Thu May 2 06:54:19 UTC 2024 I: starting to build snpsift/trixie/amd64 on jenkins on '2024-05-02 06:54' Thu May 2 06:54:19 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_24/18959/console.log Thu May 2 06:54:19 UTC 2024 I: Downloading source for trixie/snpsift=5.1+dfsg2-2 --2024-05-02 06:54:20-- http://deb.debian.org/debian/pool/main/s/snpsift/snpsift_5.1%2bdfsg2-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2422 (2.4K) [text/prs.lines.tag] Saving to: ‘snpsift_5.1+dfsg2-2.dsc’ 0K .. 100% 353M=0s 2024-05-02 06:54:20 (353 MB/s) - ‘snpsift_5.1+dfsg2-2.dsc’ saved [2422/2422] Thu May 2 06:54:20 UTC 2024 I: snpsift_5.1+dfsg2-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: snpsift Binary: libsnpsift-java, snpsift, libsnpsift-java-doc Architecture: all Version: 5.1+dfsg2-2 Maintainer: Debian Med Packaging Team Uploaders: Pierre Gruet Homepage: https://pcingola.github.io/SnpEff/ss_introduction/ Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/snpsift Vcs-Git: https://salsa.debian.org/med-team/snpsift.git Testsuite: autopkgtest Testsuite-Triggers: default-jdk-headless, junit5 Build-Depends: debhelper-compat (= 13), antlr4, antlr4-doc, javahelper, junit5, libcommons-math3-java, libcommons-math3-java-doc, libhtsjdk-java, libhtsjdk-java-doc, libmaven-assembly-plugin-java, libmaven-javadoc-plugin-java, libsnpeff-java, libsnpeff-java-doc, libtrove3-java, libtrove3-java-doc, maven-debian-helper Package-List: libsnpsift-java deb java optional arch=all libsnpsift-java-doc deb doc optional arch=all snpsift deb java optional arch=all Checksums-Sha1: b7a653e15f66d63b5c6db8d42554367364aaca68 6454944 snpsift_5.1+dfsg2.orig.tar.xz a015a8ff5ff4367d650a9faea7ae802279f7ebd6 7048 snpsift_5.1+dfsg2-2.debian.tar.xz Checksums-Sha256: ac6d61b9e4656d3f2134ffdd08f497741622d14aa41767c117cf1d6d60b01556 6454944 snpsift_5.1+dfsg2.orig.tar.xz 2a7168509b64ab6d9bbd4a590c8243dfa863be7df3c87b2226bd2f0d700b307e 7048 snpsift_5.1+dfsg2-2.debian.tar.xz Files: 68f4fc412cb0c3e8f6209c7b9af7f0e4 6454944 snpsift_5.1+dfsg2.orig.tar.xz 60661e5d20708742de85740cbb63d777 7048 snpsift_5.1+dfsg2-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEM8soQxPpC9J9y0UjYAMWptwndHYFAmIbgAAACgkQYAMWptwn dHbtjA//R/HpUyZ45Iyngd3eGm/RYKN3PcKdJapdtxoDxp4wxZ64e1qksJtISguJ TA0saGSrAQ6ZlNMfcg3DzoZNzc8JKkYMwuv0gfjWNWElTlAkxqHLB2cYsXnKfQ33 jYU3z5F5daMLqkyc5cgmmBFKo+xqyRZT+0PWqjlEzlLKOkaFb1h8xSvFq92hmMrk PbyBlTRbbnooUSp3eFdwmPKzc9u6fJXbFO/s7SpQb9PghCl+ghKv50oVvZkqAmqh BthF6KN/MTrGkCoVTzcsZi0vb1b5U3yOMgLIR0FoQji3W8dQMdL8Ade4Y37hbrDm pmgkwj/1iIyLapBY78aAMNYT2QZfbc7lHWouSl6f7XhpfRhywUlitoA5gTVLGARG yHxUfsQe7AMk8Sh4cN5peCdY989/axtm1bVKvEuAsBuwSV74SrPOv9dxUgeu3Kwq 3VAgMu+yLj5kZXD/4/xhbBMJEWkaGerbqh8HP4c2rAn5r/oubnp6rQK1kcPI3ftW PT5bAppBfC/E8HJhOz+DfespZ784JbvvFBP3d8rVXOzzOl2LaaN1yN1R+GkQAHvF MUEZZFAIlLU1nYUKuvHGcWsNW+hJ/2i0gqPsaZHod+nSnxTPVv4SpwNd6yRpU9Hg FOE+tra2VjHi36KHL256ctH0gmuz/6RsW/5DCf21hof5w+r3+tE= =GElC -----END PGP SIGNATURE----- Thu May 2 06:54:20 UTC 2024 I: Checking whether the package is not for us Thu May 2 06:54:20 UTC 2024 I: Starting 1st build on remote node ionos15-amd64.debian.net. Thu May 2 06:54:20 UTC 2024 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Thu May 2 06:59:02 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Jun 4 01:17:23 -12 2025 I: pbuilder-time-stamp: 1749043043 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 [snpsift_5.1+dfsg2-2.dsc] I: copying [./snpsift_5.1+dfsg2.orig.tar.xz] I: copying [./snpsift_5.1+dfsg2-2.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Feb 27 13:43:28 2022 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./snpsift_5.1+dfsg2-2.dsc: no acceptable signature found dpkg-source: info: extracting snpsift in snpsift-5.1+dfsg2 dpkg-source: info: unpacking snpsift_5.1+dfsg2.orig.tar.xz dpkg-source: info: unpacking snpsift_5.1+dfsg2-2.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 omit_unused_junit_classes.patch dpkg-source: info: applying Debian_specific_config_file.patch dpkg-source: info: applying test_scope_for_junit.