shared-mime-info amd64 2.4-5+b2 [760 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.46-4 [284 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-2 [140 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 gtk-update-icon-cache amd64 4.17.4+ds-4 [51.3 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 hicolor-icon-theme all 0.18-2 [11.8 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 adwaita-icon-theme all 47.0-2 [463 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 java-common all 0.76 [6776 B] Get: 61 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libnspr4 amd64 2:4.36-1 [110 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libnss3 amd64 2:3.108-1 [1393 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libpcsclite1 amd64 2.3.1-1 [56.0 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jre-headless amd64 21.0.6+7-1 [41.7 MB] Get: 66 http://deb.debian.org/debian trixie/main amd64 default-jre-headless amd64 2:1.21-76 [3192 B] Get: 67 http://deb.debian.org/debian trixie/main amd64 ant all 1.10.15-1 [2163 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 ant-optional all 1.10.15-1 [456 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 at-spi2-common all 2.55.2-1 [170 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 dbus-user-session amd64 1.16.0-1 [51.0 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libdconf1 amd64 0.40.0-5 [41.8 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 dconf-service amd64 0.40.0-5 [32.4 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 dconf-gsettings-backend amd64 0.40.0-5 [28.6 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 dctrl-tools amd64 2.24-3+b1 [104 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 86 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libatk1.0-0t64 amd64 2.55.2-1 [51.4 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libatspi2.0-0t64 amd64 2.55.2-1 [77.0 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libatk-bridge2.0-0t64 amd64 2.55.2-1 [68.1 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-2 [391 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b4 [27.8 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libcairo-gobject2 amd64 1.18.2-2 [130 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libcloudproviders0 amd64 0.3.6-1+b1 [29.2 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libcolord2 amd64 1.4.7-1+b2 [140 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libavahi-common-data amd64 0.8-16 [112 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libavahi-common3 amd64 0.8-16 [44.2 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libavahi-client3 amd64 0.8-16 [48.4 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 128 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libcups2t64 amd64 2.4.10-2+b1 [251 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libepoxy0 amd64 1.5.10-2 [193 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.2.0-1 [479 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-2 [463 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.56.1-1 [226 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.56.1-1 [55.3 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.56.1-1 [35.8 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libwayland-client0 amd64 1.23.1-1 [26.5 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 libwayland-cursor0 amd64 1.23.1-1 [11.4 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libwayland-egl1 amd64 1.23.1-1 [5452 B] Get: 145 http://deb.debian.org/debian trixie/main amd64 libxcomposite1 amd64 1:0.4.6-1 [16.3 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libxfixes3 amd64 1:6.0.0-2+b4 [20.2 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libxcursor1 amd64 1:1.2.3-1 [39.7 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libxdamage1 amd64 1:1.1.6-1+b2 [15.5 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 libxinerama1 amd64 2:1.1.4-3+b3 [16.0 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 xkb-data all 2.42-1 [790 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 libxkbcommon0 amd64 1.7.0-2 [113 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 libxrandr2 amd64 2:1.5.4-1+b3 [36.3 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libgtk-3-common all 3.24.48-4 [4873 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libgtk-3-0t64 amd64 3.24.48-4 [2767 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.123-1 [8084 B] Get: 157 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 libglapi-mesa amd64 24.3.4-3 [38.5 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 libx11-xcb1 amd64 2:1.8.10-2 [241 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b4 [19.3 kB] Get: 165 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 libdrm-intel1 amd64 2.4.123-1 [63.7 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 libdrm-radeon1 amd64 2.4.123-1 [22.3 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 libllvm19 amd64 1:19.1.7-1+b1 [26.0 MB] Get: 172 http://deb.debian.org/debian trixie/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 libsensors5 amd64 1:3.6.0-10+b1 [35.1 kB] Get: 174 http://deb.debian.org/debian trixie/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 libxshmfence1 amd64 1.3-1+b3 [8852 B] Get: 177 http://deb.debian.org/debian trixie/main amd64 mesa-libgallium amd64 24.3.4-3 [9492 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 libwayland-server0 amd64 1.23.1-1 [34.0 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 libgbm1 amd64 24.3.4-3 [43.7 kB] Get: 180 http://deb.debian.org/debian trixie/main amd64 libvulkan1 amd64 1.4.304.0-1 [129 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 libgl1-mesa-dri amd64 24.3.4-3 [45.2 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 libglx-mesa0 amd64 24.3.4-3 [143 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB] Get: 184 http://deb.debian.org/debian trixie/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 libasound2-data all 1.2.13-1 [21.1 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 libasound2t64 amd64 1.2.13-1+b1 [373 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 libgif7 amd64 5.2.2-1+b1 [44.2 kB] Get: 188 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+24 [217 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 libxtst6 amd64 2:1.2.5-1 [25.8 kB] Get: 190 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jre amd64 21.0.6+7-1 [205 kB] Get: 191 http://deb.debian.org/debian trixie/main amd64 default-jre amd64 2:1.21-76 [1068 B] Get: 192 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jdk-headless amd64 21.0.6+7-1 [82.8 MB] Get: 193 http://deb.debian.org/debian trixie/main amd64 default-jdk-headless amd64 2:1.21-76 [1124 B] Get: 194 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jdk amd64 21.0.6+7-1 [3434 kB] Get: 195 http://deb.debian.org/debian trixie/main amd64 default-jdk amd64 2:1.21-76 [1076 B] Get: 196 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 197 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 198 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui-theme-base all 1.12.1+dfsg-1.1 [44.3 kB] Get: 199 http://deb.debian.org/debian trixie/main amd64 openjdk-21-doc all 21.0.6+7-1 [13.2 MB] Get: 200 http://deb.debian.org/debian trixie/main amd64 default-jdk-doc amd64 2:1.21-76 [3264 B] Get: 201 http://deb.debian.org/debian trixie/main amd64 libgpg-error0 amd64 1.51-3 [82.2 kB] Get: 202 http://deb.debian.org/debian trixie/main amd64 libassuan9 amd64 3.0.1-2 [60.6 kB] Get: 203 http://deb.debian.org/debian trixie/main amd64 libgcrypt20 amd64 1.11.0-7 [843 kB] Get: 204 http://deb.debian.org/debian trixie/main amd64 gpgconf amd64 2.2.46-1+b1 [121 kB] Get: 205 http://deb.debian.org/debian trixie/main amd64 libksba8 amd64 1.6.7-2+b1 [136 kB] Get: 206 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8+b1 [19.9 kB] Get: 207 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8+b1 [57.6 kB] Get: 208 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB] Get: 209 http://deb.debian.org/debian trixie/main amd64 libnpth0t64 amd64 1.8-2 [22.9 kB] Get: 210 http://deb.debian.org/debian trixie/main amd64 dirmngr amd64 2.2.46-1+b1 [369 kB] Get: 211 http://deb.debian.org/debian trixie/main amd64 gnupg-l10n all 2.2.46-1 [702 kB] Get: 212 http://deb.debian.org/debian trixie/main amd64 gpg amd64 2.2.46-1+b1 [532 kB] Get: 213 http://deb.debian.org/debian trixie/main amd64 pinentry-curses amd64 1.3.1-2 [86.4 kB] Get: 214 http://deb.debian.org/debian trixie/main amd64 gpg-agent amd64 2.2.46-1+b1 [252 kB] Get: 215 http://deb.debian.org/debian trixie/main amd64 gpgsm amd64 2.2.46-1+b1 [255 kB] Get: 216 http://deb.debian.org/debian trixie/main amd64 gnupg all 2.2.46-1 [376 kB] Get: 217 http://deb.debian.org/debian trixie/main amd64 gpgv amd64 2.2.46-1+b1 [219 kB] Get: 218 http://deb.debian.org/debian trixie/main amd64 sopv-gpgv all 0.1.1-1 [10.7 kB] Get: 219 http://deb.debian.org/debian trixie/main amd64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 220 http://deb.debian.org/debian trixie/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 221 http://deb.debian.org/debian trixie/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 222 http://deb.debian.org/debian trixie/main amd64 libfile-touch-perl all 0.12-2 [8816 B] Get: 223 http://deb.debian.org/debian trixie/main amd64 libio-pty-perl amd64 1:1.20-1+b3 [34.3 kB] Get: 224 http://deb.debian.org/debian trixie/main amd64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 225 http://deb.debian.org/debian trixie/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 226 http://deb.debian.org/debian trixie/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b5 [36.1 kB] Get: 227 http://deb.debian.org/debian trixie/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b2 [10.6 kB] Get: 228 http://deb.debian.org/debian trixie/main amd64 libdynaloader-functions-perl all 0.004-1 [12.1 kB] Get: 229 http://deb.debian.org/debian trixie/main amd64 libdevel-callchecker-perl amd64 0.009-1+b1 [16.2 kB] Get: 230 http://deb.debian.org/debian trixie/main amd64 libparams-classify-perl amd64 0.015-2+b4 [22.5 kB] Get: 231 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 232 http://deb.debian.org/debian trixie/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 233 http://deb.debian.org/debian trixie/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 234 http://deb.debian.org/debian trixie/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 235 http://deb.debian.org/debian trixie/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 236 http://deb.debian.org/debian trixie/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 237 http://deb.debian.org/debian trixie/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 238 http://deb.debian.org/debian trixie/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 239 http://deb.debian.org/debian trixie/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 240 http://deb.debian.org/debian trixie/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 241 http://deb.debian.org/debian trixie/main amd64 liburi-perl all 5.30-1 [105 kB] Get: 242 http://deb.debian.org/debian trixie/main amd64 libhtml-parser-perl amd64 3.83-1+b2 [99.7 kB] Get: 243 http://deb.debian.org/debian trixie/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 244 http://deb.debian.org/debian trixie/main amd64 libclone-perl amd64 0.47-1+b1 [13.9 kB] Get: 245 http://deb.debian.org/debian trixie/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 246 http://deb.debian.org/debian trixie/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 247 http://deb.debian.org/debian trixie/main amd64 libhttp-message-perl all 7.00-2 [79.8 kB] Get: 248 http://deb.debian.org/debian trixie/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 249 http://deb.debian.org/debian trixie/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 250 http://deb.debian.org/debian trixie/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get: 251 http://deb.debian.org/debian trixie/main amd64 libnet-ssleay-perl amd64 1.94-3 [339 kB] Get: 252 http://deb.debian.org/debian trixie/main amd64 libio-socket-ssl-perl all 2.089-1 [223 kB] Get: 253 http://deb.debian.org/debian trixie/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 254 http://deb.debian.org/debian trixie/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 255 http://deb.debian.org/debian trixie/main amd64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 256 http://deb.debian.org/debian trixie/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 257 http://deb.debian.org/debian trixie/main amd64 libwww-perl all 6.77-1 [183 kB] Get: 258 http://deb.debian.org/debian trixie/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get: 259 http://deb.debian.org/debian trixie/main amd64 wdiff amd64 1.2.2-7 [122 kB] Get: 260 http://deb.debian.org/debian trixie/main amd64 devscripts all 2.25.2 [1058 kB] Get: 261 http://deb.debian.org/debian trixie/main amd64 fastjar amd64 2:0.98-7 [80.1 kB] Get: 262 http://deb.debian.org/debian trixie/main amd64 jarwrapper all 0.80 [9692 B] Get: 263 http://deb.debian.org/debian trixie/main amd64 javahelper all 0.80 [80.4 kB] Get: 264 http://deb.debian.org/debian trixie/main amd64 libhamcrest-java all 2.2-2 [121 kB] Get: 265 http://deb.debian.org/debian trixie/main amd64 junit4 all 4.13.2-5 [350 kB] Get: 266 http://deb.debian.org/debian trixie/main amd64 libapiguardian-java all 1.1.2-1 [4656 B] Get: 267 http://deb.debian.org/debian trixie/main amd64 libopentest4j-java all 1.2.0-4 [9516 B] Get: 268 http://deb.debian.org/debian trixie/main amd64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 269 http://deb.debian.org/debian trixie/main amd64 libpicocli-java all 4.6.2-2 [390 kB] Get: 270 http://deb.debian.org/debian trixie/main amd64 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 271 http://deb.debian.org/debian trixie/main amd64 junit5 all 5.10.3-1 [2459 kB] Get: 272 http://deb.debian.org/debian trixie/main amd64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 273 http://deb.debian.org/debian trixie/main amd64 libantlr4-runtime-java all 4.9.2-3 [318 kB] Get: 274 http://deb.debian.org/debian trixie/main amd64 libaopalliance-java all 20070526-7 [8572 B] Get: 275 http://deb.debian.org/debian trixie/main amd64 libapache-pom-java all 33-2 [5852 B] Get: 276 http://deb.debian.org/debian trixie/main amd64 libapfloat-java all 1.14.0-2 [725 kB] Get: 277 http://deb.debian.org/debian trixie/main amd64 libargs4j-java all 2.33-2 [138 kB] Get: 278 http://deb.debian.org/debian trixie/main amd64 libasm-java all 9.7.1-1 [391 kB] Get: 279 http://deb.debian.org/debian trixie/main amd64 libatinject-jsr330-api-java all 1.0+ds1-6 [5112 B] Get: 280 http://deb.debian.org/debian trixie/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 281 http://deb.debian.org/debian trixie/main amd64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 282 http://deb.debian.org/debian trixie/main amd64 libciftools-java all 6.0.0-1 [2211 kB] Get: 283 http://deb.debian.org/debian trixie/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 284 http://deb.debian.org/debian trixie/main amd64 libcommons-codec-java all 1.17.1-1 [303 kB] Get: 285 http://deb.debian.org/debian trixie/main amd64 libcommons-math-java all 2.2-9 [933 kB] Get: 286 http://deb.debian.org/debian trixie/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 287 http://deb.debian.org/debian trixie/main amd64 libjsr305-java all 0.1~+svn49-12 [26.6 kB] Get: 288 http://deb.debian.org/debian trixie/main amd64 libguava-java all 32.0.1-1 [2708 kB] Get: 289 http://deb.debian.org/debian trixie/main amd64 libitext5-java all 5.5.13.3-4 [2667 kB] Get: 290 http://deb.debian.org/debian trixie/main amd64 libjackson2-annotations-java all 2.14.0-1 [68.8 kB] Get: 291 http://deb.debian.org/debian trixie/main amd64 libjackson2-core-java all 2.14.1-1 [447 kB] Get: 292 http://deb.debian.org/debian trixie/main amd64 libjackson2-databind-java all 2.14.0+ds-1 [1532 kB] Get: 293 http://deb.debian.org/debian trixie/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 294 http://deb.debian.org/debian trixie/main amd64 libjaxen-java all 1.1.6-5 [214 kB] Get: 295 http://deb.debian.org/debian trixie/main amd64 libdom4j-java all 2.1.4-1 [312 kB] Get: 296 http://deb.debian.org/debian trixie/main amd64 libcommons-io-java all 2.18.0-1 [509 kB] Get: 297 http://deb.debian.org/debian trixie/main amd64 libslf4j-java all 1.7.32-1 [144 kB] Get: 298 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-utils-java all 3.4.2-1 [137 kB] Get: 299 http://deb.debian.org/debian trixie/main amd64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 300 http://deb.debian.org/debian trixie/main amd64 libguice-java all 5.1.0-1 [932 kB] Get: 301 http://deb.debian.org/debian trixie/main amd64 libmaven-parent-java all 43-2 [6252 B] Get: 302 http://deb.debian.org/debian trixie/main amd64 libcommons-lang3-java all 3.17.0-1 [641 kB] Get: 303 http://deb.debian.org/debian trixie/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 304 http://deb.debian.org/debian trixie/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 305 http://deb.debian.org/debian trixie/main amd64 libmaven-resolver-java all 1.9.22-1 [729 kB] Get: 306 http://deb.debian.org/debian trixie/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 307 http://deb.debian.org/debian trixie/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 308 http://deb.debian.org/debian trixie/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 309 http://deb.debian.org/debian trixie/main amd64 libplexus-interpolation-java all 1.27-1 [76.8 kB] Get: 310 http://deb.debian.org/debian trixie/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 311 http://deb.debian.org/debian trixie/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-5 [8444 B] Get: 312 http://deb.debian.org/debian trixie/main amd64 libcdi-api-java all 1.2-4 [55.3 kB] Get: 313 http://deb.debian.org/debian trixie/main amd64 libsisu-inject-java all 0.3.5-1 [352 kB] Get: 314 http://deb.debian.org/debian trixie/main amd64 libsisu-plexus-java all 0.3.5-1 [183 kB] Get: 315 http://deb.debian.org/debian trixie/main amd64 libmaven3-core-java all 3.9.9-1 [1661 kB] Get: 316 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 317 http://deb.debian.org/debian trixie/main amd64 libmaven-file-management-java all 3.0.0-2 [35.1 kB] Get: 318 http://deb.debian.org/debian trixie/main amd64 libcommons-compress-java all 1.27.1-2 [641 kB] Get: 319 http://deb.debian.org/debian trixie/main amd64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 320 http://deb.debian.org/debian trixie/main amd64 libsnappy1v5 amd64 1.2.1-1+b1 [29.6 kB] Get: 321 http://deb.debian.org/debian trixie/main amd64 libsnappy-jni amd64 1.1.10.7-1 [6492 B] Get: 322 http://deb.debian.org/debian trixie/main amd64 libsnappy-java all 1.1.10.7-1 [87.6 kB] Get: 323 http://deb.debian.org/debian trixie/main amd64 libxz-java all 1.9-1 [143 kB] Get: 324 http://deb.debian.org/debian trixie/main amd64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 325 http://deb.debian.org/debian trixie/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 326 http://deb.debian.org/debian trixie/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 327 http://deb.debian.org/debian trixie/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 328 http://deb.debian.org/debian trixie/main amd64 libjsoup-java all 1.15.3-1 [431 kB] Get: 329 http://deb.debian.org/debian trixie/main amd64 libwagon-http-java all 3.5.3-1 [49.5 kB] Get: 330 http://deb.debian.org/debian trixie/main amd64 libistack-commons-java all 3.0.6-5 [145 kB] Get: 331 http://deb.debian.org/debian trixie/main amd64 libcodemodel-java all 2.6+jaxb2.3.0.1-11 [164 kB] Get: 332 http://deb.debian.org/debian trixie/main amd64 librelaxng-datatype-java all 1.0+ds1-4 [11.8 kB] Get: 333 http://deb.debian.org/debian trixie/main amd64 librngom-java all 2.3.0.1-11 [292 kB] Get: 334 http://deb.debian.org/debian trixie/main amd64 libxsom-java all 2.3.0.1-11 [401 kB] Get: 335 http://deb.debian.org/debian trixie/main amd64 libtxw2-java all 2.3.0.1-11 [134 kB] Get: 336 http://deb.debian.org/debian trixie/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 337 http://deb.debian.org/debian trixie/main amd64 libdtd-parser-java all 1.2-1 [64.9 kB] Get: 338 http://deb.debian.org/debian trixie/main amd64 libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 339 http://deb.debian.org/debian trixie/main amd64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB] Get: 340 http://deb.debian.org/debian trixie/main amd64 libfastinfoset-java all 1.2.12-4 [347 kB] Get: 341 http://deb.debian.org/debian trixie/main amd64 libjaxb-java all 2.3.0.1-11 [1980 kB] Get: 342 http://deb.debian.org/debian trixie/main amd64 libmaven-archiver-java all 3.6.2-1 [26.1 kB] Get: 343 http://deb.debian.org/debian trixie/main amd64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 344 http://deb.debian.org/debian trixie/main amd64 libcommons-text-java all 1.12.0-1 [222 kB] Get: 345 http://deb.debian.org/debian trixie/main amd64 libfastutil-java all 8.5.15+dfsg-1 [20.0 MB] Get: 346 http://deb.debian.org/debian trixie/main amd64 libjheaps-java all 0.14-2 [144 kB] Get: 347 http://deb.debian.org/debian trixie/main amd64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 348 http://deb.debian.org/debian trixie/main amd64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 349 http://deb.debian.org/debian trixie/main amd64 libjgraphx-java all 2.1.0.7-5 [809 kB] Get: 350 http://deb.debian.org/debian trixie/main amd64 libjgrapht-java all 1.5.2-1 [1610 kB] Get: 351 http://deb.debian.org/debian trixie/main amd64 libinchi1.07 amd64 1.07.2+dfsg-1 [556 kB] Get: 352 http://deb.debian.org/debian trixie/main amd64 libjni-inchi-jni amd64 0.8+dfsg-8 [9188 B] Get: 353 http://deb.debian.org/debian trixie/main amd64 libcommons-exec-java all 1.3-2 [48.1 kB] Get: 354 http://deb.debian.org/debian trixie/main amd64 libexec-maven-plugin-java all 3.1.0-2 [66.7 kB] Get: 355 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-incremental-java all 1.1-6 [9916 B] Get: 356 http://deb.debian.org/debian trixie/main amd64 libcommons-lang-java all 2.6-10 [273 kB] Get: 357 http://deb.debian.org/debian trixie/main amd64 libxbean-reflect-java all 4.5-9 [132 kB] Get: 358 http://deb.debian.org/debian trixie/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 359 http://deb.debian.org/debian trixie/main amd64 libplexus-compiler-java all 2.13.0-1 [99.5 kB] Get: 360 http://deb.debian.org/debian trixie/main amd64 libqdox2-java all 2.0.3-1 [296 kB] Get: 361 http://deb.debian.org/debian