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1402880/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='7a702385c7e3413cbeef42b66529e811' 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='1402880' 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.DuYiYMto/pbuilderrc_eBbV --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.DuYiYMto/b1 --logfile b1/build.log snpsift_5.1+dfsg2-2.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 27 17:46 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1402880/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), antlr4, antlr4-doc, javahelper, junit5, libcommons-math3-java, libcommons-math3-java-doc, libhtsjdk-java, libhtsjdk-java-doc, libmaven-assembly-plugin-java, libmaven-javadoc-plugin-java, libsnpeff-java, libsnpeff-java-doc, libtrove3-java, libtrove3-java-doc, maven-debian-helper dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19699 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 antlr4; however: Package antlr4 is not installed. pbuilder-satisfydepends-dummy depends on antlr4-doc; however: Package antlr4-doc is not installed. pbuilder-satisfydepends-dummy depends on javahelper; however: Package javahelper is not installed. pbuilder-satisfydepends-dummy depends on junit5; however: Package junit5 is not installed. pbuilder-satisfydepends-dummy depends on libcommons-math3-java; however: Package libcommons-math3-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-math3-java-doc; however: Package libcommons-math3-java-doc is not installed. pbuilder-satisfydepends-dummy depends on libhtsjdk-java; however: Package libhtsjdk-java is not installed. pbuilder-satisfydepends-dummy depends on libhtsjdk-java-doc; however: Package libhtsjdk-java-doc is not installed. pbuilder-satisfydepends-dummy depends on libmaven-assembly-plugin-java; however: Package libmaven-assembly-plugin-java is not installed. pbuilder-satisfydepends-dummy depends on libmaven-javadoc-plugin-java; however: Package libmaven-javadoc-plugin-java is not installed. pbuilder-satisfydepends-dummy depends on libsnpeff-java; however: Package libsnpeff-java is not installed. pbuilder-satisfydepends-dummy depends on libsnpeff-java-doc; however: Package libsnpeff-java-doc is not installed. pbuilder-satisfydepends-dummy depends on libtrove3-java; however: Package libtrove3-java is not installed. pbuilder-satisfydepends-dummy depends on libtrove3-java-doc; however: Package libtrove3-java-doc is not installed. pbuilder-satisfydepends-dummy depends on maven-debian-helper; however: Package maven-debian-helper 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: antlr4-doc{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} default-jdk-doc{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} dwz{a} file{a} fonts-mathjax{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gnupg-utils{a} gpg{a} gpg-agent{a} gpg-wks-client{a} gpg-wks-server{a} gpgconf{a} gpgsm{a} groff-base{a} intltool-debian{a} java-wrappers{a} libaopalliance-java{a} libapache-pom-java{a} libarchive-zip-perl{a} libasm-java{a} libassuan0{a} libatinject-jsr330-api-java{a} libbatik-java{a} libcdi-api-java{a} libcommons-beanutils-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-compress-java{a} libcommons-configuration-java{a} libcommons-digester-java{a} libcommons-io-java{a} libcommons-jexl2-java{a} libcommons-lang-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-math3-java{a} libcommons-math3-java-doc{a} libcommons-parent-java{a} libcommons-text-java{a} libcommons-validator-java{a} libdebhelper-perl{a} libdom4j-java{a} libdoxia-core-java{a} libdoxia-java{a} libdoxia-sitetools-java{a} libelf1t64{a} liberror-prone-java{a} libfile-stripnondeterminism-perl{a} libfontbox2-java{a} libfop-java{a} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libguava-java{a} libguice-java{a} libhtsjdk-java{a} libhtsjdk-java-doc{a} libhttpclient-java{a} libhttpcore-java{a} libicu72{a} libitext1-java{a} libjaxen-java{a} libjaxp1.3-java{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-jquery-ui-theme-base{a} libjs-mathjax{a} libjsr305-java{a} libksba8{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1t64{a} libmaven-archiver-java{a} libmaven-artifact-transfer-java{a} libmaven-assembly-plugin-java