trixie/main amd64 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 362 http://deb.debian.org/debian trixie/main amd64 libmaven-compiler-plugin-java all 3.13.0-1 [78.8 kB] Get: 363 http://deb.debian.org/debian trixie/main amd64 liblog4j1.2-java all 1.2.17-11 [444 kB] Get: 364 http://deb.debian.org/debian trixie/main amd64 libjni-inchi-java all 0.8+dfsg-8 [33.6 kB] Get: 365 http://deb.debian.org/debian trixie/main amd64 libnaga-java all 3.0+svn80-5 [43.5 kB] Get: 366 http://deb.debian.org/debian trixie/main amd64 libjmol-java all 16.2.33+dfsg-1 [10.4 MB] Get: 367 http://deb.debian.org/debian trixie/main amd64 libjson-simple-java all 2.3.0-2 [61.7 kB] Get: 368 http://deb.debian.org/debian trixie/main amd64 libmsgpack-java all 0.9.6-1 [161 kB] Get: 369 http://deb.debian.org/debian trixie/main amd64 libmmtf-java all 1.0.11-1 [187 kB] Get: 370 http://deb.debian.org/debian trixie/main amd64 libvecmath-java all 1.5.2-7 [97.0 kB] Get: 371 http://deb.debian.org/debian trixie/main amd64 libbiojava6-java all 6.1.0+dfsg-5 [5359 kB] Get: 372 http://deb.debian.org/debian trixie/main amd64 libbiojava6-java-doc all 6.1.0+dfsg-5 [2256 kB] Get: 373 http://deb.debian.org/debian trixie/main amd64 libbsh-java all 2.0b4-20 [291 kB] Get: 374 http://deb.debian.org/debian trixie/main amd64 libcharts4j-java all 1.3-4 [162 kB] Get: 375 http://deb.debian.org/debian trixie/main amd64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 376 http://deb.debian.org/debian trixie/main amd64 libcommons-beanutils-java all 1.9.4-2 [233 kB] Get: 377 http://deb.debian.org/debian trixie/main amd64 libcommons-collections4-java all 4.4-2 [682 kB] Get: 378 http://deb.debian.org/debian trixie/main amd64 libcommons-digester-java all 1.8.1-7 [138 kB] Get: 379 http://deb.debian.org/debian trixie/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get: 380 http://deb.debian.org/debian trixie/main amd64 libcommons-math3-java all 3.6.1-4 [2040 kB] Get: 381 http://deb.debian.org/debian trixie/main amd64 libcommons-validator-java all 1:1.9.0-1 [191 kB] Get: 382 http://deb.debian.org/debian trixie/main amd64 libdistlib-java all 1.0-5 [72.5 kB] Get: 383 http://deb.debian.org/debian trixie/main amd64 libdoxia-core-java all 2.0.0-1 [149 kB] Get: 384 http://deb.debian.org/debian trixie/main amd64 libplexus-xml-java all 3.0.1-2 [93.7 kB] Get: 385 http://deb.debian.org/debian trixie/main amd64 libdoxia-java all 2.0.0-1 [113 kB] Get: 386 http://deb.debian.org/debian trixie/main amd64 libmaven-reporting-api-java all 4.0.0-1 [6724 B] Get: 387 http://deb.debian.org/debian trixie/main amd64 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB] Get: 388 http://deb.debian.org/debian trixie/main amd64 velocity all 1.7-7 [431 kB] Get: 389 http://deb.debian.org/debian trixie/main amd64 libplexus-velocity-java all 1.2-4 [9676 B] Get: 390 http://deb.debian.org/debian trixie/main amd64 liboro-java all 2.0.8a-14 [70.5 kB] Get: 391 http://deb.debian.org/debian trixie/main amd64 libvelocity-tools-java all 2.0-9 [311 kB] Get: 392 http://deb.debian.org/debian trixie/main amd64 libdoxia-sitetools-java all 2.0.0-1 [176 kB] Get: 393 http://deb.debian.org/debian trixie/main amd64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 394 http://deb.debian.org/debian trixie/main amd64 libezmorph-java all 1.0.6-4 [75.9 kB] Get: 395 http://deb.debian.org/debian trixie/main amd64 libfreemarker-java all 2.3.32-2 [1546 kB] Get: 396 http://deb.debian.org/debian trixie/main amd64 libxom-java all 1.3.9-1 [174 kB] Get: 397 http://deb.debian.org/debian trixie/main amd64 libjson-java all 3.1.0+dfsg-2 [142 kB] Get: 398 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto16 amd64 3.6.2-3 [355 kB] Get: 399 http://deb.debian.org/debian trixie/main amd64 libmbedx509-7 amd64 3.6.2-3 [147 kB] Get: 400 http://deb.debian.org/debian trixie/main amd64 libmbedtls21 amd64 3.6.2-3 [234 kB] Get: 401 http://deb.debian.org/debian trixie/main amd64 ncbi-vdb-data all 3.0.9+dfsg-2 [74.0 kB] Get: 402 http://deb.debian.org/debian trixie/main amd64 libncbi-vdb3 amd64 3.0.9+dfsg-2 [1189 kB] Get: 403 http://deb.debian.org/debian trixie/main amd64 libncbi-ngs3 amd64 3.0.9+dfsg-7+b2 [156 kB] Get: 404 http://deb.debian.org/debian trixie/main amd64 libngs-jni amd64 3.0.9+dfsg-7+b2 [25.9 kB] Get: 405 http://deb.debian.org/debian trixie/main amd64 libngs-java amd64 3.0.9+dfsg-7+b2 [112 kB] Get: 406 http://deb.debian.org/debian trixie/main amd64 librhino-java all 1.7.15-1 [1382 kB] Get: 407 http://deb.debian.org/debian trixie/main amd64 libhtsjdk-java all 4.1.3+dfsg-2 [1841 kB] Get: 408 http://deb.debian.org/debian trixie/main amd64 libjansi-java all 2.4.1-2 [100 kB] Get: 409 http://deb.debian.org/debian trixie/main amd64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 410 http://deb.debian.org/debian trixie/main amd64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 411 http://deb.debian.org/debian trixie/main amd64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 412 http://deb.debian.org/debian trixie/main amd64 libjetty9-java all 9.4.56-1 [2964 kB] Get: 413 http://deb.debian.org/debian trixie/main amd64 libjtidy-java all 7+svn20110807-6 [251 kB] Get: 414 http://deb.debian.org/debian trixie/main amd64 libmaven-common-artifact-filters-java all 3.4.0-1 [47.7 kB] Get: 415 http://deb.debian.org/debian trixie/main amd64 libmaven-artifact-transfer-java all 0.13.1-2 [158 kB] Get: 416 http://deb.debian.org/debian trixie/main amd64 libplexus-build-api-java all 0.0.7-4 [10.3 kB] Get: 417 http://deb.debian.org/debian trixie/main amd64 libmaven-filtering-java all 3.4.0-1 [51.4 kB] Get: 418 http://deb.debian.org/debian trixie/main amd64 libmaven-assembly-plugin-java all 3.4.2-2 [242 kB] Get: 419 http://deb.debian.org/debian trixie/main amd64 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB] Get: 420 http://deb.debian.org/debian trixie/main amd64 libmaven-invoker-java all 3.3.0-1 [29.1 kB] Get: 421 http://deb.debian.org/debian trixie/main amd64 libplexus-interactivity-api-java all 1.3-1 [11.6 kB] Get: 422 http://deb.debian.org/debian trixie/main amd64 libmaven-javadoc-plugin-java all 3.10.1-2 [451 kB] Get: 423 http://deb.debian.org/debian trixie/main amd64 libplexus-container-default1.5-java all 2.1.1-1 [4476 B] Get: 424 http://deb.debian.org/debian trixie/main amd64 libplexus-ant-factory-java all 1.0~alpha2.1-4 [11.4 kB] Get: 425 http://deb.debian.org/debian trixie/main amd64 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B] Get: 426 http://deb.debian.org/debian trixie/main amd64 libmaven-plugin-tools-java all 3.10.2-1 [245 kB] Get: 427 http://deb.debian.org/debian trixie/main amd64 libmaven-reporting-exec-java all 2.0.0-1 [23.9 kB] Get: 428 http://deb.debian.org/debian trixie/main amd64 libmaven-resources-plugin-java all 3.3.1-1 [27.5 kB] Get: 429 http://deb.debian.org/debian trixie/main amd64 libmaven-site-plugin-java all 3.21.0-1 [106 kB] Get: 430 http://deb.debian.org/debian trixie/main amd64 libsurefire-java all 2.22.3-3 [1284 kB] Get: 431 http://deb.debian.org/debian trixie/main amd64 libtrove3-java all 3.0.3-5 [2146 kB] Get: 432 http://deb.debian.org/debian trixie/main amd64 libtrove3-java-doc all 3.0.3-5 [823 kB] Get: 433 http://deb.debian.org/debian trixie/main amd64 libwagon-file-java all 3.5.3-1 [8388 B] Get: 434 http://deb.debian.org/debian trixie/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 trixie/main amd64 maven all 3.9.9-1 [19.7 kB] Get: 436 http://deb.debian.org/debian trixie/main amd64 maven-repo-helper all 1.11 [142 kB] Get: 437 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get: 438 http://deb.debian.org/debian trixie/main amd64 maven-debian-helper all 2.6.7 [108 kB] Fetched 361 MB in 19s (19.2 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 ... 19809 files and directories currently installed.) Preparing to unpack .../libsystemd-shared_257.3-1_amd64.deb ... Unpacking libsystemd-shared:amd64 (257.3-1) ... Selecting previously unselected package libapparmor1:amd64. Preparing to unpack .../libapparmor1_3.1.7-4_amd64.deb ... Unpacking libapparmor1:amd64 (3.1.7-4) ... Setting up libsystemd-shared:amd64 (257.3-1) ... 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 ... 19822 files and directories currently installed.) Preparing to unpack .../systemd_257.3-1_amd64.deb ... Unpacking systemd (257.3-1) ... Setting up libapparmor1:amd64 (3.1.7-4) ... Setting up systemd (257.3-1) ... Created symlink '/etc/systemd/system/getty.target.wants/getty@tty1.service' -> '/usr/lib/systemd/system/getty@.service'. Created symlink '/etc/systemd/system/multi-user.target.wants/remote-fs.target' -> '/usr/lib/systemd/system/remote-fs.target'. Created symlink '/etc/systemd/system/sysinit.target.wants/systemd-pstore.service' -> '/usr/lib/systemd/system/systemd-pstore.service'. Initializing machine ID from random generator. Creating group 'systemd-journal' with GID 999. Creating group 'systemd-network' with GID 998. Creating user 'systemd-network' (systemd Network Management) with UID 998 and GID 998. /usr/lib/tmpfiles.d/legacy.conf: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 ... 20765 files and directories currently installed.) Preparing to unpack .../00-systemd-sysv_257.3-1_amd64.deb ... Unpacking systemd-sysv (257.3-1) ... 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) ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21213 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) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_amd64.deb ... Unpacking python3.13 (3.13.2-1) ... 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 ... 22223 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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Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../008-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../009-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../010-gettext-base_0.23.1-1_amd64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../011-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../012-groff-base_1.23.0-7_amd64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package libpam-systemd:amd64. Preparing to unpack .../013-libpam-systemd_257.3-1_amd64.deb ... Unpacking libpam-systemd:amd64 (257.3-1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../014-bsdextrautils_2.40.4-3_amd64.deb ... Unpacking bsdextrautils (2.40.4-3) ... Selecting previously unselected package man-db. Preparing to unpack .../015-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package libgdk-pixbuf2.0-common. Preparing to unpack .../016-libgdk-pixbuf2.0-common_2.42.12+dfsg-2_all.deb ... Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ... Selecting previously unselected package libglib2.0-0t64:amd64. Preparing to unpack .../017-libglib2.0-0t64_2.83.3-2_amd64.deb ... Unpacking libglib2.0-0t64:amd64 (2.83.3-2) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../018-libicu72_72.1-6_amd64.deb ... Unpacking libicu72:amd64 (72.1-6) ... Selecting previously unselected package libxml2:amd64. 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Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Created symlink '/etc/systemd/system/multi-user.target.wants/binfmt-support.service' -> '/usr/lib/systemd/system/binfmt-support.service'. Setting up libb-hooks-op-check-perl:amd64 (0.22-3+b2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up libpcsclite1:amd64 (2.3.1-1) ... Setting up libtrove3-java-doc (3.0.3-5) ... Setting up libsensors5:amd64 (1:3.6.0-10+b1) ... Setting up libk5crypto3:amd64 (1.21.3-4) ... Setting up libactivation-java (1.2.0-2) ... Setting up libhamcrest-java (2.2-2) ... Setting up libglapi-mesa:amd64 (24.3.4-3) ... Setting up libbsh-java (2.0b4-20) ... Setting up libjsp-api-java (2.3.4-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8+b1) ... Setting up libvulkan1:amd64 (1.4.304.0-1) ... Setting up autoconf (2.72-3) ... Setting up libapfloat-java (1.14.0-2) ... Setting up libwebp7:amd64 (1.5.0-0.1) ... 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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+ds1-4) ... Setting up openssl (3.4.1-1) ... 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 (1.23.1-1) ... Setting up libnet-ssleay-perl:amd64 (1.94-3) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 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 (1.14.1-2) ... 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+b1) ... Setting up libwayland-server0:amd64 (1.23.1-1) ... 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+b4) ... Setting up jarwrapper (0.80) ... Setting up libtool (2.5.4-3) ... 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 (2:3.108-1) ... 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+ds-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 (2.83.3-2) ... 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+b4) ... 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+b2) ... 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+b3) ... 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 (1.14.1-2) ... 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 (1.23.1-1) ... Setting up libhtml-parser-perl:amd64 (3.83-1+b2) ... Setting up gpgconf (2.2.46-1+b1) ... Setting up libpam-systemd:amd64 (257.3-1) ... 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-2) ... 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 (3.13.2-1) ... 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 (3.8.9-2) ... Setting up gtk-update-icon-cache (4.17.4+ds-4) ... 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 (2.55.2-1) ... Setting up openjdk-21-jre-headless:amd64 (21.0.6+7-1) ... 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 (3.13.2-1) ... Setting up libcommons-io-java (2.18.0-1) ... Setting up libdrm-radeon1:amd64 (2.4.123-1) ... Setting up libcommons-digester-java (1.8.1-7) ... Setting up libxtst6:amd64 (2:1.2.5-1) ... 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+7-1) ... 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 (2.55.2-1) ... 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 (1.2.12-4) ... 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+b2) ... Setting up libatk-bridge2.0-0t64:amd64 (2.55.2-1) ... Setting up mesa-libgallium:amd64 (24.3.4-3) ... Setting up libngs-jni:amd64 (3.0.9+dfsg-7+b2) ... 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 (24.3.4-3) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up libgl1-mesa-dri:amd64 (24.3.4-3) ... 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+b2) ... Setting up libglx-mesa0:amd64 (24.3.4-3) ... 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 (3.24.48-4) ... Setting up libgtk-3-0t64:amd64 (3.24.48-4) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libwww-perl (6.77-1) ... Setting up devscripts (2.25.2) ... 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 (3.0.0-2) ... 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 (2.40-6) ... Processing triggers for systemd (257.3-1) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian: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+7-1) ... Setting up ant (1.10.15-1) ... Setting up junit4 (4.13.2-5) ... Setting up openjdk-21-jdk-headless:amd64 (21.0.6+7-1) ... 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+7-1) ... 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.f+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.f+dfsg-1_source.changes dpkg-buildpackage: info: source package snpeff dpkg-buildpackage: info: source version 5.2.f+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.f+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.f+dfsg' jh_clean Duplicate specification "u=s" 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.f+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="@1739702387" +"%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.f\+dfsg/debian/maven-repo Failed to parse /build/reproducible-path/snpeff-5.2.f+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) Failed to parse /build/reproducible-path/snpeff-5.2.f+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) make[1]: Leaving directory '/build/reproducible-path/snpeff-5.2.f+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.f\+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.f\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/snpeff-5.2.f\+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+dfsg/src/main/java/org/snpeff/vcf/PedigreeEntry.java:9: warning: invalid input: '<' [WARNING] * ##PEDIGREE= [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.f+dfsg/src/main/java/org/snpeff/vcf/PedigreeEntry.java:12: warning: invalid input: '<' [WARNING] * ##PEDIGREE= [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.f+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.f+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.f+dfsg/target/snpeff-5.2.jar to /build/reproducible-path/snpeff-5.2.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+dfsg/src/main/java/org/snpeff/vcf/PedigreeEntry.java:9: warning: invalid input: '<' [WARNING] * ##PEDIGREE= [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.f+dfsg/src/main/java/org/snpeff/vcf/PedigreeEntry.java:12: warning: invalid input: '<' [WARNING] * ##PEDIGREE= [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.f+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: 02:19 min [INFO] Finished at: 2025-02-21T08:21:17-12:00 [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.f\+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.f\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/snpeff-5.2.f\+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.f+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.f+dfsg/pom.xml.save with options: [INFO] --keep-pom-version --package=libsnpeff-java [INFO] --rules=/build/reproducible-path/snpeff-5.2.f+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/snpeff-5.2.f+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/snpeff-5.2.f+dfsg/debian/maven.publishedRules [INFO] Install jar for snpeff into /usr/share/java [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 5.696 s [INFO] Finished at: 2025-02-21T08:51:17-12:00 [INFO] ------------------------------------------------------------------------ mh_resolve_dependencies --non-interactive --offline --build -plibsnpeff-java --javadoc --base-directory=/build/reproducible-path/snpeff-5.2.f\+dfsg --non-explore Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) at org.debian.maven.repo.POMReader.readPom(POMReader.java:82) at org.debian.maven.repo.POMReader.readPom(POMReader.java:57) at org.debian.maven.repo.Repository.scan(Repository.java:397) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:201) at org.debian.maven.repo.Repository.scanOnce(Repository.java:196) at org.debian.maven.repo.POMTransformer.usePluginVersionsFromRepository(POMTransformer.java:107) at org.debian.maven.packager.DependenciesSolver.main(DependenciesSolver.java:907) Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) at org.debian.maven.repo.POMReader.readPom(POMReader.java:82) at org.debian.maven.repo.POMReader.readPom(POMReader.java:57) at org.debian.maven.repo.Repository.scan(Repository.java:397) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:201) at org.debian.maven.repo.Repository.scanOnce(Repository.java:196) at org.debian.maven.repo.POMTransformer.usePluginVersionsFromRepository(POMTransformer.java:107) at org.debian.maven.packager.DependenciesSolver.main(DependenciesSolver.java:907) Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) at org.debian.maven.repo.POMReader.readPom(POMReader.java:82) at org.debian.maven.repo.POMReader.readPom(POMReader.java:57) at org.debian.maven.repo.Repository.scan(Repository.java:397) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:201) at org.debian.maven.packager.DependenciesSolver.getRepository(DependenciesSolver.java:231) at org.debian.maven.packager.DependenciesSolver.solveDependencies(DependenciesSolver.java:237) at org.debian.maven.packager.DependenciesSolver.main(DependenciesSolver.java:922) Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) at org.debian.maven.repo.POMReader.readPom(POMReader.java:82) at org.debian.maven.repo.POMReader.readPom(POMReader.java:57) at org.debian.maven.repo.Repository.scan(Repository.java:397) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:201) at org.debian.maven.packager.DependenciesSolver.getRepository(DependenciesSolver.java:231) at org.debian.maven.packager.DependenciesSolver.solveDependencies(DependenciesSolver.java:237) at org.debian.maven.packager.DependenciesSolver.main(DependenciesSolver.java:922) Analysing pom.xml... > dpkg --search /usr/share/maven-repo/org/biojava/biojava-structure/*/* Found /usr/share/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom in libbiojava6-java Found /usr/share/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom in libbiojava6-java > dpkg --status libbiojava6-java [error] Package libbiojava6-java (6.1.0+dfsg) is already installed and contains a possible match, but I cannot resolve library org.biojava:biojava-structure:jar:6.x in it. [error] Please check manually that the library is up to date, otherwise it may be necessary to package version 6.x in Debian. Feb 21, 2025 8:51:45 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve SEVERE: Cannot resolve dependencies in /build/reproducible-path/snpeff-5.2.f+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-doc' in '../libsnpeff-java-doc_5.2.f+dfsg-1_all.deb'. dpkg-deb: building package 'libsnpeff-java' in '../libsnpeff-java_5.2.f+dfsg-1_all.deb'. dpkg-deb: building package 'snpeff' in '../snpeff_5.2.f+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../snpeff_5.2.f+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../snpeff_5.2.f+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/1686575 and its subdirectories I: Current time: Fri Feb 21 08:56:07 -12 2025 I: pbuilder-time-stamp: 1740171367 Fri Feb 21 20:56:11 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Fri Feb 21 20:56:11 UTC 2025 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Fri Feb 21 20:56:11 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Fri Feb 21 20:56:11 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-FPek8f' ==================================================================================== Fri Mar 27 03:19:12 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos15-amd64, called using "2 snpeff trixie /srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc 5.2.f+dfsg-1" as arguments. Fri Mar 27 03:19:12 UTC 2026 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-12ncfKOQ" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Mar 27 03:19:12 UTC 2026 I: Downloading source for trixie/snpeff=5.2.f+dfsg-1 Reading package lists... NOTICE: 'snpeff' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/snpeff.git Please use: git clone https://salsa.debian.org/med-team/snpeff.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 155 MB of source archives. Get:1 http://deb.debian.org/debian trixie/main snpeff 5.2.f+dfsg-1 (dsc) [2569 B] Get:2 http://deb.debian.org/debian trixie/main snpeff 5.2.f+dfsg-1 (tar) [155 MB] Get:3 http://deb.debian.org/debian trixie/main snpeff 5.2.f+dfsg-1 (diff) [14.3 kB] Fetched 155 MB in 5s (32.9 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'snpeff' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/snpeff.git Please use: git clone https://salsa.debian.org/med-team/snpeff.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 155 MB of source archives. Get:1 http://deb.debian.org/debian trixie/main snpeff 5.2.f+dfsg-1 (dsc) [2569 B] Get:2 http://deb.debian.org/debian trixie/main snpeff 5.2.f+dfsg-1 (tar) [155 MB] Get:3 http://deb.debian.org/debian trixie/main snpeff 5.2.f+dfsg-1 (diff) [14.3 kB] Fetched 155 MB in 5s (32.9 MB/s) Download complete and in download only mode ============================================================================= Re-Building snpeff in trixie on amd64 on ionos15-amd64 now. Date: Fri Mar 27 03:19:17 UTC 2026 Date UTC: Fri Mar 27 03:19:17 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc/pbuilderrc_Vxix + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' snpeff = debian-installer -o snpeff = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' snpeff = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc/pbuilderrc_Vxix --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc/b2 --logfile b2/build.log snpeff_5.2.f+dfsg-1.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Fri Mar 27 17:19:17 +14 2026 I: pbuilder-time-stamp: 1774581557 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [snpeff_5.2.f+dfsg-1.dsc] I: copying [./snpeff_5.2.f+dfsg.orig.tar.xz] I: copying [./snpeff_5.2.f+dfsg-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./snpeff_5.2.f+dfsg-1.dsc: unsupported subcommand dpkg-source: info: extracting snpeff in snpeff-5.2.f+dfsg dpkg-source: info: unpacking snpeff_5.2.f+dfsg.orig.tar.xz dpkg-source: info: unpacking snpeff_5.2.f+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/3760331/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Mar 27 03:19 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/3760331/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3760331/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=506dee5f54c94e84a727ad95eb304a4d LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3760331 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc/pbuilderrc_Vxix --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc/b2 --logfile b2/build.log snpeff_5.2.f+dfsg-1.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3760331/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 ... 19809 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 1301 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libsystemd-shared amd64 257.3-1 [2138 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libapparmor1 amd64 3.1.7-4 [42.0 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 systemd amd64 257.3-1 [3092 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 systemd-sysv amd64 257.3-1 [61.4 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libdbus-1-3 amd64 1.16.0-1 [177 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 dbus-bin amd64 1.16.0-1 [78.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 dbus-session-bus-common all 1.16.0-1 [51.1 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 dbus-daemon amd64 1.16.0-1 [157 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 dbus-system-bus-common all 1.16.0-1 [52.2 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 dbus amd64 1.16.0-1 [70.5 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 binfmt-support amd64 2.2.2-7 [64.3 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025a-2 [259 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.2-1 [745 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B] Get: 26 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.1-2 [28.0 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-7 [878 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.4.1-1 [1427 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20241223 [164 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libpam-systemd amd64 257.3-1 [293 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-3 [92.1 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [311 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.83.3-2 [1511 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 shared-mime-info amd64 2.4-5+b2 [760 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.46-4 [284 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-2 [140 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 gtk-update-icon-cache amd64 4.17.4+ds-4 [51.3 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 hicolor-icon-theme all 0.18-2 [11.8 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 adwaita-icon-theme all 47.0-2 [463 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 java-common all 0.76 [6776 B] Get: 61 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libnspr4 amd64 2:4.36-1 [110 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libnss3 amd64 2:3.108-1 [1393 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libpcsclite1 amd64 2.3.1-1 [56.0 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jre-headless amd64 21.0.6+7-1 [41.7 MB] Get: 66 http://deb.debian.org/debian trixie/main amd64 default-jre-headless amd64 2:1.21-76 [3192 B] Get: 67 http://deb.debian.org/debian trixie/main amd64 ant all 1.10.15-1 [2163 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 ant-optional all 1.10.15-1 [456 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 at-spi2-common all 2.55.2-1 [170 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 dbus-user-session amd64 1.16.0-1 [51.0 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libdconf1 amd64 0.40.0-5 [41.8 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 dconf-service amd64 0.40.0-5 [32.4 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 dconf-gsettings-backend amd64 0.40.0-5 [28.6 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 dctrl-tools amd64 2.24-3+b1 [104 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 86 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libatk1.0-0t64 amd64 2.55.2-1 [51.4 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libatspi2.0-0t64 amd64 2.55.2-1 [77.0 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libatk-bridge2.0-0t64 amd64 2.55.2-1 [68.1 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-2 [391 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b4 [27.8 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libcairo-gobject2 amd64 1.18.2-2 [130 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libcloudproviders0 amd64 0.3.6-1+b1 [29.2 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libcolord2 amd64 1.4.7-1+b2 [140 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libavahi-common-data amd64 0.8-16 [112 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libavahi-common3 amd64 0.8-16 [44.2 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libavahi-client3 amd64 0.8-16 [48.4 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 128 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libcups2t64 amd64 2.4.10-2+b1 [251 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libepoxy0 amd64 1.5.10-2 [193 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.2.0-1 [479 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-2 [463 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.56.1-1 [226 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.56.1-1 [55.3 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.56.1-1 [35.8 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libwayland-client0 amd64 1.23.1-1 [26.5 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 libwayland-cursor0 amd64 1.23.1-1 [11.4 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libwayland-egl1 amd64 1.23.1-1 [5452 B] Get: 145 http://deb.debian.org/debian trixie/main amd64 libxcomposite1 amd64 1:0.4.6-1 [16.3 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libxfixes3 amd64 1:6.0.0-2+b4 [20.2 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libxcursor1 amd64 1:1.2.3-1 [39.7 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libxdamage1 amd64 1:1.1.6-1+b2 [15.5 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 libxinerama1 amd64 2:1.1.4-3+b3 [16.0 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 xkb-data all 2.42-1 [790 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 libxkbcommon0 amd64 1.7.0-2 [113 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 libxrandr2 amd64 2:1.5.4-1+b3 [36.3 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libgtk-3-common all 3.24.48-4 [4873 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libgtk-3-0t64 amd64 3.24.48-4 [2767 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.123-1 [8084 B] Get: 157 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 libglapi-mesa amd64 24.3.4-3 [38.5 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 libx11-xcb1 amd64 2:1.8.10-2 [241 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b4 [19.3 kB] Get: 165 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 libdrm-intel1 amd64 2.4.123-1 [63.7 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 libdrm-radeon1 amd64 2.4.123-1 [22.3 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 libllvm19 amd64 1:19.1.7-1+b1 [26.0 MB] Get: 172 http://deb.debian.org/debian trixie/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 libsensors5 amd64 1:3.6.0-10+b1 [35.1 kB] Get: 174 http://deb.debian.org/debian trixie/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 libxshmfence1 amd64 1.3-1+b3 [8852 B] Get: 177 http://deb.debian.org/debian trixie/main amd64 mesa-libgallium amd64 24.3.4-3 [9492 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 libwayland-server0 amd64 1.23.1-1 [34.0 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 libgbm1 amd64 24.3.4-3 [43.7 kB] Get: 180 http://deb.debian.org/debian trixie/main amd64 libvulkan1 amd64 1.4.304.0-1 [129 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 libgl1-mesa-dri amd64 24.3.4-3 [45.2 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 libglx-mesa0 amd64 24.3.4-3 [143 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB] Get: 184 http://deb.debian.org/debian trixie/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 libasound2-data all 1.2.13-1 [21.1 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 libasound2t64 amd64 1.2.13-1+b1 [373 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 libgif7 amd64 5.2.2-1+b1 [44.2 kB] Get: 188 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+24 [217 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 libxtst6 amd64 2:1.2.5-1 [25.8 kB] Get: 190 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jre amd64 21.0.6+7-1 [205 kB] Get: 191 http://deb.debian.org/debian trixie/main amd64 default-jre amd64 2:1.21-76 [1068 B] Get: 192 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jdk-headless amd64 21.0.6+7-1 [82.8 MB] Get: 193 http://deb.debian.org/debian trixie/main amd64 default-jdk-headless amd64 2:1.21-76 [1124 B] Get: 194 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jdk amd64 21.0.6+7-1 [3434 kB] Get: 195 http://deb.debian.org/debian trixie/main amd64 default-jdk amd64 2:1.21-76 [1076 B] Get: 196 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 197 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 198 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui-theme-base all 1.12.1+dfsg-1.1 [44.3 kB] Get: 199 http://deb.debian.org/debian trixie/main amd64 openjdk-21-doc all 21.0.6+7-1 [13.2 MB] Get: 200 http://deb.debian.org/debian trixie/main amd64 default-jdk-doc amd64 2:1.21-76 [3264 B] Get: 201 http://deb.debian.org/debian trixie/main amd64 libgpg-error0 amd64 1.51-3 [82.2 kB] Get: 202 http://deb.debian.org/debian trixie/main amd64 libassuan9 amd64 3.0.1-2 [60.6 kB] Get: 203 http://deb.debian.org/debian trixie/main amd64 libgcrypt20 amd64 1.11.0-7 [843 kB] Get: 204 http://deb.debian.org/debian trixie/main amd64 gpgconf amd64 2.2.46-1+b1 [121 kB] Get: 205 http://deb.debian.org/debian trixie/main amd64 libksba8 amd64 1.6.7-2+b1 [136 kB] Get: 206 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8+b1 [19.9 kB] Get: 207 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8+b1 [57.6 kB] Get: 208 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB] Get: 209 http://deb.debian.org/debian trixie/main amd64 libnpth0t64 amd64 1.8-2 [22.9 kB] Get: 210 http://deb.debian.org/debian trixie/main amd64 dirmngr amd64 2.2.46-1+b1 [369 kB] Get: 211 http://deb.debian.org/debian trixie/main amd64 gnupg-l10n all 2.2.46-1 [702 kB] Get: 212 http://deb.debian.org/debian trixie/main amd64 gpg amd64 2.2.46-1+b1 [532 kB] Get: 213 http://deb.debian.org/debian trixie/main amd64 pinentry-curses amd64 1.3.1-2 [86.4 kB] Get: 214 http://deb.debian.org/debian trixie/main amd64 gpg-agent amd64 2.2.46-1+b1 [252 kB] Get: 215 http://deb.debian.org/debian trixie/main amd64 gpgsm amd64 2.2.46-1+b1 [255 kB] Get: 216 http://deb.debian.org/debian trixie/main amd64 gnupg all 2.2.46-1 [376 kB] Get: 217 http://deb.debian.org/debian trixie/main amd64 gpgv amd64 2.2.46-1+b1 [219 kB] Get: 218 http://deb.debian.org/debian trixie/main amd64 sopv-gpgv all 0.1.1-1 [10.7 kB] Get: 219 http://deb.debian.org/debian trixie/main amd64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 220 http://deb.debian.org/debian trixie/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 221 http://deb.debian.org/debian trixie/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 222 http://deb.debian.org/debian trixie/main amd64 libfile-touch-perl all 0.12-2 [8816 B] Get: 223 http://deb.debian.org/debian trixie/main amd64 libio-pty-perl amd64 1:1.20-1+b3 [34.3 kB] Get: 224 http://deb.debian.org/debian trixie/main amd64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 225 http://deb.debian.org/debian trixie/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 226 http://deb.debian.org/debian trixie/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b5 [36.1 kB] Get: 227 http://deb.debian.org/debian trixie/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b2 [10.6 kB] Get: 228 http://deb.debian.org/debian trixie/main amd64 libdynaloader-functions-perl all 0.004-1 [12.1 kB] Get: 229 http://deb.debian.org/debian trixie/main amd64 libdevel-callchecker-perl amd64 0.009-1+b1 [16.2 kB] Get: 230 http://deb.debian.org/debian trixie/main amd64 libparams-classify-perl amd64 0.015-2+b4 [22.5 kB] Get: 231 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 232 http://deb.debian.org/debian trixie/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 233 http://deb.debian.org/debian trixie/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 234 http://deb.debian.org/debian trixie/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 235 http://deb.debian.org/debian trixie/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 236 http://deb.debian.org/debian trixie/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 237 http://deb.debian.org/debian trixie/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 238 http://deb.debian.org/debian trixie/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 239 http://deb.debian.org/debian trixie/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 240 http://deb.debian.org/debian trixie/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 241 http://deb.debian.org/debian trixie/main amd64 liburi-perl all 5.30-1 [105 kB] Get: 242 http://deb.debian.org/debian trixie/main amd64 libhtml-parser-perl amd64 3.83-1+b2 [99.7 kB] Get: 243 http://deb.debian.org/debian trixie/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 244 http://deb.debian.org/debian trixie/main amd64 libclone-perl amd64 0.47-1+b1 [13.9 kB] Get: 245 http://deb.debian.org/debian trixie/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 246 http://deb.debian.org/debian trixie/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 247 http://deb.debian.org/debian trixie/main amd64 libhttp-message-perl all 7.00-2 [79.8 kB] Get: 248 http://deb.debian.org/debian trixie/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 249 http://deb.debian.org/debian trixie/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 250 http://deb.debian.org/debian trixie/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get: 251 http://deb.debian.org/debian trixie/main amd64 libnet-ssleay-perl amd64 1.94-3 [339 kB] Get: 252 http://deb.debian.org/debian trixie/main amd64 libio-socket-ssl-perl all 2.089-1 [223 kB] Get: 253 http://deb.debian.org/debian trixie/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 254 http://deb.debian.org/debian trixie/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 255 http://deb.debian.org/debian trixie/main amd64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 256 http://deb.debian.org/debian trixie/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 257 http://deb.debian.org/debian trixie/main amd64 libwww-perl all 6.77-1 [183 kB] Get: 258 http://deb.debian.org/debian trixie/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get: 259 http://deb.debian.org/debian trixie/main amd64 wdiff amd64 1.2.2-7 [122 kB] Get: 260 http://deb.debian.org/debian trixie/main amd64 devscripts all 2.25.2 [1058 kB] Get: 261 http://deb.debian.org/debian trixie/main amd64 fastjar amd64 2:0.98-7 [80.1 kB] Get: 262 http://deb.debian.org/debian trixie/main amd64 jarwrapper all 0.80 [9692 B] Get: 263 http://deb.debian.org/debian trixie/main amd64 javahelper all 0.80 [80.4 kB] Get: 264 http://deb.debian.org/debian trixie/main amd64 libhamcrest-java all 2.2-2 [121 kB] Get: 265 http://deb.debian.org/debian trixie/main amd64 junit4 all 4.13.2-5 [350 kB] Get: 266 http://deb.debian.org/debian trixie/main amd64 libapiguardian-java all 1.1.2-1 [4656 B] Get: 267 http://deb.debian.org/debian trixie/main amd64 libopentest4j-java all 1.2.0-4 [9516 B] Get: 268 http://deb.debian.org/debian trixie/main amd64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 269 http://deb.debian.org/debian trixie/main amd64 libpicocli-java all 4.6.2-2 [390 kB] Get: 270 http://deb.debian.org/debian trixie/main amd64 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 271 http://deb.debian.org/debian trixie/main amd64 junit5 all 5.10.3-1 [2459 kB] Get: 272 http://deb.debian.org/debian trixie/main amd64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 273 http://deb.debian.org/debian trixie/main amd64 libantlr4-runtime-java all 4.9.2-3 [318 kB] Get: 274 http://deb.debian.org/debian trixie/main amd64 libaopalliance-java all 20070526-7 [8572 B] Get: 275 http://deb.debian.org/debian trixie/main amd64 libapache-pom-java all 33-2 [5852 B] Get: 276 http://deb.debian.org/debian trixie/main amd64 libapfloat-java all 1.14.0-2 [725 kB] Get: 277 http://deb.debian.org/debian trixie/main amd64 libargs4j-java all 2.33-2 [138 kB] Get: 278 http://deb.debian.org/debian trixie/main amd64 libasm-java all 9.7.1-1 [391 kB] Get: 279 http://deb.debian.org/debian trixie/main amd64 libatinject-jsr330-api-java all 1.0+ds1-6 [5112 B] Get: 280 http://deb.debian.org/debian trixie/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 281 http://deb.debian.org/debian trixie/main amd64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 282 http://deb.debian.org/debian trixie/main amd64 libciftools-java all 6.0.0-1 [2211 kB] Get: 283 http://deb.debian.org/debian trixie/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 284 http://deb.debian.org/debian trixie/main amd64 libcommons-codec-java all 1.17.1-1 [303 kB] Get: 285 http://deb.debian.org/debian trixie/main amd64 libcommons-math-java all 2.2-9 [933 kB] Get: 286 http://deb.debian.org/debian trixie/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 287 http://deb.debian.org/debian trixie/main amd64 libjsr305-java all 0.1~+svn49-12 [26.6 kB] Get: 288 http://deb.debian.org/debian trixie/main amd64 libguava-java all 32.0.1-1 [2708 kB] Get: 289 http://deb.debian.org/debian trixie/main amd64 libitext5-java all 5.5.13.3-4 [2667 kB] Get: 290 http://deb.debian.org/debian trixie/main amd64 libjackson2-annotations-java all 2.14.0-1 [68.8 kB] Get: 291 http://deb.debian.org/debian trixie/main amd64 libjackson2-core-java all 2.14.1-1 [447 kB] Get: 292 http://deb.debian.org/debian trixie/main amd64 libjackson2-databind-java all 2.14.0+ds-1 [1532 kB] Get: 293 http://deb.debian.org/debian trixie/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 294 http://deb.debian.org/debian trixie/main amd64 libjaxen-java all 1.1.6-5 [214 kB] Get: 295 http://deb.debian.org/debian trixie/main amd64 libdom4j-java all 2.1.4-1 [312 kB] Get: 296 http://deb.debian.org/debian trixie/main amd64 libcommons-io-java all 2.18.0-1 [509 kB] Get: 297 http://deb.debian.org/debian trixie/main amd64 libslf4j-java all 1.7.32-1 [144 kB] Get: 298 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-utils-java all 3.4.2-1 [137 kB] Get: 299 http://deb.debian.org/debian trixie/main amd64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 300 http://deb.debian.org/debian trixie/main amd64 libguice-java all 5.1.0-1 [932 kB] Get: 301 http://deb.debian.org/debian trixie/main amd64 libmaven-parent-java all 43-2 [6252 B] Get: 302 http://deb.debian.org/debian trixie/main amd64 libcommons-lang3-java all 3.17.0-1 [641 kB] Get: 303 http://deb.debian.org/debian trixie/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 304 http://deb.debian.org/debian trixie/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 305 http://deb.debian.org/debian trixie/main amd64 libmaven-resolver-java all 1.9.22-1 [729 kB] Get: 306 http://deb.debian.org/debian trixie/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 307 http://deb.debian.org/debian trixie/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 308 http://deb.debian.org/debian trixie/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 309 http://deb.debian.org/debian trixie/main amd64 libplexus-interpolation-java all 1.27-1 [76.8 kB] Get: 310 http://deb.debian.org/debian trixie/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 311 http://deb.debian.org/debian