{a} libmaven-common-artifact-filters-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-reporting-api-java{a} libmaven-resolver-java{a} libmaven-shared-io-java{a} libmaven-shared-utils-java{a} libmaven3-core-java{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libmjson-java{a} libncbi-ngs3{a} libncbi-vdb3{a} libngs-java{a} libngs-jni{a} libnpth0t64{a} liboro-java{a} libpipeline1{a} libplexus-archiver-java{a} libplexus-build-api-java{a} libplexus-cipher-java{a} libplexus-classworlds-java{a} libplexus-component-annotations-java{a} libplexus-container-default-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} libqdox-java{a} libqdox2-java{a} libreadline8t64{a} librhino-java{a} libsasl2-2{a} libsasl2-modules-db{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libsnpeff-java-doc{a} libsub-override-perl{a} libtool{a} libtrove3-java{a} libtrove3-java-doc{a} libuchardet0{a} libvelocity-tools-java{a} libwagon-provider-api-java{a} libxalan2-java{a} libxbean-reflect-java{a} libxerces2-java{a} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxmlgraphics-commons-java{a} libxz-java{a} m4{a} man-db{a} ncbi-vdb-data{a} openjdk-17-doc{a} pinentry-curses{a} po-debconf{a} readline-common{a} sensible-utils{a} sgml-base{a} unzip{a} velocity{a} The following packages are RECOMMENDED but will NOT be installed: curl icc-profiles-free javascript-common libarchive-cpio-perl libbiojava6-java-doc libjansi-java libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libsaxon-java lynx wget 0 packages upgraded, 163 newly installed, 0 to remove and 0 not upgraded. Need to get 105 MB of archives. After unpacking 649 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: antlr4 but it is not installable Depends: javahelper but it is not installable Depends: junit5 but it is not installable Depends: libsnpeff-java but it is not installable Depends: maven-debian-helper but it is not installable The following actions will resolve these dependencies: Remove the following packages: 1) libdb5.3 [5.3.28+dfsg2-4+b1 (now)] 2) libssl3 [3.1.5-1 (now)] Install the following packages: 3) ant [1.10.14-1 (testing)] 4) ant-optional [1.10.14-1 (testing)] 5) antlr4 [4.9.2-2 (testing)] 6) binfmt-support [2.2.2-7 (testing)] 7) ca-certificates [20240203 (testing)] 8) ca-certificates-java [20240118 (testing)] 9) dctrl-tools [2.24-3+b1 (testing)] 10) default-jdk-headless [2:1.17-75 (testing)] 11) default-jre-headless [2:1.17-75 (testing)] 12) devscripts [2.23.7 (testing)] 13) fastjar [2:0.98-7 (testing)] 14) jarwrapper [0.79 (testing)] 15) java-common [0.75 (testing)] 16) javahelper [0.79 (testing)] 17) junit4 [4.13.2-4 (testing)] 18) junit5 [5.10.1-1 (testing)] 19) libactivation-java [1.2.0-2 (testing)] 20) libantlr3-runtime-java [3.5.3-2 (testing)] 21) libantlr4-runtime-java [4.9.2-2 (testing)] 22) libapfloat-java [1.13.0-1 (testing)] 23) libapiguardian-java [1.1.2-1 (testing)] 24) libargs4j-java [2.33-2 (testing)] 25) libb-hooks-op-check-perl [0.22-2+b2 (testing)] 26) libbiojava6-java [6.1.0+dfsg-4 (testing)] 27) libbsh-java [2.0b4-20 (testing)] 28) libcharts4j-java [1.3-4 (testing)] 29) libciftools-java [6.0.0-1 (testing)] 30) libclass-method-modifiers-perl [2.15-1 (testing)] 31) libclass-xsaccessor-perl [1.19-4+b2 (testing)] 32) libclone-perl [0.46-1+b1 (testing)] 33) libcodemodel-java [2.6+jaxb2.3.0.1-10.1 (testing)] 34) libcommons-exec-java [1.3-2 (testing)] 35) libcommons-math-java [2.2-8 (testing)] 36) libdb5.3t64 [5.3.28+dfsg2-7 (testing)] 37) libdevel-callchecker-perl [0.008-2+b1 (testing)] 38) libdistlib-java [1.0-4 (testing)] 39) libdtd-parser-java [1.2-1 (testing)] 40) libdynaloader-functions-perl [0.003-3 (testing)] 41) libel-api-java [3.0.0-3 (testing)] 42) libencode-locale-perl [1.05-3 (testing)] 43) libexec-maven-plugin-java [3.1.0-2 (testing)] 44) libexpat1 [2.6.2-1 (testing)] 45) libfastinfoset-java [1.2.12-3 (testing)] 46) libfastutil-java [8.5.12+dfsg-1 (testing)] 47) libfile-dirlist-perl [0.05-3 (testing)] 48) libfile-homedir-perl [1.006-2 (testing)] 49) libfile-listing-perl [6.16-1 (testing)] 50) libfile-touch-perl [0.12-2 (testing)] 51) libfile-which-perl [1.27-2 (testing)] 52) libfreemarker-java [2.3.32-2 (testing)] 53) libgoogle-gson-java [2.10.1-1 (testing)] 54) libhamcrest-java [2.2-2 (testing)] 55) libhtml-parser-perl [3.81-1+b1 (testing)] 56) libhtml-tagset-perl [3.24-1 (testing)] 57) libhtml-tree-perl [5.07-3 (testing)] 58) libhttp-cookies-perl [6.11-1 (testing)] 59) libhttp-date-perl [6.06-1 (testing)] 60) libhttp-message-perl [6.45-1 (testing)] 61) libhttp-negotiate-perl [6.01-2 (testing)] 62) libicu4j-java [73.2-1 (testing)] 63) libimport-into-perl [1.002005-2 (testing)] 64) libinchi1 [1.03+dfsg-4+b2 (testing)] 65) libio-html-perl [1.004-3 (testing)] 66) libio-pty-perl [1:1.20-1 (testing)] 67) libio-socket-ssl-perl [2.085-1 (testing)] 68) libipc-run-perl [20231003.0-2 (testing)] 69) libistack-commons-java [3.0.6-5 (testing)] 70) libitext5-java [5.5.13.3-4 (testing)] 71) libjackson2-annotations-java [2.14.0-1 (testing)] 72) libjackson2-core-java [2.14.1-1 (testing)] 73) libjackson2-databind-java [2.14.0-1 (testing)] 74) libjansi-java [2.4.1-2 (testing)] 75) libjaxb-api-java [2.3.1-1 (testing)] 76) libjaxb-java [2.3.0.1-10.1 (testing)] 77) libjetty9-java [9.4.54-1 (testing)] 78) libjgrapht-java [1.5.2-1 (testing)] 79) libjgraphx-java [2.1.0.7-3 (testing)] 80) libjheaps-java [0.14-2 (testing)] 81) libjmol-java [14.32.83+dfsg-3 (testing)] 82) libjni-inchi-java [0.8+dfsg-7 (testing)] 83) libjni-inchi-jni [0.8+dfsg-7 (testing)] 84) libjpeg62-turbo [1:2.1.5-3 (testing)] 85) libjson-simple-java [2.3.0-1 (testing)] 86) libjsonp-java [1.1.2-4 (testing)] 87) libjsoup-java [1.15.3-1 (testing)] 88) libjsp-api-java [2.3.4-3 (testing)] 89) libjtidy-java [7+svn20110807-5 (testing)] 90) liblcms2-2 [2.14-2+b1 (testing)] 91) liblog4j1.2-java [1.2.17-11 (testing)] 92) liblwp-mediatypes-perl [6.04-2 (testing)] 93) liblwp-protocol-https-perl [6.14-1 (testing)] 94) libmaven-clean-plugin-java [3.2.0-2 (testing)] 95) libmaven-compiler-plugin-java [3.10.1-2 (testing)] 96) libmaven-plugin-tools-java [3.7.1-1 (testing)] 97) libmaven-reporting-exec-java [1.6.0-1 (testing)] 98) libmaven-reporting-impl-java [3.2.0-2 (testing)] 99) libmaven-resources-plugin-java [3.3.0-1 (testing)] 100) libmaven-shared-incremental-java [1.1-4 (testing)] 101) libmaven-site-plugin-java [3.12.1-2 (testing)] 102) libmmtf-java [1.0.11-1 (testing)] 103) libmodule-runtime-perl [0.016-2 (testing)] 104) libmoo-perl [2.005005-1 (testing)] 105) libmsgpack-java [0.9.6-1 (testing)] 106) libnaga-java [3.0+svn80-5 (testing)] 107) libnet-http-perl [6.23-1 (testing)] 108) libnet-ssleay-perl [1.94-1 (testing)] 109) libnspr4 [2:4.35-1.1+b1 (testing)] 110) libnss3 [2:3.99-1 (testing)] 111) libopentest4j-java [1.2.0-4 (testing)] 112) libopentest4j-reporting-java [0.1.0-M1-2 (testing)] 113) libparams-classify-perl [0.015-2+b2 (testing)] 114) libpcsclite1 [2.0.1-1+b1 (testing)] 115) libpicocli-java [4.6.2-2 (testing)] 116) libplexus-ant-factory-java [1.0~alpha2.1-4 (testing)] 117) libplexus-bsh-factory-java [1.0~alpha7-5 (testing)] 118) libplexus-compiler-java [2.12.1-2 (testing)] 119) libplexus-container-default1.5-java [2.1.1-1 (testing)] 120) libproc2-0 [2:4.0.4-4 (testing)] 121) libpython3-stdlib [3.11.8-1 (testing)] 122) libpython3.11-minimal [3.11.9-1 (testing)] 123) libpython3.11-stdlib [3.11.9-1 (testing)] 124) librelaxng-datatype-java [1.0+ds1-3.1 (testing)] 125) librngom-java [2.3.0.1-10.1 (testing)] 126) librole-tiny-perl [2.002004-1 (testing)] 127) libservlet-api-java [4.0.1-2 (testing)] 128) libsnpeff-java [5.2.b+dfsg-1 (testing)] 129) libssl3t64 [3.2.1-3 (testing)] 130) libstax-ex-java [1.7.8-3 (testing)] 131) libstreambuffer-java [1.5.4-1.1 (testing)] 132) libstringtemplate4-java [4.0.8-2.1 (testing)] 133) libsub-quote-perl [2.006008-1 (testing)] 134) libsurefire-java [2.22.3-2 (testing)] 135) libtimedate-perl [2.3300-2 (testing)] 136) libtreelayout-java [1.0.3-2 (testing)] 137) libtry-tiny-perl [0.31-2 (testing)] 138) libtxw2-java [2.3.0.1-10.1 (testing)] 139) libunivocity-parsers-java [2.9.1-1 (testing)] 140) liburi-perl [5.28-1 (testing)] 141) libvecmath-java [1.5.2-7 (testing)] 142) libwagon-file-java [3.5.3-1 (testing)] 143) libwagon-http-java [3.5.3-1 (testing)] 144) libwagon-http-shaded-java [3.5.3-1 (testing)] 145) libwebsocket-api-java [1.1-2 (testing)] 146) libwww-perl [6.77-1 (testing)] 147) libwww-robotrules-perl [6.02-1 (testing)] 148) libxml2-utils [2.9.14+dfsg-1.3+b3 (testing)] 149) libxsom-java [2.3.0.1-10.1 (testing)] 150) maven [3.8.7-2 (testing)] 151) maven-debian-helper [2.6.4 (testing)] 152) maven-repo-helper [1.11 (testing)] 153) media-types [10.1.0 (testing)] 154) netbase [6.4 (testing)] 155) openjdk-17-jdk-headless [17.0.11+9-1 (testing)] 156) openjdk-17-jre-headless [17.0.11+9-1 (testing)] 157) openssl [3.2.1-3 (testing)] 158) patchutils [0.4.2-1 (testing)] 159) perl-openssl-defaults [7+b2 (testing)] 160) procps [2:4.0.4-4 (testing)] 161) python3 [3.11.8-1 (testing)] 162) python3-minimal [3.11.8-1 (testing)] 163) python3.11 [3.11.9-1 (testing)] 164) python3.11-minimal [3.11.9-1 (testing)] 165) tzdata [2024a-3 (testing)] 166) wdiff [1.2.2-6 (testing)] The following NEW packages will be installed: ant{a} ant-optional{a} antlr4{a} antlr4-doc{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} binfmt-support{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} dctrl-tools{a} debhelper{a} default-jdk-doc{a} default-jdk-headless{a} default-jre-headless{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} dwz{a} fastjar{a} file{a} fonts-mathjax{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gnupg-utils{a} gpg{a} gpg-agent{a} gpg-wks-client{a} gpg-wks-server{a} gpgconf{a} gpgsm{a} groff-base{a} intltool-debian{a} jarwrapper{a} java-common{a} java-wrappers{a} javahelper{a} junit4{a} junit5{a} libactivation-java{a} libantlr3-runtime-java{a} libantlr4-runtime-java{a} libaopalliance-java{a} libapache-pom-java{a} libapfloat-java{a} libapiguardian-java{a} libarchive-zip-perl{a} libargs4j-java{a} libasm-java{a} libassuan0{a} libatinject-jsr330-api-java{a} libb-hooks-op-check-perl{a} libbatik-java{a} libbiojava6-java{a} libbsh-java{a} libcdi-api-java{a} libcharts4j-java{a} libciftools-java{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcodemodel-java{a} libcommons-beanutils-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-compress-java{a} libcommons-configuration-java{a} libcommons-digester-java{a} libcommons-exec-java{a} libcommons-io-java{a} libcommons-jexl2-java{a} libcommons-lang-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-math-java{a} libcommons-math3-java{a} libcommons-math3-java-doc{a} libcommons-parent-java{a} libcommons-text-java{a} libcommons-validator-java{a} libdb5.3t64{a} libdebhelper-perl{a} libdevel-callchecker-perl{a} libdistlib-java{a} libdom4j-java{a} libdoxia-core-java{a} libdoxia-java{a} libdoxia-sitetools-java{a} libdtd-parser-java{a} libdynaloader-functions-perl{a} libel-api-java{a} libelf1t64{a} libencode-locale-perl{a} liberror-prone-java{a} libexec-maven-plugin-java{a} libexpat1{a} libfastinfoset-java{a} libfastutil-java{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} libfontbox2-java{a} libfop-java{a} libfreemarker-java{a} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libgoogle-gson-java{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhtsjdk-java{a} libhtsjdk-java-doc{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libhttpclient-java{a} libhttpcore-java{a} libicu4j-java{a} libicu72{a} libimport-into-perl{a} libinchi1{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libistack-commons-java{a} libitext1-java{a} libitext5-java{a} libjackson2-annotations-java{a} libjackson2-core-java{a} libjackson2-databind-java{a} libjansi-java{a} libjaxb-api-java{a} libjaxb-java{a} libjaxen-java{a} libjaxp1.3-java{a} 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} libjs-mathjax{a} libjson-simple-java{a} libjsonp-java{a} libjsoup-java{a} libjsp-api-java{a} libjsr305-java{a} libjtidy-java{a} libksba8{a} liblcms2-2{a} libldap-2.5-0{a} 