trixie/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-5 [8444 B] Get: 312 http://deb.debian.org/debian trixie/main amd64 libcdi-api-java all 1.2-4 [55.3 kB] Get: 313 http://deb.debian.org/debian trixie/main amd64 libsisu-inject-java all 0.3.5-1 [352 kB] Get: 314 http://deb.debian.org/debian trixie/main amd64 libsisu-plexus-java all 0.3.5-1 [183 kB] Get: 315 http://deb.debian.org/debian trixie/main amd64 libmaven3-core-java all 3.9.9-1 [1661 kB] Get: 316 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 317 http://deb.debian.org/debian trixie/main amd64 libmaven-file-management-java all 3.0.0-2 [35.1 kB] Get: 318 http://deb.debian.org/debian trixie/main amd64 libcommons-compress-java all 1.27.1-2 [641 kB] Get: 319 http://deb.debian.org/debian trixie/main amd64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 320 http://deb.debian.org/debian trixie/main amd64 libsnappy1v5 amd64 1.2.1-1+b1 [29.6 kB] Get: 321 http://deb.debian.org/debian trixie/main amd64 libsnappy-jni amd64 1.1.10.7-1 [6492 B] Get: 322 http://deb.debian.org/debian trixie/main amd64 libsnappy-java all 1.1.10.7-1 [87.6 kB] Get: 323 http://deb.debian.org/debian trixie/main amd64 libxz-java all 1.9-1 [143 kB] Get: 324 http://deb.debian.org/debian trixie/main amd64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 325 http://deb.debian.org/debian trixie/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 326 http://deb.debian.org/debian trixie/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 327 http://deb.debian.org/debian trixie/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 328 http://deb.debian.org/debian trixie/main amd64 libjsoup-java all 1.15.3-1 [431 kB] Get: 329 http://deb.debian.org/debian trixie/main amd64 libwagon-http-java all 3.5.3-1 [49.5 kB] Get: 330 http://deb.debian.org/debian trixie/main amd64 libistack-commons-java all 3.0.6-5 [145 kB] Get: 331 http://deb.debian.org/debian trixie/main amd64 libcodemodel-java all 2.6+jaxb2.3.0.1-11 [164 kB] Get: 332 http://deb.debian.org/debian trixie/main amd64 librelaxng-datatype-java all 1.0+ds1-4 [11.8 kB] Get: 333 http://deb.debian.org/debian trixie/main amd64 librngom-java all 2.3.0.1-11 [292 kB] Get: 334 http://deb.debian.org/debian trixie/main amd64 libxsom-java all 2.3.0.1-11 [401 kB] Get: 335 http://deb.debian.org/debian trixie/main amd64 libtxw2-java all 2.3.0.1-11 [134 kB] Get: 336 http://deb.debian.org/debian trixie/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 337 http://deb.debian.org/debian trixie/main amd64 libdtd-parser-java all 1.2-1 [64.9 kB] Get: 338 http://deb.debian.org/debian trixie/main amd64 libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 339 http://deb.debian.org/debian trixie/main amd64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB] Get: 340 http://deb.debian.org/debian trixie/main amd64 libfastinfoset-java all 1.2.12-4 [347 kB] Get: 341 http://deb.debian.org/debian trixie/main amd64 libjaxb-java all 2.3.0.1-11 [1980 kB] Get: 342 http://deb.debian.org/debian trixie/main amd64 libmaven-archiver-java all 3.6.2-1 [26.1 kB] Get: 343 http://deb.debian.org/debian trixie/main amd64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 344 http://deb.debian.org/debian trixie/main amd64 libcommons-text-java all 1.12.0-1 [222 kB] Get: 345 http://deb.debian.org/debian trixie/main amd64 libfastutil-java all 8.5.15+dfsg-1 [20.0 MB] Get: 346 http://deb.debian.org/debian trixie/main amd64 libjheaps-java all 0.14-2 [144 kB] Get: 347 http://deb.debian.org/debian trixie/main amd64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 348 http://deb.debian.org/debian trixie/main amd64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 349 http://deb.debian.org/debian trixie/main amd64 libjgraphx-java all 2.1.0.7-5 [809 kB] Get: 350 http://deb.debian.org/debian trixie/main amd64 libjgrapht-java all 1.5.2-1 [1610 kB] Get: 351 http://deb.debian.org/debian trixie/main amd64 libinchi1.07 amd64 1.07.2+dfsg-1 [556 kB] Get: 352 http://deb.debian.org/debian trixie/main amd64 libjni-inchi-jni amd64 0.8+dfsg-8 [9188 B] Get: 353 http://deb.debian.org/debian trixie/main amd64 libcommons-exec-java all 1.3-2 [48.1 kB] Get: 354 http://deb.debian.org/debian trixie/main amd64 libexec-maven-plugin-java all 3.1.0-2 [66.7 kB] Get: 355 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-incremental-java all 1.1-6 [9916 B] Get: 356 http://deb.debian.org/debian trixie/main amd64 libcommons-lang-java all 2.6-10 [273 kB] Get: 357 http://deb.debian.org/debian trixie/main amd64 libxbean-reflect-java all 4.5-9 [132 kB] Get: 358 http://deb.debian.org/debian trixie/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 359 http://deb.debian.org/debian trixie/main amd64 libplexus-compiler-java all 2.13.0-1 [99.5 kB] Get: 360 http://deb.debian.org/debian trixie/main amd64 libqdox2-java all 2.0.3-1 [296 kB] Get: 361 http://deb.debian.org/debian trixie/main amd64 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 362 http://deb.debian.org/debian trixie/main amd64 libmaven-compiler-plugin-java all 3.13.0-1 [78.8 kB] Get: 363 http://deb.debian.org/debian trixie/main amd64 liblog4j1.2-java all 1.2.17-11 [444 kB] Get: 364 http://deb.debian.org/debian trixie/main amd64 libjni-inchi-java all 0.8+dfsg-8 [33.6 kB] Get: 365 http://deb.debian.org/debian trixie/main amd64 libnaga-java all 3.0+svn80-5 [43.5 kB] Get: 366 http://deb.debian.org/debian trixie/main amd64 libjmol-java all 16.2.33+dfsg-1 [10.4 MB] Get: 367 http://deb.debian.org/debian trixie/main amd64 libjson-simple-java all 2.3.0-2 [61.7 kB] Get: 368 http://deb.debian.org/debian trixie/main amd64 libmsgpack-java all 0.9.6-1 [161 kB] Get: 369 http://deb.debian.org/debian trixie/main amd64 libmmtf-java all 1.0.11-1 [187 kB] Get: 370 http://deb.debian.org/debian trixie/main amd64 libvecmath-java all 1.5.2-7 [97.0 kB] Get: 371 http://deb.debian.org/debian trixie/main amd64 libbiojava6-java all 6.1.0+dfsg-5 [5359 kB] Get: 372 http://deb.debian.org/debian trixie/main amd64 libbiojava6-java-doc all 6.1.0+dfsg-5 [2256 kB] Get: 373 http://deb.debian.org/debian trixie/main amd64 libbsh-java all 2.0b4-20 [291 kB] Get: 374 http://deb.debian.org/debian trixie/main amd64 libcharts4j-java all 1.3-4 [162 kB] Get: 375 http://deb.debian.org/debian trixie/main amd64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 376 http://deb.debian.org/debian trixie/main amd64 libcommons-beanutils-java all 1.9.4-2 [233 kB] Get: 377 http://deb.debian.org/debian trixie/main amd64 libcommons-collections4-java all 4.4-2 [682 kB] Get: 378 http://deb.debian.org/debian trixie/main amd64 libcommons-digester-java all 1.8.1-7 [138 kB] Get: 379 http://deb.debian.org/debian trixie/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get: 380 http://deb.debian.org/debian trixie/main amd64 libcommons-math3-java all 3.6.1-4 [2040 kB] Get: 381 http://deb.debian.org/debian trixie/main amd64 libcommons-validator-java all 1:1.9.0-1 [191 kB] Get: 382 http://deb.debian.org/debian trixie/main amd64 libdistlib-java all 1.0-5 [72.5 kB] Get: 383 http://deb.debian.org/debian trixie/main amd64 libdoxia-core-java all 2.0.0-1 [149 kB] Get: 384 http://deb.debian.org/debian trixie/main amd64 libplexus-xml-java all 3.0.1-2 [93.7 kB] Get: 385 http://deb.debian.org/debian trixie/main amd64 libdoxia-java all 2.0.0-1 [113 kB] Get: 386 http://deb.debian.org/debian trixie/main amd64 libmaven-reporting-api-java all 4.0.0-1 [6724 B] Get: 387 http://deb.debian.org/debian trixie/main amd64 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB] Get: 388 http://deb.debian.org/debian trixie/main amd64 velocity all 1.7-7 [431 kB] Get: 389 http://deb.debian.org/debian trixie/main amd64 libplexus-velocity-java all 1.2-4 [9676 B] Get: 390 http://deb.debian.org/debian trixie/main amd64 liboro-java all 2.0.8a-14 [70.5 kB] Get: 391 http://deb.debian.org/debian trixie/main amd64 libvelocity-tools-java all 2.0-9 [311 kB] Get: 392 http://deb.debian.org/debian trixie/main amd64 libdoxia-sitetools-java all 2.0.0-1 [176 kB] Get: 393 http://deb.debian.org/debian trixie/main amd64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 394 http://deb.debian.org/debian trixie/main amd64 libezmorph-java all 1.0.6-4 [75.9 kB] Get: 395 http://deb.debian.org/debian trixie/main amd64 libfreemarker-java all 2.3.32-2 [1546 kB] Get: 396 http://deb.debian.org/debian trixie/main amd64 libxom-java all 1.3.9-1 [174 kB] Get: 397 http://deb.debian.org/debian trixie/main amd64 libjson-java all 3.1.0+dfsg-2 [142 kB] Get: 398 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto16 amd64 3.6.2-3 [355 kB] Get: 399 http://deb.debian.org/debian trixie/main amd64 libmbedx509-7 amd64 3.6.2-3 [147 kB] Get: 400 http://deb.debian.org/debian trixie/main amd64 libmbedtls21 amd64 3.6.2-3 [234 kB] Get: 401 http://deb.debian.org/debian trixie/main amd64 ncbi-vdb-data all 3.0.9+dfsg-2 [74.0 kB] Get: 402 http://deb.debian.org/debian trixie/main amd64 libncbi-vdb3 amd64 3.0.9+dfsg-2 [1189 kB] Get: 403 http://deb.debian.org/debian trixie/main amd64 libncbi-ngs3 amd64 3.0.9+dfsg-7+b2 [156 kB] Get: 404 http://deb.debian.org/debian trixie/main amd64 libngs-jni amd64 3.0.9+dfsg-7+b2 [25.9 kB] Get: 405 http://deb.debian.org/debian trixie/main amd64 libngs-java amd64 3.0.9+dfsg-7+b2 [112 kB] Get: 406 http://deb.debian.org/debian trixie/main amd64 librhino-java all 1.7.15-1 [1382 kB] Get: 407 http://deb.debian.org/debian trixie/main amd64 libhtsjdk-java all 4.1.3+dfsg-2 [1841 kB] Get: 408 http://deb.debian.org/debian trixie/main amd64 libjansi-java all 2.4.1-2 [100 kB] Get: 409 http://deb.debian.org/debian trixie/main amd64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 410 http://deb.debian.org/debian trixie/main amd64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 411 http://deb.debian.org/debian trixie/main amd64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 412 http://deb.debian.org/debian trixie/main amd64 libjetty9-java all 9.4.56-1 [2964 kB] Get: 413 http://deb.debian.org/debian trixie/main amd64 libjtidy-java all 7+svn20110807-6 [251 kB] Get: 414 http://deb.debian.org/debian trixie/main amd64 libmaven-common-artifact-filters-java all 3.4.0-1 [47.7 kB] Get: 415 http://deb.debian.org/debian trixie/main amd64 libmaven-artifact-transfer-java all 0.13.1-2 [158 kB] Get: 416 http://deb.debian.org/debian trixie/main amd64 libplexus-build-api-java all 0.0.7-4 [10.3 kB] Get: 417 http://deb.debian.org/debian trixie/main amd64 libmaven-filtering-java all 3.4.0-1 [51.4 kB] Get: 418 http://deb.debian.org/debian trixie/main amd64 libmaven-assembly-plugin-java all 3.4.2-2 [242 kB] Get: 419 http://deb.debian.org/debian trixie/main amd64 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB] Get: 420 http://deb.debian.org/debian trixie/main amd64 libmaven-invoker-java all 3.3.0-1 [29.1 kB] Get: 421 http://deb.debian.org/debian trixie/main amd64 libplexus-interactivity-api-java all 1.3-1 [11.6 kB] Get: 422 http://deb.debian.org/debian trixie/main amd64 libmaven-javadoc-plugin-java all 3.10.1-2 [451 kB] Get: 423 http://deb.debian.org/debian trixie/main amd64 libplexus-container-default1.5-java all 2.1.1-1 [4476 B] Get: 424 http://deb.debian.org/debian trixie/main amd64 libplexus-ant-factory-java all 1.0~alpha2.1-4 [11.4 kB] Get: 425 http://deb.debian.org/debian trixie/main amd64 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B] Get: 426 http://deb.debian.org/debian trixie/main amd64 libmaven-plugin-tools-java all 3.10.2-1 [245 kB] Get: 427 http://deb.debian.org/debian trixie/main amd64 libmaven-reporting-exec-java all 2.0.0-1 [23.9 kB] Get: 428 http://deb.debian.org/debian trixie/main amd64 libmaven-resources-plugin-java all 3.3.1-1 [27.5 kB] Get: 429 http://deb.debian.org/debian trixie/main amd64 libmaven-site-plugin-java all 3.21.0-1 [106 kB] Get: 430 http://deb.debian.org/debian trixie/main amd64 libsurefire-java all 2.22.3-3 [1284 kB] Get: 431 http://deb.debian.org/debian trixie/main amd64 libtrove3-java all 3.0.3-5 [2146 kB] Get: 432 http://deb.debian.org/debian trixie/main amd64 libtrove3-java-doc all 3.0.3-5 [823 kB] Get: 433 http://deb.debian.org/debian trixie/main amd64 libwagon-file-java all 3.5.3-1 [8388 B] Get: 434 http://deb.debian.org/debian trixie/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 trixie/main amd64 maven all 3.9.9-1 [19.7 kB] Get: 436 http://deb.debian.org/debian trixie/main amd64 maven-repo-helper all 1.11 [142 kB] Get: 437 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get: 438 http://deb.debian.org/debian trixie/main amd64 maven-debian-helper all 2.6.7 [108 kB] Fetched 361 MB in 12s (29.1 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 ... 19809 files and directories currently installed.) Preparing to unpack .../libsystemd-shared_257.3-1_amd64.deb ... Unpacking libsystemd-shared:amd64 (257.3-1) ... Selecting previously unselected package libapparmor1:amd64. Preparing to unpack .../libapparmor1_3.1.7-4_amd64.deb ... Unpacking libapparmor1:amd64 (3.1.7-4) ... 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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 ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_amd64.deb ... Unpacking python3.13 (3.13.2-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Unpacking maven-debian-helper (2.6.7) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up fastjar (2:0.98-7) ... Setting up libgraphite2-3:amd64 (1.3.14-2+b1) ... Setting up liblcms2-2:amd64 (2.16-2) ... Setting up libpixman-1-0:amd64 (0.44.0-3) ... Setting up libfastutil-java (8.5.15+dfsg-1) ... Setting up libjackson2-annotations-java (2.14.0-1) ... Setting up libdtd-parser-java (1.2-1) ... Setting up wdiff (1.2.2-7) ... Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... Setting up libpciaccess0:amd64 (0.17-3+b3) ... Setting up libslf4j-java (1.7.32-1) ... Setting up libfile-which-perl (1.27-2) ... Setting up systemd-sysv (257.3-1) ... Setting up libxau6:amd64 (1:1.0.11-1) ... Setting up libxdmcp6:amd64 (1:1.1.5-1) ... Setting up libplexus-utils2-java (3.4.2-1) ... Setting up libnpth0t64:amd64 (1.8-2) ... Setting up libkeyutils1:amd64 (1.6.3-4) ... Setting up libplexus-classworlds-java (2.7.0-1) ... Setting up libxcb1:amd64 (1.17.0-2+b1) ... Setting up libopentest4j-reporting-java (0.1.0-M1-2) ... Setting up libicu72:amd64 (72.1-6) ... Setting up libplexus-build-api-java (0.0.7-4) ... Setting up libxcb-xfixes0:amd64 (1.17.0-2+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-5) ... Setting up libjsr305-java (0.1~+svn49-12) ... Setting up bsdextrautils (2.40.4-3) ... Setting up hicolor-icon-theme (0.18-2) ... Setting up libgpg-error0:amd64 (1.51-3) ... Setting up java-common (0.76) ... Setting up libdynaloader-functions-perl (0.004-1) ... Setting up libdatrie1:amd64 (0.2.13-3+b1) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up libqdox2-java (2.0.3-1) ... Setting up libaopalliance-java (20070526-7) ... Setting up libcommons-cli-java (1.6.0-1) ... Setting up libjheaps-java (0.14-2) ... Setting up libio-pty-perl (1:1.20-1+b3) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libcommons-exec-java (1.3-2) ... Setting up libvecmath-java (1.5.2-7) ... Setting up libxcb-render0:amd64 (1.17.0-2+b1) ... Setting up libclone-perl:amd64 (0.47-1+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglvnd0:amd64 (1.7.0-1+b2) ... Setting up libgoogle-gson-java (2.10.1-1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libxcb-glx0:amd64 (1.17.0-2+b1) ... Setting up unzip (6.0-28) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libedit2:amd64 (3.1-20250104-1) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up libpicocli-java (4.6.2-2) ... Setting up libasm-java (9.7.1-1) ... Setting up libjs-jquery-ui-theme-base (1.12.1+dfsg-1.1) ... Setting up x11-common (1:7.7+24) ... Running in chroot, ignoring request. Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libtry-tiny-perl (0.32-1) ... Setting up libsensors-config (1:3.6.0-10) ... Setting up libdeflate0:amd64 (1.23-1+b1) ... Setting up perl-openssl-defaults:amd64 (7+b2) ... Setting up liblog4j1.2-java (1.2.17-11) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up libel-api-java (3.0.0-3) ... Setting up libgcrypt20:amd64 (1.11.0-7) ... Setting up xkb-data (2.42-1) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libplexus-component-annotations-java (2.1.1-1) ... Setting up libantlr4-runtime-java (4.9.2-3) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up libcom-err2:amd64 (1.47.2-1) ... Setting up file (1:5.45-3+b1) ... Setting up libjson-simple-java (2.3.0-2) ... Setting up libunivocity-parsers-java (2.9.1-1) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up liboro-java (2.0.8a-14) ... Setting up libsnappy1v5:amd64 (1.2.1-1+b1) ... Setting up libcharts4j-java (1.3-4) ... Setting up libkrb5support0:amd64 (1.21.3-4) ... Setting up libexec-maven-plugin-java (3.1.0-2) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8+b1) ... Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Mar 27 03:20:44 UTC 2026. Universal Time is now: Fri Mar 27 03:20:44 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:amd64 (1.17.0-2+b1) ... Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... Setting up libgeronimo-interceptor-3.0-spec-java (1.0.1-5) ... Setting up libcommons-collections3-java (3.2.2-3) ... Setting up libasound2-data (1.2.13-1) ... Setting up librhino-java (1.7.15-1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.13.3-1) ... Setting up libasound2t64:amd64 (1.2.13-1+b1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Setting up libjaxen-java (1.1.6-5) ... Setting up libapiguardian-java (1.1.2-1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libepoxy0:amd64 (1.5.10-2) ... Setting up libnspr4:amd64 (2:4.36-1) ... Setting up gnupg-l10n (2.2.46-1) ... Setting up libxcb-sync1:amd64 (1.17.0-2+b1) ... Setting up libjtidy-java (7+svn20110807-6) ... Setting up libjansi-java (2.4.1-2) ... Setting up libapache-pom-java (33-2) ... Setting up libavahi-common-data:amd64 (0.8-16) ... Setting up libatinject-jsr330-api-java (1.0+ds1-6) ... Setting up libdbus-1-3:amd64 (1.16.0-1) ... Setting up libwebsocket-api-java (1.1-2) ... Setting up libfribidi0:amd64 (1.0.16-1) ... Setting up libproc2-0:amd64 (2:4.0.4-7) ... Setting up libplexus-interpolation-java (1.27-1) ... Setting up libunistring5:amd64 (1.3-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libitext5-java (5.5.13.3-4) ... Setting up libpng16-16t64:amd64 (1.6.46-4) ... Setting up libxml-commons-resolver1.1-java (1.2-11) ... Setting up libxz-java (1.9-1) ... Setting up libio-html-perl (1.004-3) ... Setting up autopoint (0.23.1-1) ... Setting up binfmt-support (2.2.2-7) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Created symlink '/etc/systemd/system/multi-user.target.wants/binfmt-support.service' -> '/usr/lib/systemd/system/binfmt-support.service'. Setting up libb-hooks-op-check-perl:amd64 (0.22-3+b2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up libpcsclite1:amd64 (2.3.1-1) ... Setting up libtrove3-java-doc (3.0.3-5) ... Setting up libsensors5:amd64 (1:3.6.0-10+b1) ... Setting up libk5crypto3:amd64 (1.21.3-4) ... Setting up libactivation-java (1.2.0-2) ... Setting up libhamcrest-java (2.2-2) ... Setting up libglapi-mesa:amd64 (24.3.4-3) ... Setting up libbsh-java (2.0b4-20) ... Setting up libjsp-api-java (2.3.4-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8+b1) ... Setting up libvulkan1:amd64 (1.4.304.0-1) ... Setting up autoconf (2.72-3) ... Setting up libapfloat-java (1.14.0-2) ... Setting up libwebp7:amd64 (1.5.0-0.1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libgif7:amd64 (5.2.2-1+b1) ... Setting up libffi8:amd64 (3.4.7-1) ... 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 (2.55.2-1) ... 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 (2:4.0.4-7) ... 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 (4.20.0-2) ... 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+b5) ... Setting up libkrb5-3:amd64 (1.21.3-4) ... Setting up libwayland-egl1:amd64 (1.23.1-1) ... 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+ds1-4) ... Setting up openssl (3.4.1-1) ... 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 (1.23.1-1) ... Setting up libnet-ssleay-perl:amd64 (1.94-3) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 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 (1.14.1-2) ... 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+b1) ... Setting up libwayland-server0:amd64 (1.23.1-1) ... 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+b4) ... Setting up jarwrapper (0.80) ... Setting up libtool (2.5.4-3) ... 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 (2:3.108-1) ... 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+ds-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 (2.83.3-2) ... 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+b4) ... 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+b2) ... 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+b3) ... 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 (1.14.1-2) ... 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 (1.23.1-1) ... Setting up libhtml-parser-perl:amd64 (3.83-1+b2) ... Setting up gpgconf (2.2.46-1+b1) ... Setting up libpam-systemd:amd64 (257.3-1) ... 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-2) ... 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 (3.13.2-1) ... 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 (3.8.9-2) ... Setting up gtk-update-icon-cache (4.17.4+ds-4) ... 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 (2.55.2-1) ... Setting up openjdk-21-jre-headless:amd64 (21.0.6+7-1) ... 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 (3.13.2-1) ... Setting up libcommons-io-java (2.18.0-1) ... Setting up libdrm-radeon1:amd64 (2.4.123-1) ... Setting up libcommons-digester-java (1.8.1-7) ... Setting up libxtst6:amd64 (2:1.2.5-1) ... 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+7-1) ... 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 (2.55.2-1) ... 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 (1.2.12-4) ... 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+b2) ... Setting up libatk-bridge2.0-0t64:amd64 (2.55.2-1) ... Setting up mesa-libgallium:amd64 (24.3.4-3) ... Setting up libngs-jni:amd64 (3.0.9+dfsg-7+b2) ... 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 (24.3.4-3) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up libgl1-mesa-dri:amd64 (24.3.4-3) ... 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+b2) ... Setting up libglx-mesa0:amd64 (24.3.4-3) ... 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 (3.24.48-4) ... Setting up libgtk-3-0t64:amd64 (3.24.48-4) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libwww-perl (6.77-1) ... Setting up devscripts (2.25.2) ... 