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-reporting-impl-java{a} libmaven-resolver-java{a} libmaven-resources-plugin-java{a} libmaven-shared-incremental-java{a} libmaven-shared-io-java{a} libmaven-shared-utils-java{a} libmaven-site-plugin-java{a} libmaven3-core-java{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libmjson-java{a} libmmtf-java{a} libmodule-runtime-perl{a} libmoo-perl{a} libmsgpack-java{a} libnaga-java{a} libncbi-ngs3{a} libncbi-vdb3{a} libnet-http-perl{a} libnet-ssleay-perl{a} libngs-java{a} libngs-jni{a} libnpth0t64{a} libnspr4{a} libnss3{a} libopentest4j-java{a} libopentest4j-reporting-java{a} liboro-java{a} libparams-classify-perl{a} libpcsclite1{a} libpicocli-java{a} libpipeline1{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} libproc2-0{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqdox-java{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} libservlet-api-java{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libsnpeff-java{a} libsnpeff-java-doc{a} libssl3t64{a} libstax-ex-java{a} libstreambuffer-java{a} libstringtemplate4-java{a} libsub-override-perl{a} libsub-quote-perl{a} libsurefire-java{a} libtimedate-perl{a} libtool{a} libtreelayout-java{a} libtrove3-java{a} libtrove3-java-doc{a} libtry-tiny-perl{a} libtxw2-java{a} libuchardet0{a} libunivocity-parsers-java{a} liburi-perl{a} libvecmath-java{a} libvelocity-tools-java{a} libwagon-file-java{a} libwagon-http-java{a} libwagon-http-shaded-java{a} libwagon-provider-api-java{a} libwebsocket-api-java{a} libwww-perl{a} libwww-robotrules-perl{a} libxalan2-java{a} libxbean-reflect-java{a} libxerces2-java{a} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxml2-utils{a} libxmlgraphics-commons-java{a} libxsom-java{a} libxz-java{a} m4{a} man-db{a} maven{a} maven-debian-helper{a} maven-repo-helper{a} media-types{a} ncbi-vdb-data{a} netbase{a} openjdk-17-doc{a} openjdk-17-jdk-headless{a} openjdk-17-jre-headless{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} procps{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} tzdata{a} unzip{a} velocity{a} wdiff{a} The following packages will be REMOVED: libdb5.3{a} libssl3{a} The following packages are RECOMMENDED but will NOT be installed: curl debian-keyring dput dput-ng dupload equivs icc-profiles-free javascript-common libarchive-cpio-perl libasound2t64 libbiojava6-java-doc libcups2t64 libdata-dump-perl libdistlib-java-doc libdistro-info-perl libfontconfig1 libfreetype6 libgit-wrapper-perl libgitlab-api-v4-perl libharfbuzz0b libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjson-perl libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl libsasl2-modules libsaxon-java libsoap-lite-perl libstring-shellquote-perl libxstring-perl licensecheck lintian lynx pristine-tar psmisc python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg strace wget 0 packages upgraded, 327 newly installed, 2 to remove and 0 not upgraded. Need to get 324 MB of archives. After unpacking 1091 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-7 [697 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libssl3t64 amd64 3.2.1-3 [2244 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 binfmt-support amd64 2.2.2-7 [64.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-3 [255 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 17 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-3+b1 [1180 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.0-3 [1401 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 java-common all 0.75 [6640 B] Get: 34 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libnspr4 amd64 2:4.35-1.1+b1 [109 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libnss3 amd64 2:3.99-1 [1408 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libpcsclite1 amd64 2.0.1-1+b1 [51.1 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 openjdk-17-jre-headless amd64 17.0.11+9-1 [43.8 MB] Get: 40 http://deb.debian.org/debian trixie/main amd64 default-jre-headless amd64 2:1.17-75 [3068 B] Get: 41 http://deb.debian.org/debian trixie/main amd64 ant all 1.10.14-1 [2162 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 ant-optional all 1.10.14-1 [455 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libantlr4-runtime-java all 4.9.2-2 [317 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libantlr3-runtime-java all 3.5.3-2 [165 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libicu4j-java all 73.2-1 [16.4 MB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libjsonp-java all 1.1.2-4 [127 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libstringtemplate4-java all 4.0.8-2.1 [241 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libtreelayout-java all 1.0.3-2 [27.0 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 antlr4 all 4.9.2-2 [1399 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui-theme-base all 1.12.1+dfsg-1.1 [44.3 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 openjdk-17-doc all 17.0.11+9-1 [12.8 MB] Get: 54 http://deb.debian.org/debian trixie/main amd64 default-jdk-doc amd64 2:1.17-75 [3148 B] Get: 55 http://deb.debian.org/debian trixie/main amd64 antlr4-doc all 4.9.2-2 [852 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 dctrl-tools amd64 2.24-3+b1 [104 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 69 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 openjdk-17-jdk-headless amd64 17.0.11+9-1 [71.4 MB] Get: 78 http://deb.debian.org/debian trixie/main amd64 default-jdk-headless amd64 2:1.17-75 [1108 B] Get: 79 http://deb.debian.org/debian trixie/main amd64 libassuan0 amd64 2.5.6-1+b1 [50.4 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 gpgconf amd64 2.2.40-1.1+b1 [565 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libksba8 amd64 1.6.6-1 [131 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-4+b1 [19.7 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-4+b1 [57.0 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5+b3 [184 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libnpth0t64 amd64 1.6-3.1 [17.9 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 dirmngr amd64 2.2.40-1.1+b1 [793 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 gnupg-l10n all 2.2.40-1.1 [1093 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 gnupg-utils amd64 2.2.40-1.1+b1 [928 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 gpg amd64 2.2.40-1.1+b1 [950 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 pinentry-curses amd64 1.2.1-3 [78.1 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 gpg-agent amd64 2.2.40-1.1+b1 [695 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 gpg-wks-client amd64 2.2.40-1.1+b1 [541 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 gpg-wks-server amd64 2.2.40-1.1+b1 [532 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 gpgsm amd64 2.2.40-1.1+b1 [671 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 gnupg all 2.2.40-1.1 [846 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 97 http://deb.debian.org/debian trixie/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libfile-touch-perl all 0.12-2 [8816 B] Get: 100 http://deb.debian.org/debian trixie/main amd64 libio-pty-perl amd64 1:1.20-1 [34.1 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b2 [36.3 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libb-hooks-op-check-perl amd64 0.22-2+b2 [10.7 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libdevel-callchecker-perl amd64 0.008-2+b1 [15.1 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libparams-classify-perl amd64 0.015-2+b2 [22.4 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 liburi-perl all 5.28-1 [98.6 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libhtml-parser-perl amd64 3.81-1+b1 [99.0 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libclone-perl amd64 0.46-1+b1 [13.8 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libhttp-message-perl all 6.45-1 [82.0 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get: 128 http://deb.debian.org/debian trixie/main amd64 libnet-ssleay-perl amd64 1.94-1 [338 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libio-socket-ssl-perl all 2.085-1 [218 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libwww-perl all 6.77-1 [183 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 wdiff amd64 1.2.2-6 [119 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 devscripts all 2.23.7 [1068 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 fastjar amd64 2:0.98-7 [80.1 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 jarwrapper all 0.79 [10.1 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 