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 (3.0.0-2) ... 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 (2.40-6) ... Processing triggers for systemd (257.3-1) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian: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+7-1) ... Setting up ant (1.10.15-1) ... Setting up junit4 (4.13.2-5) ... Setting up openjdk-21-jdk-headless:amd64 (21.0.6+7-1) ... 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+7-1) ... 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: user script /srv/workspace/pbuilder/3760331/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/3760331/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/snpeff-5.2.f+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../snpeff_5.2.f+dfsg-1_source.changes dpkg-buildpackage: info: source package snpeff dpkg-buildpackage: info: source version 5.2.f+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.f+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.f+dfsg' jh_clean Duplicate specification "u=s" 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.f+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="@1739702387" +"%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.f\+dfsg/debian/maven-repo Failed to parse /build/reproducible-path/snpeff-5.2.f+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.f+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.f+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.f\+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.f\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/snpeff-5.2.f\+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+dfsg/src/main/java/org/snpeff/vcf/PedigreeEntry.java:9: warning: invalid input: '<' [WARNING] * ##PEDIGREE= [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.f+dfsg/src/main/java/org/snpeff/vcf/PedigreeEntry.java:12: warning: invalid input: '<' [WARNING] * ##PEDIGREE= [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.f+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.f+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.f+dfsg/target/snpeff-5.2.jar to /build/reproducible-path/snpeff-5.2.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+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.f+dfsg/src/main/java/org/snpeff/vcf/PedigreeEntry.java:9: warning: invalid input: '<' [WARNING] * ##PEDIGREE= [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.f+dfsg/src/main/java/org/snpeff/vcf/PedigreeEntry.java:12: warning: invalid input: '<' [WARNING] * ##PEDIGREE= [WARNING] ^ [WARNING] /build/reproducible-path/snpeff-5.2.f+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: 18.718 s [INFO] Finished at: 2026-03-27T17:21:31+14:00 [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.f\+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.f\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/snpeff-5.2.f\+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.f+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.f+dfsg/pom.xml.save with options: [INFO] --keep-pom-version --package=libsnpeff-java [INFO] --rules=/build/reproducible-path/snpeff-5.2.f+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/snpeff-5.2.f+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/snpeff-5.2.f+dfsg/debian/maven.publishedRules [INFO] Install jar for snpeff into /usr/share/java [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.461 s [INFO] Finished at: 2026-03-27T17:25:56+14:00 [INFO] ------------------------------------------------------------------------ mh_resolve_dependencies --non-interactive --offline --build -plibsnpeff-java --javadoc --base-directory=/build/reproducible-path/snpeff-5.2.f\+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. Mar 27, 2026 5:26:07 PM org.debian.maven.packager.DependenciesSolver$ToResolve resolve SEVERE: Cannot resolve dependencies in /build/reproducible-path/snpeff-5.2.f+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.f+dfsg-1_all.deb'. dpkg-deb: building package 'libsnpeff-java-doc' in '../libsnpeff-java-doc_5.2.f+dfsg-1_all.deb'. dpkg-deb: building package 'snpeff' in '../snpeff_5.2.f+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../snpeff_5.2.f+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../snpeff_5.2.f+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: user script /srv/workspace/pbuilder/3760331/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3760331/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3760331 and its subdirectories I: Current time: Fri Mar 27 17:29:29 +14 2026 I: pbuilder-time-stamp: 1774582169 + false + set +x Fri Mar 27 03:29:29 UTC 2026 I: Signing ./b2/snpeff_5.2.f+dfsg-1_amd64.buildinfo as snpeff_5.2.f+dfsg-1_amd64.buildinfo.asc Fri Mar 27 03:29:29 UTC 2026 I: Signed ./b2/snpeff_5.2.f+dfsg-1_amd64.buildinfo as ./b2/snpeff_5.2.f+dfsg-1_amd64.buildinfo.asc Fri Mar 27 03:29:29 UTC 2026 - build #2 for snpeff/trixie/amd64 on ionos15-amd64 done. Starting cleanup. All cleanup done. Fri Mar 27 03:29:29 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-12ncfKOQ, removing. /srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc: total 316 drwxr-xr-x 2 jenkins jenkins 4096 Feb 21 20:56 b1 drwxr-xr-x 2 jenkins jenkins 4096 Feb 21 21:06 b2 -rw------- 1 jenkins jenkins 305592 Feb 21 20:56 rbuildlog.UsLFtmK -rw-r--r-- 1 jenkins jenkins 2569 Feb 16 11:26 snpeff_5.2.f+dfsg-1.dsc /srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc/b1: total 155216 -rw-r--r-- 1 jenkins jenkins 301616 Feb 21 20:56 build.log -rw-r--r-- 1 jenkins jenkins 1295308 Feb 21 20:56 libsnpeff-java-doc_5.2.f+dfsg-1_all.deb -rw-r--r-- 1 jenkins jenkins 2155868 Feb 21 20:56 libsnpeff-java_5.2.f+dfsg-1_all.deb -rw-r--r-- 1 jenkins jenkins 14288 Feb 21 20:56 snpeff_5.2.f+dfsg-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2569 Feb 21 20:56 snpeff_5.2.f+dfsg-1.dsc -rw-r--r-- 1 jenkins jenkins 7244 Feb 21 20:56 snpeff_5.2.f+dfsg-1_all.deb -rw-r--r-- 1 jenkins jenkins 18677 Feb 21 20:56 snpeff_5.2.f+dfsg-1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 19559 Feb 21 20:56 snpeff_5.2.f+dfsg-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1848 Feb 21 20:56 snpeff_5.2.f+dfsg-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 1532 Feb 21 20:56 snpeff_5.2.f+dfsg-1_source.changes -rw-r--r-- 1 jenkins jenkins 154934504 Feb 21 20:56 snpeff_5.2.f+dfsg.orig.tar.xz /srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc/b2: total 155056 -rw-r--r-- 1 jenkins jenkins 303517 Feb 21 21:06 build.log -rw-r--r-- 1 jenkins jenkins 1295308 Feb 21 21:06 libsnpeff-java-doc_5.2.f+dfsg-1_all.deb -rw-r--r-- 1 jenkins jenkins 2155868 Feb 21 21:06 libsnpeff-java_5.2.f+dfsg-1_all.deb -rw-r--r-- 1 jenkins jenkins 14288 Feb 21 21:06 snpeff_5.2.f+dfsg-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2569 Feb 21 21:06 snpeff_5.2.f+dfsg-1.dsc -rw-r--r-- 1 jenkins jenkins 7244 Feb 21 21:06 snpeff_5.2.f+dfsg-1_all.deb -rw-r--r-- 1 jenkins jenkins 18686 Feb 21 21:06 snpeff_5.2.f+dfsg-1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 19568 Feb 21 21:06 snpeff_5.2.f+dfsg-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1848 Feb 21 21:06 snpeff_5.2.f+dfsg-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 1532 Feb 21 21:06 snpeff_5.2.f+dfsg-1_source.changes -rw-r--r-- 1 jenkins jenkins 154934504 Feb 21 21:06 snpeff_5.2.f+dfsg.orig.tar.xz Fri Feb 21 21:06:30 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Fri Feb 21 21:06:31 UTC 2025 I: snpeff_5.2.f+dfsg-1_amd64.changes: Format: 1.8 Date: Sun, 16 Feb 2025 11:39:47 +0100 Source: snpeff Binary: libsnpeff-java libsnpeff-java-doc snpeff Architecture: all Version: 5.2.f+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.f+dfsg-1) unstable; urgency=medium . * New upstream version 5.2.f+dfsg * Restricting autopkgtest architectures Checksums-Sha1: 7acd2980e6d979200c24083c0f01f81a5a2cfcfc 1295308 libsnpeff-java-doc_5.2.f+dfsg-1_all.deb 5789409287ba1e836af25908b751a1385f21a0d7 2155868 libsnpeff-java_5.2.f+dfsg-1_all.deb c811674fcbeb6706d508520e178630fba2f4d963 7244 snpeff_5.2.f+dfsg-1_all.deb 2a7ac8717b3d1296eadd6c1302878de1df4ba265 18677 snpeff_5.2.f+dfsg-1_amd64.buildinfo Checksums-Sha256: cec04dbd26bc736452d62fc2862ebc79d3ddd058d29522c8ff97cd930f3810aa 1295308 libsnpeff-java-doc_5.2.f+dfsg-1_all.deb 48ea93fa6752a5b2625818a4113278f5d0b43d4480cb08feacba95dcc17973ba 2155868 libsnpeff-java_5.2.f+dfsg-1_all.deb 26d97606e5416e8173cc252dcf520f0f4d900af388c9296623b84838d5e03fcc 7244 snpeff_5.2.f+dfsg-1_all.deb f3f92e9623362110d8cee4a003392f5f5394e4f484b792ecd08245d7495df880 18677 snpeff_5.2.f+dfsg-1_amd64.buildinfo Files: f683be885298bbc07a4166677a452811 1295308 doc optional libsnpeff-java-doc_5.2.f+dfsg-1_all.deb 70a15fbd05757019b593e339e61f5b65 2155868 java optional libsnpeff-java_5.2.f+dfsg-1_all.deb 6286a5cf01979f5ce9ab90177363f6bc 7244 java optional snpeff_5.2.f+dfsg-1_all.deb fae4b8c818e69e3a78d5ff6b92de6165 18677 java optional snpeff_5.2.f+dfsg-1_amd64.buildinfo Diff of the two buildlogs: -- --- b1/build.log 2025-02-21 20:56:08.473612462 +0000 +++ b2/build.log 2025-02-21 21:06:29.825423199 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Feb 21 08:07:33 -12 2025 -I: pbuilder-time-stamp: 1740168453 +I: Current time: Fri Mar 27 17:19:17 +14 2026 +I: pbuilder-time-stamp: 1774581557 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -29,52 +29,84 @@ 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/1686575/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3760331/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Mar 27 03:19 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3760331/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3760331/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='b715f5724f154bf19a933374d9143114' - 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='1686575' - PS1='# ' - PS2='> ' + INVOCATION_ID=506dee5f54c94e84a727ad95eb304a4d + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3760331 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.ssl2lMWc/pbuilderrc_yzVc --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc/b1 --logfile b1/build.log snpeff_5.2.f+dfsg-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc/pbuilderrc_Vxix --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc/b2 --logfile b2/build.log snpeff_5.2.f+dfsg-1.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) 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/1686575/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3760331/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -590,7 +622,7 @@ Get: 436 http://deb.debian.org/debian trixie/main amd64 maven-repo-helper all 1.11 [142 kB] Get: 437 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get: 438 http://deb.debian.org/debian trixie/main amd64 maven-debian-helper all 2.6.7 [108 kB] -Fetched 361 MB in 19s (19.2 MB/s) +Fetched 361 MB in 12s (29.1 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 ... 19809 files and directories currently installed.) @@ -2024,8 +2056,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Feb 21 20:15:19 UTC 2025. -Universal Time is now: Fri Feb 21 20:15:19 UTC 2025. +Local time is now: Fri Mar 27 03:20:44 UTC 2026. +Universal Time is now: Fri Mar 27 03:20:44 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:amd64 (1.17.0-2+b1) ... @@ -2595,7 +2627,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/snpeff-5.2.f+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.f+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/3760331/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3760331/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/snpeff-5.2.f+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../snpeff_5.2.f+dfsg-1_source.changes dpkg-buildpackage: info: source package snpeff dpkg-buildpackage: info: source version 5.2.f+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -2629,7 +2665,7 @@ sed "s/Gpr\.compile.*/\"$(date --utc --date="@1739702387" +"%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.f\+dfsg/debian/maven-repo -Failed to parse /build/reproducible-path/snpeff-5.2.f+dfsg/debian/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom +Failed to parse /build/reproducible-path/snpeff-5.2.f+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) @@ -2645,7 +2681,7 @@ 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.f+dfsg/debian/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom +Failed to parse /build/reproducible-path/snpeff-5.2.f+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) @@ -3343,8 +3379,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 02:19 min -[INFO] Finished at: 2025-02-21T08:21:17-12:00 +[INFO] Total time: 18.718 s +[INFO] Finished at: 2026-03-27T17:21:31+14:00 [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.f\+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.f\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/snpeff-5.2.f\+dfsg/debian/maven-repo --batch-mode test @@ -3376,75 +3412,23 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesProteinInteraction -TestCasesProteinInteraction.test_02_split_codon_base(58): Test -TestCasesProteinInteraction.test_01_split_codon_base(26): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.363 s - in org.snpeff.snpEffect.testCases.unity.TestCasesProteinInteraction -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCircular -TestCasesCircular.test_circular_01(26): Test -TestCasesCircular.test_circular_02(54): Test -TestCasesCircular.test_circular_03(83): Test -TestCasesCircular.test_circular_04(103): Test -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCircular -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse -TestCasesEffectCollapse.test_01(68): Test -TestCasesEffectCollapse.test_02(74): Test -TestCasesEffectCollapse.test_03(80): Test -TestCasesEffectCollapse.test_04(86): Test -TestCasesEffectCollapse.test_05(92): Test -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 17.139 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv -TestCasesStructuralInv.test01_invGene(214): Test -TestCasesStructuralInv.test02(249): Test -TestCasesStructuralInv.test03(266): Test -TestCasesStructuralInv.test04(283): Test -TestCasesStructuralInv.test05(300): Test -TestCasesStructuralInv.test06(317): Test -TestCasesStructuralInv.test07(334): Test -TestCasesStructuralInv.test08(352): Test -TestCasesStructuralInv.test09(370): Test -TestCasesStructuralInv.test10(387): Test -TestCasesStructuralInv.test01_invTr(231): Test -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 29.828 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray -TestCasesIntervalTree.test_01(141): Test -. -0 .................................................................................................... -10000 .................................................................................................... -20000 .................................................................................................... -30000 .................................................................................................... -40000 .................................................................................................... -50000 .................................................................................................... -60000 .................................................................................................... -70000 .................................................................................................... -80000 .................................................................................................... -90000 ................................................................................................... -TestCasesIntervalTree.test_02(164): Test -. -0 .................................................................................................... -1000 .................................................................................................... -2000 .................................................................................................... -3000 .................................................................................................... -4000 .................................................................................................... -5000 .................................................................................................... -6000 .................................................................................................... -7000 .................................................................................................... -8000 .................................................................................................... -9000 ................................................................................................... -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 24.339 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant -TestCasesIntervalVariant.test_01(36): Test -.................................................................................................... -100 .................................................................................................... -200 .................................................................................................... -300 .................................................................................................... -400 .................................................................................................... -500 .................................................................................................... -600 .................................................................................................... -700 .................................................................................................... -800 .................................................................................................... -900 .................................................................................................... -1000 [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 18.135 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron +TestCasesHgvsIntron.test_01_intron(23): Test +............................................................... +100 ............................................................ +200 ................................................................ +300 ......................................................... +400 ......................................................................................................................... +600 ......................................................................................................... +800 ....................................................... +900 .................................................................. +1000 ............................................................. +1100 .................................................................. +1200 ......................................................... +1300 ........................................................................................................... +1500 ....................................................... +1600 ............................................................... +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.988 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns TestCasesApplyIns.test_apply_variant_01(21): Test TestCasesApplyIns.test_apply_variant_02(32): Test @@ -3459,110 +3443,43 @@ TestCasesApplyIns.test_apply_variant_11(159): Test TestCasesApplyIns.test_apply_variant_12(178): Test TestCasesApplyIns.test_apply_variant_13(192): Test -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 33.908 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed -TestCasesApplyMixed.test_apply_variant_04_shorter(116): Test -TestCasesApplyMixed.test_apply_variant_06_longer(169): Test -TestCasesApplyMixed.test_apply_variant_06_shorter(186): Test -TestCasesApplyMixed.test_apply_variant_04_longer(98): Test -TestCasesApplyMixed.test_apply_variant_09_longer(259): Test -TestCasesApplyMixed.test_apply_variant_01_shorter(32): Test -TestCasesApplyMixed.test_apply_variant_08_shorter(248): Test -TestCasesApplyMixed.test_apply_variant_02_longer(42): Test -TestCasesApplyMixed.test_apply_variant_07_longer(203): Test -TestCasesApplyMixed.test_apply_variant_03_shorter(81): Test -TestCasesApplyMixed.test_apply_variant_05_shorter(152): Test -TestCasesApplyMixed.test_apply_variant_05_longer(134): Test -TestCasesApplyMixed.test_apply_variant_07_shorter(220): Test -TestCasesApplyMixed.test_apply_variant_03_longer(64): Test -TestCasesApplyMixed.test_apply_variant_08_longer(237): Test -TestCasesApplyMixed.test_apply_variant_02_shorter(53): Test -TestCasesApplyMixed.test_apply_variant_09_shorter(270): Test -TestCasesApplyMixed.test_apply_variant_01_longer(22): Test -[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 56.664 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVcf -[INFO] Tests run: 44, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 166.836 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVcf -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIubString -TestCasesIubString.test_01(29): Test -TestCasesIubString.test_02(39): Test -TestCasesIubString.test_03(49): Test -TestCasesIubString.test_04(68): Test -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIubString -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSeekableReader -TestCasesSeekableReader.test_00(59): Test -TestCasesSeekableReader.test_01(71): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.248 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSeekableReader -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVariantDecompose -TestCasesVariantDecompose.test_00_decomposeVariant_01(35): Test -TestCasesVariantDecompose.test_00_decomposeVariant_02(45): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantDecompose -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvs -TestCasesHgvs.test_01(56): Test -TestCasesHgvs.test_02(69): Test -TestCasesHgvs.test_03(83): Test -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.682 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvs -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesReactome -TestCasesReactome.test_01(32): Test -TestCasesReactome.test_02(56): Test -TestCasesReactome.test_03(86): Test -TestCasesReactome.test_04(114): Test -TestCasesReactome.test_05(142): Test -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.snpeff.snpEffect.testCases.unity.TestCasesReactome -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp -TestCasesApplyMnp.test_apply_variant_01(22): Test -TestCasesApplyMnp.test_apply_variant_02(33): Test -TestCasesApplyMnp.test_apply_variant_03(44): Test -TestCasesApplyMnp.test_apply_variant_04(61): Test -TestCasesApplyMnp.test_apply_variant_05(79): Test -TestCasesApplyMnp.test_apply_variant_06(97): Test -TestCasesApplyMnp.test_apply_variant_07(115): Test -TestCasesApplyMnp.test_apply_variant_08(133): Test -TestCasesApplyMnp.test_apply_variant_09(144): Test -TestCasesApplyMnp.test_apply_variant_10(155): Test -TestCasesApplyMnp.test_apply_variant_11(176): Test -TestCasesApplyMnp.test_apply_variant_12(197): Test -TestCasesApplyMnp.test_apply_variant_13(219): Test -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 53.411 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment -TestCasesVariantRealignment.test_07_savant(203): Test -TestCasesVariantRealignment.test_01(56): Test -TestCasesVariantRealignment.test_02(82): Test -TestCasesVariantRealignment.test_03(105): Test -TestCasesVariantRealignment.test_05_savant(157): Test -TestCasesVariantRealignment.test_04_Intron(131): Test -TestCasesVariantRealignment.test_06_savant(194): Test -TestCasesVariantRealignment.test_09_reallyLongRealign(224): Test -TestCasesVariantRealignment.test_05_savant_opposite(174): Test -TestCasesVariantRealignment.test_08_reallyLongRealign(213): Test -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 30.976 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesNmers -TestCasesNmers.test_03_Nmers(33): Test -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.019 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNmers -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequenceByte -TestCasesDnaSequenceByte.test_01(18): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.143 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequenceByte -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntStats -TestCasesIntStats.test_01(31): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.684 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntStats +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.561 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesMarkerUtils +TestCasesMarkerUtils.test_collapseZeroGap(107): Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.087 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMarkerUtils +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite +TestCasesSpliceSite.test_01(34): Test +.................................................................................................... +100 .................................................................................................... +200 .................................................................................................... +300 .................................................................................................... +400 .................................................................................................... +500 .................................................................................................... +600 .................................................................................................... +700 .................................................................................................... +800 .................................................................................................... +900 .................................................................................................... +1000 +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.612 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant +TestCasesIntervalVariant.test_01(36): Test +.................................................................................................... +100 .................................................................................................... +200 .................................................................................................... +300 .................................................................................................... +400 .................................................................................................... +500 .................................................................................................... +600 .................................................................................................... +700 .................................................................................................... +800 .................................................................................................... +900 .................................................................................................... +1000 [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.088 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesBuild TestCasesBuild.test_01_chromoNamesDoNotMatch_Gff(18): Test TestCasesBuild.test_02_chromoNamesDoNotMatch_GffFasta(54): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 10.455 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBuild -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup -TestCasesStructuralDup.test01_dupGene(157): Test -TestCasesStructuralDup.test02(194): Test -TestCasesStructuralDup.test03(212): Test -TestCasesStructuralDup.test04(229): Test -TestCasesStructuralDup.test05(247): Test -TestCasesStructuralDup.test06(265): Test -TestCasesStructuralDup.test07(286): Test -TestCasesStructuralDup.test08(303): Test -TestCasesStructuralDup.test09(324): Test -TestCasesStructuralDup.test10(345): Test -TestCasesStructuralDup.test01_dupTr(175): Test -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 34.965 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesMnps -TestCasesMnps.test_01(187): Test +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.993 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBuild +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon +TestCasesHgvsExon.test_01_coding(27): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... @@ -3574,22 +3491,24 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 78.937 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMnps +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.881 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv +TestCasesStructuralInv.test01_invGene(214): Test +TestCasesStructuralInv.test02(249): Test +TestCasesStructuralInv.test03(266): Test +TestCasesStructuralInv.test04(283): Test +TestCasesStructuralInv.test05(300): Test +TestCasesStructuralInv.test06(317): Test +TestCasesStructuralInv.test07(334): Test +TestCasesStructuralInv.test08(352): Test +TestCasesStructuralInv.test09(370): Test +TestCasesStructuralInv.test10(387): Test +TestCasesStructuralInv.test01_invTr(231): Test +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.476 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCytoBands -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.004 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCytoBands -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable -TestCasesCodonTable.test_01(28): Test -TestCasesCodonTable.test_02(59): Test -00:09:48 Codon table 'Blepharisma_Macronuclear' for genome 'test_ctab' -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.152 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse -TestCasesAnnParse.test_EffectType(29): Test -TestCasesAnnParse.test_old_SO(45): Test -TestCasesAnnParse.test_old_SO_vcf(53): Test -TestCasesAnnParse.testCase_tfbs_ablation(71): Test -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 12.849 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCds -TestCasesCds.test_CdsPos(35): Test +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCytoBands +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIns +TestCasesIns.test_01(38): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... @@ -3601,10 +3520,32 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -TestCasesCds.test_cdsStartEnd_1(73): Test -TestCasesCds.test_cdsStartEnd_2(96): Test -WARNING_EXON_NOT_FOUND: WARNING: Cannot find first exonic position after 101 for transcript 'tr1' -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.9 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCds +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.376 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIns +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment +TestCasesVariantRealignment.test_07_savant(203): Test +TestCasesVariantRealignment.test_01(56): Test +TestCasesVariantRealignment.test_02(82): Test +TestCasesVariantRealignment.test_03(105): Test +TestCasesVariantRealignment.test_05_savant(157): Test +TestCasesVariantRealignment.test_04_Intron(131): Test +TestCasesVariantRealignment.test_06_savant(194): Test +TestCasesVariantRealignment.test_09_reallyLongRealign(224): Test +TestCasesVariantRealignment.test_05_savant_opposite(174): Test +TestCasesVariantRealignment.test_08_reallyLongRealign(213): Test +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.921 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesReactome +TestCasesReactome.test_01(32): Test +TestCasesReactome.test_02(56): Test +TestCasesReactome.test_03(86): Test +TestCasesReactome.test_04(114): Test +TestCasesReactome.test_05(142): Test +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.snpeff.snpEffect.testCases.unity.TestCasesReactome +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIubString +TestCasesIubString.test_01(29): Test +TestCasesIubString.test_02(39): Test +TestCasesIubString.test_03(49): Test +TestCasesIubString.test_04(68): Test +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIubString [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos TestCasesFileIndexChrPos.test_00_short_file(79): Test .................................................................................................... @@ -3654,28 +3595,107 @@ 700 .................................................................................................... 800 .................................................................................................... 900 ................................................................................................... -[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 181.85 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence -TestCasesDnaNSequence.test_02_long_replaceBase(243): Test -TestCasesDnaNSequence.test_13_reverseWc(253): Test -TestCasesDnaNSequence.test_02_long_getBases(233): Test -TestCasesDnaNSequence.test_01_short_getBases(194): Test -TestCasesDnaNSequence.test_01_short(175): Test -TestCasesDnaNSequence.test_02_long(214): Test -TestCasesDnaNSequence.test_02_long_getBase(223): Test -TestCasesDnaNSequence.test_01_short_getBase(184): Test -TestCasesDnaNSequence.test_01_short_replaceBase(204): Test -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 21.984 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSpliceRegion -TestCasesSpliceRegion.test_01(33): Test -..................[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.141 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceRegion -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesBinomial -TestCasesBinomial.test_01(86): Test -TestCasesBinomial.test_02(191): Test -TestCasesBinomial.test_03(299): Test -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBinomial -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon -TestCasesHgvsExon.test_01_coding(27): Test +[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 27.097 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvs +TestCasesHgvs.test_01(56): Test +TestCasesHgvs.test_02(69): Test +TestCasesHgvs.test_03(83): Test +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.348 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvs +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray +TestCasesIntervalTree.test_01(141): Test +. +0 .................................................................................................... +10000 .................................................................................................... +20000 .................................................................................................... +30000 .................................................................................................... +40000 .................................................................................................... +50000 .................................................................................................... +60000 .................................................................................................... +70000 .................................................................................................... +80000 .................................................................................................... +90000 ................................................................................................... +TestCasesIntervalTree.test_02(164): Test +. +0 .................................................................................................... +1000 .................................................................................................... +2000 .................................................................................................... +3000 .................................................................................................... +4000 .................................................................................................... +5000 .................................................................................................... +6000 .................................................................................................... +7000 .................................................................................................... +8000 .................................................................................................... +9000 ................................................................................................... +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.437 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed +TestCasesApplyMixed.test_apply_variant_04_shorter(116): Test +TestCasesApplyMixed.test_apply_variant_06_longer(169): Test +TestCasesApplyMixed.test_apply_variant_06_shorter(186): Test +TestCasesApplyMixed.test_apply_variant_04_longer(98): Test +TestCasesApplyMixed.test_apply_variant_09_longer(259): Test +TestCasesApplyMixed.test_apply_variant_01_shorter(32): Test +TestCasesApplyMixed.test_apply_variant_08_shorter(248): Test +TestCasesApplyMixed.test_apply_variant_02_longer(42): Test +TestCasesApplyMixed.test_apply_variant_07_longer(203): Test +TestCasesApplyMixed.test_apply_variant_03_shorter(81): Test +TestCasesApplyMixed.test_apply_variant_05_shorter(152): Test +TestCasesApplyMixed.test_apply_variant_05_longer(134): Test +TestCasesApplyMixed.test_apply_variant_07_shorter(220): Test +TestCasesApplyMixed.test_apply_variant_03_longer(64): Test +TestCasesApplyMixed.test_apply_variant_08_longer(237): Test +TestCasesApplyMixed.test_apply_variant_02_shorter(53): Test +TestCasesApplyMixed.test_apply_variant_09_shorter(270): Test +TestCasesApplyMixed.test_apply_variant_01_longer(22): Test +[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.24 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDel +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.956 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDel +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp +TestCasesApplyMnp.test_apply_variant_01(22): Test +TestCasesApplyMnp.test_apply_variant_02(33): Test +TestCasesApplyMnp.test_apply_variant_03(44): Test +TestCasesApplyMnp.test_apply_variant_04(61): Test +TestCasesApplyMnp.test_apply_variant_05(79): Test +TestCasesApplyMnp.test_apply_variant_06(97): Test +TestCasesApplyMnp.test_apply_variant_07(115): Test +TestCasesApplyMnp.test_apply_variant_08(133): Test +TestCasesApplyMnp.test_apply_variant_09(144): Test +TestCasesApplyMnp.test_apply_variant_10(155): Test +TestCasesApplyMnp.test_apply_variant_11(176): Test +TestCasesApplyMnp.test_apply_variant_12(197): Test +TestCasesApplyMnp.test_apply_variant_13(219): Test +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.967 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesProteinInteraction +TestCasesProteinInteraction.test_02_split_codon_base(58): Test +TestCasesProteinInteraction.test_01_split_codon_base(26): Test +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.93 s - in org.snpeff.snpEffect.testCases.unity.TestCasesProteinInteraction +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree +TestCasesIntervalTree.test_01(141): Test +. +0 .................................................................................................... +10000 .................................................................................................... +20000 .................................................................................................... +30000 .................................................................................................... +40000 .................................................................................................... +50000 .................................................................................................... +60000 .................................................................................................... +70000 .................................................................................................... +80000 .................................................................................................... +90000 ................................................................................................... +TestCasesIntervalTree.test_02(164): Test +. +0 .................................................................................................... +1000 .................................................................................................... +2000 .................................................................................................... +3000 .................................................................................................... +4000 .................................................................................................... +5000 .................................................................................................... +6000 .................................................................................................... +7000 .................................................................................................... +8000 .................................................................................................... +9000 ................................................................................................... +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.711 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSnps +TestCasesSnps.test_01(43): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... @@ -3687,35 +3707,31 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 12.151 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage -TestCasesCochranArmitage.test_01(18): Test -TestCasesCochranArmitage.test_02(28): Test -TestCasesCochranArmitage.test_03(37): Test -TestCasesCochranArmitage.test_04(46): Test -TestCasesCochranArmitage.test_05(57): Test -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.125 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSnps +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList +TestCasesGenePvalueList.test_01(28): Test +TestCasesGenePvalueList.test_02(46): Test +TestCasesGenePvalueList.test_03(64): Test +TestCasesGenePvalueList.test_04(82): Test +TestCasesGenePvalueList.test_05(111): Test +TestCasesGenePvalueList.test_06(129): Test +TestCasesGenePvalueList.test_07(155): Test +TestCasesGenePvalueList.test_08(187): Test +TestCasesGenePvalueList.test_09(209): Test +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.719 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsProtDup TestCasesHgvsProtDup.test_01(31): Test TestCasesHgvsProtDup.test_02(70): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.716 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsProtDup -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel -TestCasesApplyDel.test_apply_variant_01(21): Test -TestCasesApplyDel.test_apply_variant_02(31): Test -TestCasesApplyDel.test_apply_variant_03(42): Test -TestCasesApplyDel.test_apply_variant_04(59): Test -TestCasesApplyDel.test_apply_variant_05(77): Test -TestCasesApplyDel.test_apply_variant_06(95): Test -TestCasesApplyDel.test_apply_variant_07(113): Test -TestCasesApplyDel.test_apply_variant_08(131): Test -TestCasesApplyDel.test_apply_variant_09(142): Test -TestCasesApplyDel.test_apply_variant_10(153): Test -TestCasesApplyDel.test_apply_variant_11(176): Test -TestCasesApplyDel.test_apply_variant_12(199): Test -TestCasesApplyDel.test_apply_variant_13(223): Test -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 78.14 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSnps -TestCasesSnps.test_01(43): Test +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.977 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsProtDup +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesAlign +TestCasesAlign.test_01(23): Test +TestCasesAlign.test_02(112): Test +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAlign +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesNmers +TestCasesNmers.test_03_Nmers(33): Test +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.005 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNmers +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCds +TestCasesCds.test_CdsPos(35): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... @@ -3727,75 +3743,28 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 16.676 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSnps -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap -TestCasesDnaOverlap.test_10_overlap(332): Test -TestCasesDnaOverlap.test_07_overlap(297): Test -TestCasesDnaOverlap.test_12_overlap(356): Test -TestCasesDnaOverlap.test_09_overlap(320): Test -TestCasesDnaOverlap.test_17_overlap_rand(459): Test - -Overlap random test: -.................................................................................................... -100 .................................................................................................... -200 .................................................................................................... -300 .................................................................................................... -400 .................................................................................................... -500 .................................................................................................... -600 .................................................................................................... -700 .................................................................................................... -800 .................................................................................................... -900 ................................................................................................... -Done. -TestCasesDnaOverlap.test_15_DnaCoder_copy_1(380): Test -.........TestCasesDnaOverlap.test_11_overlap(344): Test -TestCasesDnaOverlap.test_08_overlap(308): Test -TestCasesDnaOverlap.test_18_DnaCoder_score_rand(474): Test -DnaCoder.score test: -.................................................................................................... -100 .................................................................................................... -200 .................................................................................................... -300 .................................................................................................... -400 .................................................................................................... -500 .................................................................................................... -600 .................................................................................................... -700 .................................................................................................... -800 .................................................................................................... -900 ...................................................................................................Done. -TestCasesDnaOverlap.test_13_overlap(368): Test -TestCasesDnaOverlap.test_19_score_threshold_rand(493): Test - -Score (threshold) random test: -.................................................................................................... -100 .................................................................................................... -200 .................................................................................................... -300 .................................................................................................... -400 .................................................................................................... -500 .................................................................................................... -600 .................................................................................................... -700 .................................................................................................... -800 .................................................................................................... -900 ................................................................................................... -Done. -TestCasesDnaOverlap.test_16_DnaCoder_copy_2(438): Test -.................................................................................[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 107.549 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron -TestCasesHgvsIntron.test_01_intron(23): Test -............................................................... -100 ............................................................ -200 ................................................................ -300 ......................................................... -400 ......................................................................................................................... -600 ......................................................................................................... -800 ....................................................... -900 .................................................................. -1000 ............................................................. -1100 .................................................................. -1200 ......................................................... -1300 ........................................................................................................... -1500 ....................................................... -1600 ............................................................... -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 12.942 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron +TestCasesCds.test_cdsStartEnd_1(73): Test +TestCasesCds.test_cdsStartEnd_2(96): Test +WARNING_EXON_NOT_FOUND: WARNING: Cannot find first exonic position after 101 for transcript 'tr1' +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.544 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCds +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVcf +[INFO] Tests run: 44, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 20.952 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVcf +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup +TestCasesStructuralDup.test01_dupGene(157): Test +TestCasesStructuralDup.test02(194): Test +TestCasesStructuralDup.test03(212): Test +TestCasesStructuralDup.test04(229): Test +TestCasesStructuralDup.test05(247): Test +TestCasesStructuralDup.test06(265): Test +TestCasesStructuralDup.test07(286): Test +TestCasesStructuralDup.test08(303): Test +TestCasesStructuralDup.test09(324): Test +TestCasesStructuralDup.test10(345): Test +TestCasesStructuralDup.test01_dupTr(175): Test +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.255 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesFasta +TestCasesFasta.test_01(23): Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.448 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFasta [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup TestCasesHgvsDnaDup.test_01(31): Test TestCasesHgvsDnaDup.test_02(54): Test @@ -3808,7 +3777,94 @@ TestCasesHgvsDnaDup.test_09(247): Test TestCasesHgvsDnaDup.test_10(277): Test TestCasesHgvsDnaDup.test_11(308): Test -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 43.931 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.034 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable +TestCasesCodonTable.test_01(28): Test +TestCasesCodonTable.test_02(59): Test +00:02:11 Codon table 'Blepharisma_Macronuclear' for genome 'test_ctab' +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.453 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp +TestCasesApplySnp.test_apply_variant_01(21): Test +TestCasesApplySnp.test_apply_variant_02(31): Test +TestCasesApplySnp.test_apply_variant_04(41): Test +TestCasesApplySnp.test_apply_variant_05(59): Test +TestCasesApplySnp.test_apply_variant_06(77): Test +TestCasesApplySnp.test_apply_variant_08(95): Test +TestCasesApplySnp.test_apply_variant_09(106): Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.415 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest +TestCasesFisherExactTest.test_05_fisher(313): Test +TestCasesFisherExactTest.test_0(97): Test +TestCasesFisherExactTest.test_03_fisher(103): Test +TestCasesFisherExactTest.test_06_fisher_vs_chi2(352): Test +TestCasesFisherExactTest.test_04_fisher(208): Test +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer +TestCasesSequenceIndexer.test_01(69): Test +TestCasesSequenceIndexer.test_02(100): Test +TestCasesSequenceIndexer.test_03(125): Test +TestCasesSequenceIndexer.test_04(152): Test +TestCasesSequenceIndexer.test_05(182): Test +TestCasesSequenceIndexer.test_06(207): Test +TestCasesSequenceIndexer.test_07(225): Test +TestCasesSequenceIndexer.test_08(247): Test +TestCasesSequenceIndexer.test_09(267): Test +TestCasesSequenceIndexer.test_10(287): Test +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.848 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntStats +TestCasesIntStats.test_01(31): Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.484 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntStats +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse +TestCasesEffectCollapse.test_01(68): Test +TestCasesEffectCollapse.test_02(74): Test +TestCasesEffectCollapse.test_03(80): Test +TestCasesEffectCollapse.test_04(86): Test +TestCasesEffectCollapse.test_05(92): Test +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.359 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesOverlap +TestCasesOverlap.test_binSeq_01(26): Test +TestCasesOverlap.test_binSeq_02(32): Test +TestCasesOverlap.test_binSeq_03(38): Test +TestCasesOverlap.test_binSeq_04(44): Test +TestCasesOverlap.test_binSeq_05(50): Test +TestCasesOverlap.test_binSeq_06(56): Test +TestCasesOverlap.test_binSeq_07(62): Test +TestCasesOverlap.test_binSeq_08(68): Test +TestCasesOverlap.test_binSeq_09(74): Test +TestCasesOverlap.test_binSeq_10(80): Test +TestCasesOverlap.test_binSeq_11(87): Test +TestCasesOverlap.test_binSeq_12(94): Test +TestCasesOverlap.test_binSeq_13(100): Test +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.snpeff.snpEffect.testCases.unity.TestCasesOverlap +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations +TestCasesStructuralTranslocations.test02_2_nonFs(532): Test +TestCasesStructuralTranslocations.test01_0_nonFs(286): Test +TestCasesStructuralTranslocations.test01_0(260): Test +TestCasesStructuralTranslocations.test01_1(314): Test +TestCasesStructuralTranslocations.test01_2(341): Test +TestCasesStructuralTranslocations.test01_3(368): Test +TestCasesStructuralTranslocations.test02_0(423): Test +TestCasesStructuralTranslocations.test02_1(450): Test +TestCasesStructuralTranslocations.test02_2(505): Test +TestCasesStructuralTranslocations.test02_3(560): Test +TestCasesStructuralTranslocations.test03_0(587): Test +TestCasesStructuralTranslocations.test03_1(614): Test +TestCasesStructuralTranslocations.test03_2(669): Test +TestCasesStructuralTranslocations.test03_3(724): Test +TestCasesStructuralTranslocations.test04_0(751): Test +TestCasesStructuralTranslocations.test04_1(806): Test +TestCasesStructuralTranslocations.test04_2(833): Test +TestCasesStructuralTranslocations.test04_3(860): Test +TestCasesStructuralTranslocations.test05_2_one_gene(951): Test +TestCasesStructuralTranslocations.test04_3_nonFs(887): Test +TestCasesStructuralTranslocations.test03_1_nonFs(641): Test +TestCasesStructuralTranslocations.test05_1_one_gene(919): Test +TestCasesStructuralTranslocations.test03_2_nonFs(696): Test +TestCasesStructuralTranslocations.test01_3_noFs(395): Test +TestCasesStructuralTranslocations.test04_0_nonFs(778): Test +TestCasesStructuralTranslocations.test02_1_nonFs(477): Test +TestCasesStructuralTranslocations.test06_no_gene(981): Test +[INFO] Tests run: 27, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 12.892 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervals TestCasesIntervals.test_00(140): Test TestCasesIntervals.test_01(152): Test @@ -3827,46 +3883,21 @@ TestCasesIntervals.test_07_05(362): Test TestCasesIntervals.test_08_02(413): Test TestCasesIntervals.test_08_03(438): Test -[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 81.952 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervals -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesOverlap -TestCasesOverlap.test_binSeq_01(26): Test -TestCasesOverlap.test_binSeq_02(32): Test -TestCasesOverlap.test_binSeq_03(38): Test -TestCasesOverlap.test_binSeq_04(44): Test -TestCasesOverlap.test_binSeq_05(50): Test -TestCasesOverlap.test_binSeq_06(56): Test -TestCasesOverlap.test_binSeq_07(62): Test -TestCasesOverlap.test_binSeq_08(68): Test -TestCasesOverlap.test_binSeq_09(74): Test -TestCasesOverlap.test_binSeq_10(80): Test -TestCasesOverlap.test_binSeq_11(87): Test -TestCasesOverlap.test_binSeq_12(94): Test -TestCasesOverlap.test_binSeq_13(100): Test -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.snpeff.snpEffect.testCases.unity.TestCasesOverlap -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntergenic -TestCasesIntergenic.test_01(30): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.8 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntergenic +[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.298 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervals [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDupNegative TestCasesHgvsDnaDupNegative.test_01(34): Test TestCasesHgvsDnaDupNegative.test_02(61): Test TestCasesHgvsDnaDupNegative.test_03(91): Test TestCasesHgvsDnaDupNegative.test_04(122): Test -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 19.439 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDupNegative -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel -TestCasesStructuralDel.test02(249): Test -TestCasesStructuralDel.test03(266): Test -TestCasesStructuralDel.test04(283): Test -TestCasesStructuralDel.test05(302): Test -TestCasesStructuralDel.test06(321): Test -TestCasesStructuralDel.test07(342): Test -TestCasesStructuralDel.test08(360): Test -TestCasesStructuralDel.test09(379): Test -TestCasesStructuralDel.test10(398): Test -TestCasesStructuralDel.test01_delTr(230): Test -TestCasesStructuralDel.test01_delGene(212): Test -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 54.288 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDels -TestCasesDels.test_01(138): Test +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.821 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDupNegative +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap +TestCasesDnaOverlap.test_10_overlap(332): Test +TestCasesDnaOverlap.test_07_overlap(297): Test +TestCasesDnaOverlap.test_12_overlap(356): Test +TestCasesDnaOverlap.test_09_overlap(320): Test +TestCasesDnaOverlap.test_17_overlap_rand(459): Test + +Overlap random test: .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... @@ -3876,11 +3907,13 @@ 600 .................................................................................................... 700 .................................................................................................... 800 .................................................................................................... -900 .................................................................................................... -1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 26.492 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDels -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIns -TestCasesIns.test_01(38): Test +900 ................................................................................................... +Done. +TestCasesDnaOverlap.test_15_DnaCoder_copy_1(380): Test +.........TestCasesDnaOverlap.test_11_overlap(344): Test +TestCasesDnaOverlap.test_08_overlap(308): Test +TestCasesDnaOverlap.test_18_DnaCoder_score_rand(474): Test +DnaCoder.score test: .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... @@ -3890,36 +3923,29 @@ 600 .................................................................................................... 700 .................................................................................................... 800 .................................................................................................... -900 .................................................................................................... -1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 14.196 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIns -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp -TestCasesApplySnp.test_apply_variant_01(21): Test -TestCasesApplySnp.test_apply_variant_02(31): Test -TestCasesApplySnp.test_apply_variant_04(41): Test -TestCasesApplySnp.test_apply_variant_05(59): Test -TestCasesApplySnp.test_apply_variant_06(77): Test -TestCasesApplySnp.test_apply_variant_08(95): Test -TestCasesApplySnp.test_apply_variant_09(106): Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 32.392 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesChiSquare -TestCasesChiSquare.test_1(26): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.snpeff.snpEffect.testCases.unity.TestCasesChiSquare -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDel -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 10.452 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDel -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesFasta -TestCasesFasta.test_01(23): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.984 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFasta -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesGenotypeVector -TestCasesGenotypeVector.test_01(23): Test -TestCasesGenotypeVector.test_02(48): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenotypeVector -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesAlign -TestCasesAlign.test_01(23): Test -TestCasesAlign.test_02(112): Test -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAlign -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesGenomicSequences -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenomicSequences +900 ...................................................................................................Done. +TestCasesDnaOverlap.test_13_overlap(368): Test +TestCasesDnaOverlap.test_19_score_threshold_rand(493): Test + +Score (threshold) random test: +.................................................................................................... +100 .................................................................................................... +200 .................................................................................................... +300 .................................................................................................... +400 .................................................................................................... +500 .................................................................................................... +600 .................................................................................................... +700 .................................................................................................... +800 .................................................................................................... +900 ................................................................................................... +Done. +TestCasesDnaOverlap.test_16_DnaCoder_copy_2(438): Test +.................................................................................[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 13.909 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesBinomial +TestCasesBinomial.test_01(86): Test +TestCasesBinomial.test_02(191): Test +TestCasesBinomial.test_03(299): Test +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBinomial [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence TestCasesDnaSequence.test_02_long_replaceBase(277): Test TestCasesDnaSequence.test_05_fastqReader(320): Test @@ -3933,37 +3959,10 @@ TestCasesDnaSequence.test_01_short_getBase(218): Test TestCasesDnaSequence.test_04_Pe(287): Test TestCasesDnaSequence.test_01_short_replaceBase(238): Test -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 69.143 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite -TestCasesSpliceSite.test_01(34): Test -.................................................................................................... -100 .................................................................................................... -200 .................................................................................................... -300 .................................................................................................... -400 .................................................................................................... -500 .................................................................................................... -600 .................................................................................................... -700 .................................................................................................... -800 .................................................................................................... -900 .................................................................................................... -1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.222 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHypergeometric -TestCasesHypergeometric.test_0(77): Test -TestCasesHypergeometric.test_01_hyper(83): Test -TestCasesHypergeometric.test_02_hyper(202): Test -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHypergeometric -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList -TestCasesGenePvalueList.test_01(28): Test -TestCasesGenePvalueList.test_02(46): Test -TestCasesGenePvalueList.test_03(64): Test -TestCasesGenePvalueList.test_04(82): Test -TestCasesGenePvalueList.test_05(111): Test -TestCasesGenePvalueList.test_06(129): Test -TestCasesGenePvalueList.test_07(155): Test -TestCasesGenePvalueList.test_08(187): Test -TestCasesGenePvalueList.test_09(209): Test -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 28.663 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.845 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSpliceRegion +TestCasesSpliceRegion.test_01(33): Test +..................[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.49 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceRegion [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesNextProt TestCasesNextProt.test_10_nextprotFactory(205): Test TestCasesNextProt.test_09_nextprotFactory(182): Test @@ -3984,87 +3983,68 @@ TestCasesNextProt.test_05_nextprotFactory(98): Test TestCasesNextProt.test_02_nextprotFactory(42): Test TestCasesNextProt.test_13_nextprotFactory(277): Test -[INFO] Tests run: 19, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.172 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNextProt -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer -TestCasesSequenceIndexer.test_01(69): Test -TestCasesSequenceIndexer.test_02(100): Test -TestCasesSequenceIndexer.test_03(125): Test -TestCasesSequenceIndexer.test_04(152): Test -TestCasesSequenceIndexer.test_05(182): Test -TestCasesSequenceIndexer.test_06(207): Test -TestCasesSequenceIndexer.test_07(225): Test -TestCasesSequenceIndexer.test_08(247): Test -TestCasesSequenceIndexer.test_09(267): Test -TestCasesSequenceIndexer.test_10(287): Test -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 47.26 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse2 -TestCasesEffectCollapse2.test_01(40): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.916 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse2 -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesMarkerUtils -TestCasesMarkerUtils.test_collapseZeroGap(107): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.444 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMarkerUtils -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations -TestCasesStructuralTranslocations.test02_2_nonFs(532): Test -TestCasesStructuralTranslocations.test01_0_nonFs(286): Test -TestCasesStructuralTranslocations.test01_0(260): Test -TestCasesStructuralTranslocations.test01_1(314): Test -TestCasesStructuralTranslocations.test01_2(341): Test -TestCasesStructuralTranslocations.test01_3(368): Test -TestCasesStructuralTranslocations.test02_0(423): Test -TestCasesStructuralTranslocations.test02_1(450): Test -TestCasesStructuralTranslocations.test02_2(505): Test -TestCasesStructuralTranslocations.test02_3(560): Test -TestCasesStructuralTranslocations.test03_0(587): Test -TestCasesStructuralTranslocations.test03_1(614): Test -TestCasesStructuralTranslocations.test03_2(669): Test -TestCasesStructuralTranslocations.test03_3(724): Test -TestCasesStructuralTranslocations.test04_0(751): Test -TestCasesStructuralTranslocations.test04_1(806): Test -TestCasesStructuralTranslocations.test04_2(833): Test -TestCasesStructuralTranslocations.test04_3(860): Test -TestCasesStructuralTranslocations.test05_2_one_gene(951): Test -TestCasesStructuralTranslocations.test04_3_nonFs(887): Test -TestCasesStructuralTranslocations.test03_1_nonFs(641): Test -TestCasesStructuralTranslocations.test05_1_one_gene(919): Test -TestCasesStructuralTranslocations.test03_2_nonFs(696): Test -TestCasesStructuralTranslocations.test01_3_noFs(395): Test -TestCasesStructuralTranslocations.test04_0_nonFs(778): Test -TestCasesStructuralTranslocations.test02_1_nonFs(477): Test -TestCasesStructuralTranslocations.test06_no_gene(981): Test -[INFO] Tests run: 27, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 124.73 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree -TestCasesIntervalTree.test_01(141): Test -. -0 .................................................................................................... -10000 .................................................................................................... -20000 .................................................................................................... -30000 .................................................................................................... -40000 .................................................................................................... -50000 .................................................................................................... -60000 .................................................................................................... -70000 .................................................................................................... -80000 .................................................................................................... -90000 ................................................................................................... -TestCasesIntervalTree.test_02(164): Test -. -0 .................................................................................................... -1000 .................................................................................................... -2000 .................................................................................................... -3000 .................................................................................................... -4000 .................................................................................................... -5000 .................................................................................................... -6000 .................................................................................................... -7000 .................................................................................................... -8000 .................................................................................................... -9000 ................................................................................................... -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 46.336 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest -TestCasesFisherExactTest.test_05_fisher(313): Test -TestCasesFisherExactTest.test_0(97): Test -TestCasesFisherExactTest.test_03_fisher(103): Test -TestCasesFisherExactTest.test_06_fisher_vs_chi2(352): Test -TestCasesFisherExactTest.test_04_fisher(208): Test -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest +[INFO] Tests run: 19, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNextProt +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel +TestCasesApplyDel.test_apply_variant_01(21): Test +TestCasesApplyDel.test_apply_variant_02(31): Test +TestCasesApplyDel.test_apply_variant_03(42): Test +TestCasesApplyDel.test_apply_variant_04(59): Test +TestCasesApplyDel.test_apply_variant_05(77): Test +TestCasesApplyDel.test_apply_variant_06(95): Test +TestCasesApplyDel.test_apply_variant_07(113): Test +TestCasesApplyDel.test_apply_variant_08(131): Test +TestCasesApplyDel.test_apply_variant_09(142): Test +TestCasesApplyDel.test_apply_variant_10(153): Test +TestCasesApplyDel.test_apply_variant_11(176): Test +TestCasesApplyDel.test_apply_variant_12(199): Test +TestCasesApplyDel.test_apply_variant_13(223): Test +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.341 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDels +TestCasesDels.test_01(138): Test +.................................................................................................... +100 .................................................................................................... +200 .................................................................................................... +300 .................................................................................................... +400 .................................................................................................... +500 .................................................................................................... +600 .................................................................................................... +700 .................................................................................................... +800 .................................................................................................... +900 .................................................................................................... +1000 +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.157 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDels +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesMnps +TestCasesMnps.test_01(187): Test +.................................................................................................... +100 .................................................................................................... +200 .................................................................................................... +300 .................................................................................................... +400 .................................................................................................... +500 .................................................................................................... +600 .................................................................................................... +700 .................................................................................................... +800 .................................................................................................... +900 .................................................................................................... +1000 +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 12.375 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMnps +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesGenotypeVector +TestCasesGenotypeVector.test_01(23): Test +TestCasesGenotypeVector.test_02(48): Test +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenotypeVector +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage +TestCasesCochranArmitage.test_01(18): Test +TestCasesCochranArmitage.test_02(28): Test +TestCasesCochranArmitage.test_03(37): Test +TestCasesCochranArmitage.test_04(46): Test +TestCasesCochranArmitage.test_05(57): Test +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSeekableReader +TestCasesSeekableReader.test_00(59): Test +TestCasesSeekableReader.test_01(71): Test +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.019 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSeekableReader +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesChiSquare +TestCasesChiSquare.test_1(26): Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesChiSquare [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeOri TestCasesIntervalTree.test_01(141): Test . @@ -4090,11 +4070,67 @@ 7000 .................................................................................................... 8000 .................................................................................................... 9000 ................................................................................................... -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 39.87 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeOri +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.557 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeOri +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesGenomicSequences +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenomicSequences +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse +TestCasesAnnParse.test_EffectType(29): Test +TestCasesAnnParse.test_old_SO(45): Test +TestCasesAnnParse.test_old_SO_vcf(53): Test +TestCasesAnnParse.testCase_tfbs_ablation(71): Test +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.806 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesJaspar TestCasesJaspar.test_01(22): Test TestCasesJaspar.test_02(56): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 11.479 s - in org.snpeff.snpEffect.testCases.unity.TestCasesJaspar +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.026 s - in org.snpeff.snpEffect.testCases.unity.TestCasesJaspar +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse2 +TestCasesEffectCollapse2.test_01(40): Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.457 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse2 +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVariantDecompose +TestCasesVariantDecompose.test_00_decomposeVariant_01(35): Test +TestCasesVariantDecompose.test_00_decomposeVariant_02(45): Test +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantDecompose +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCircular +TestCasesCircular.test_circular_01(26): Test +TestCasesCircular.test_circular_02(54): Test +TestCasesCircular.test_circular_03(83): Test +TestCasesCircular.test_circular_04(103): Test +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCircular +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence +TestCasesDnaNSequence.test_02_long_replaceBase(243): Test +TestCasesDnaNSequence.test_13_reverseWc(253): Test +TestCasesDnaNSequence.test_02_long_getBases(233): Test +TestCasesDnaNSequence.test_01_short_getBases(194): Test +TestCasesDnaNSequence.test_01_short(175): Test +TestCasesDnaNSequence.test_02_long(214): Test +TestCasesDnaNSequence.test_02_long_getBase(223): Test +TestCasesDnaNSequence.test_01_short_getBase(184): Test +TestCasesDnaNSequence.test_01_short_replaceBase(204): Test +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.136 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHypergeometric +TestCasesHypergeometric.test_0(77): Test +TestCasesHypergeometric.test_01_hyper(83): Test +TestCasesHypergeometric.test_02_hyper(202): Test +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHypergeometric +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntergenic +TestCasesIntergenic.test_01(30): Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.466 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntergenic +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequenceByte +TestCasesDnaSequenceByte.test_01(18): Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.104 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequenceByte +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel +TestCasesStructuralDel.test02(249): Test +TestCasesStructuralDel.test03(266): Test +TestCasesStructuralDel.test04(283): Test +TestCasesStructuralDel.test05(302): Test +TestCasesStructuralDel.test06(321): Test +TestCasesStructuralDel.test07(342): Test +TestCasesStructuralDel.test08(360): Test +TestCasesStructuralDel.test09(379): Test +TestCasesStructuralDel.test10(398): Test +TestCasesStructuralDel.test01_delTr(230): Test +TestCasesStructuralDel.test01_delGene(212): Test +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.953 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel [INFO] [INFO] Results: [INFO] @@ -4103,8 +4139,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 29:28 min -[INFO] Finished at: 2025-02-21T08:50:56-12:00 +[INFO] Total time: 04:22 min +[INFO] Finished at: 2026-03-27T17:25:55+14:00 [INFO] ------------------------------------------------------------------------ create-stamp debian/debhelper-build-stamp dh_prep @@ -4128,11 +4164,11 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 5.696 s -[INFO] Finished at: 2025-02-21T08:51:17-12:00 +[INFO] Total time: 0.461 s +[INFO] Finished at: 2026-03-27T17:25:56+14:00 [INFO] ------------------------------------------------------------------------ mh_resolve_dependencies --non-interactive --offline --build -plibsnpeff-java --javadoc --base-directory=/build/reproducible-path/snpeff-5.2.f\+dfsg --non-explore -Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom +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) @@ -4148,7 +4184,7 @@ 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 +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) @@ -4164,7 +4200,7 @@ 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 +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) @@ -4180,7 +4216,7 @@ at org.debian.maven.packager.DependenciesSolver.solveDependencies(DependenciesSolver.java:237) at org.debian.maven.packager.DependenciesSolver.main(DependenciesSolver.java:922) -Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom +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) @@ -4204,7 +4240,7 @@ [error] Package libbiojava6-java (6.1.0+dfsg) is already installed and contains a possible match, but I cannot resolve library org.biojava:biojava-structure:jar:6.x in it. [error] Please check manually that the library is up to date, otherwise it may be necessary to package version 6.x in Debian. -Feb 21, 2025 8:51:45 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve +Mar 27, 2026 5:26:07 PM org.debian.maven.packager.DependenciesSolver$ToResolve resolve SEVERE: Cannot resolve dependencies in /build/reproducible-path/snpeff-5.2.f+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 @@ -4346,8 +4382,8 @@ 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-doc' in '../libsnpeff-java-doc_5.2.f+dfsg-1_all.deb'. dpkg-deb: building package 'libsnpeff-java' in '../libsnpeff-java_5.2.f+dfsg-1_all.deb'. +dpkg-deb: building package 'libsnpeff-java-doc' in '../libsnpeff-java-doc_5.2.f+dfsg-1_all.deb'. dpkg-deb: building package 'snpeff' in '../snpeff_5.2.f+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../snpeff_5.2.f+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../snpeff_5.2.f+dfsg-1_amd64.changes @@ -4356,12 +4392,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3760331/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3760331/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/1686575 and its subdirectories -I: Current time: Fri Feb 21 08:56:07 -12 2025 -I: pbuilder-time-stamp: 1740171367 +I: removing directory /srv/workspace/pbuilder/3760331 and its subdirectories +I: Current time: Fri Mar 27 17:29:29 +14 2026 +I: pbuilder-time-stamp: 1774582169 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/snpeff_5.2.f+dfsg-1.diff: 87.5% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/snpeff_5.2.f+dfsg-1.diff.gz b2/build.log: 85.3% -- replaced with stdout Compressing the 1st log... b1/build.log: 85.5% -- replaced with stdout Fri Feb 21 21:06:32 UTC 2025 I: diffoscope 288 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_snpeff_trixie_amd64_1740171992 + touch /var/log/reproducible-builds/diffoscope_stamp_snpeff_trixie_amd64_1740171992 + RESULT=0 + systemd-run '--description=diffoscope on snpeff/5.2.f+dfsg-1 in trixie/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_23-47642 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc --run-session -c jenkins-reproducible-trixie-diffoscope-f52aa427-bed0-43d2-a4ef-1abb766a9cd4 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc/dbd-tmp-WiSQPY6 ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc/snpeff_5.2.f+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc/snpeff_5.2.f+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc/snpeff_5.2.f+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc/b1/snpeff_5.2.f+dfsg-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc/b2/snpeff_5.2.f+dfsg-1_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_23-47642.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc/snpeff_5.2.f+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc/snpeff_5.2.f+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc/snpeff_5.2.f+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc/b1/snpeff_5.2.f+dfsg-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.ssl2lMWc/b2/snpeff_5.2.f+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 diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 223ms CPU time consumed: 224ms __ __ ___ _ __ _ __ ___ / _|/ _| / __| '_ \| '_ \ / _ \ |_| |_ \__ \ | | | |_) | __/ _| _| |___/_| |_| .__/ \___|_| |_| |_| Fri Feb 21 21:06:33 UTC 2025 I: diffoscope 288 found no differences in the changes files, and a .buildinfo file also exists. Fri Feb 21 21:06:33 UTC 2025 I: snpeff from trixie built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-02-21 21:06:34] INFO: Starting at 2025-02-21 21:06:34.243460 [2025-02-21 21:06:34] INFO: Generating the pages of 1 package(s) [2025-02-21 21:06:34] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/snpeff_5.2.e+dfsg-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/snpeff_5.2.e+dfsg-1.diff.gz is missing [2025-02-21 21:06:34] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/snpeff_5.2.f+dfsg-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/snpeff_5.2.f+dfsg-1.diff.gz is missing [2025-02-21 21:06:34] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/amd64/snpeff didn't produce a buildlog, even though it has been built. [2025-02-21 21:06:34] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/armhf/snpeff_5.1+d+dfsg-3.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/armhf/snpeff_5.1+d+dfsg-3.diff.gz is missing [2025-02-21 21:06:34] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/i386/snpeff_5.1+d+dfsg-3.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/i386/snpeff_5.1+d+dfsg-3.diff.gz is missing [2025-02-21 21:06:34] INFO: Finished at 2025-02-21 21:06:34.585037, took: 0:00:00.341581 Fri Feb 21 21:06:34 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/amd64/snpeff.html Fri Feb 21 21:06:34 UTC 2025 I: Submitting .buildinfo files to external archives: Fri Feb 21 21:06:34 UTC 2025 I: Submitting 20K b1/snpeff_5.2.f+dfsg-1_amd64.buildinfo.asc https://buildinfo.debian.net/2a7ac8717b3d1296eadd6c1302878de1df4ba265/snpeff_5.2.f+dfsg-1_all Fri Feb 21 21:06:42 UTC 2025 I: Submitting 20K b2/snpeff_5.2.f+dfsg-1_amd64.buildinfo.asc https://buildinfo.debian.net/f33e42645467dc07986be76ae4403e8d96c92553/snpeff_5.2.f+dfsg-1_all Fri Feb 21 21:06:49 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Feb 21 21:06:49 UTC 2025 I: Done submitting .buildinfo files. Fri Feb 21 21:06:49 UTC 2025 I: Removing signed snpeff_5.2.f+dfsg-1_amd64.buildinfo.asc files: removed './b1/snpeff_5.2.f+dfsg-1_amd64.buildinfo.asc' removed './b2/snpeff_5.2.f+dfsg-1_amd64.buildinfo.asc' 1740172009 amd64 trixie snpeff Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/snpeff_5.2.f+dfsg-1.rbuild.log: 84.8% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/snpeff_5.2.f+dfsg-1.rbuild.log.gz [2025-02-21 21:06:49] INFO: Starting at 2025-02-21 21:06:49.858523 [2025-02-21 21:06:49] INFO: Generating the pages of 1 package(s) [2025-02-21 21:06:50] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/snpeff_5.2.e+dfsg-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/snpeff_5.2.e+dfsg-1.diff.gz is missing [2025-02-21 21:06:50] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/snpeff_5.2.f+dfsg-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/snpeff_5.2.f+dfsg-1.diff.gz is missing [2025-02-21 21:06:50] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/armhf/snpeff_5.1+d+dfsg-3.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/armhf/snpeff_5.1+d+dfsg-3.diff.gz is missing [2025-02-21 21:06:50] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/i386/snpeff_5.1+d+dfsg-3.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/i386/snpeff_5.1+d+dfsg-3.diff.gz is missing [2025-02-21 21:06:50] INFO: Finished at 2025-02-21 21:06:50.402974, took: 0:00:00.544462 All cleanup done. Fri Feb 21 21:06:50 UTC 2025 - total duration: 0h 59m 14s. Fri Feb 21 21:06:50 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-NOqrNVVC, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 59min 31.061s CPU time consumed: 14.241s