java-wrappers all 0.4 [8916 B] Get: 143 http://deb.debian.org/debian trixie/main amd64 javahelper all 0.79 [84.6 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libhamcrest-java all 2.2-2 [121 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 junit4 all 4.13.2-4 [349 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libapiguardian-java all 1.1.2-1 [4656 B] Get: 147 http://deb.debian.org/debian trixie/main amd64 libopentest4j-java all 1.2.0-4 [9516 B] Get: 148 http://deb.debian.org/debian trixie/main amd64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 libpicocli-java all 4.6.2-2 [390 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 junit5 all 5.10.1-1 [2458 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libaopalliance-java all 20070526-7 [8572 B] Get: 154 http://deb.debian.org/debian trixie/main amd64 libapache-pom-java all 29-2 [5276 B] Get: 155 http://deb.debian.org/debian trixie/main amd64 libapfloat-java all 1.13.0-1 [700 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 libargs4j-java all 2.33-2 [138 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 libasm-java all 9.7-1 [394 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 159 http://deb.debian.org/debian trixie/main amd64 libjaxp1.3-java all 1.3.05-6 [227 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 libcommons-io-java all 2.16.1-1 [480 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 libxmlgraphics-commons-java all 2.8-2 [623 kB] Get: 165 http://deb.debian.org/debian trixie/main amd64 libbatik-java all 1.17+dfsg-1 [3923 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 libciftools-java all 6.0.0-1 [2211 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 libcommons-codec-java all 1.16.0-1 [297 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 libcommons-math-java all 2.2-8 [926 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 172 http://deb.debian.org/debian trixie/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 libguava-java all 32.0.1-1 [2708 kB] Get: 174 http://deb.debian.org/debian trixie/main amd64 libitext5-java all 5.5.13.3-4 [2667 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 libjackson2-annotations-java all 2.14.0-1 [68.8 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 libjackson2-core-java all 2.14.1-1 [447 kB] Get: 177 http://deb.debian.org/debian trixie/main amd64 libjackson2-databind-java all 2.14.0-1 [1584 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 libjaxen-java all 1.1.6-4 [214 kB] Get: 180 http://deb.debian.org/debian trixie/main amd64 libdom4j-java all 2.1.4-1 [312 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-utils-java all 3.3.4-1 [138 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 libcommons-lang3-java all 3.14.0-1 [621 kB] Get: 184 http://deb.debian.org/debian trixie/main amd64 libguice-java all 4.2.3-2 [1435 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 libmaven-parent-java all 35-1 [6140 B] Get: 186 http://deb.debian.org/debian trixie/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 188 http://deb.debian.org/debian trixie/main amd64 libmaven-resolver-java all 1.6.3-1 [548 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 190 http://deb.debian.org/debian trixie/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 191 http://deb.debian.org/debian trixie/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 192 http://deb.debian.org/debian trixie/main amd64 libplexus-interpolation-java all 1.26-1 [76.8 kB] Get: 193 http://deb.debian.org/debian trixie/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 194 http://deb.debian.org/debian trixie/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 195 http://deb.debian.org/debian trixie/main amd64 libcdi-api-java all 1.2-3 [54.3 kB] Get: 196 http://deb.debian.org/debian trixie/main amd64 libslf4j-java all 1.7.32-1 [144 kB] Get: 197 http://deb.debian.org/debian trixie/main amd64 libsisu-inject-java all 0.3.4-2 [347 kB] Get: 198 http://deb.debian.org/debian trixie/main amd64 libsisu-plexus-java all 0.3.4-3 [181 kB] Get: 199 http://deb.debian.org/debian trixie/main amd64 libmaven3-core-java all 3.8.7-2 [1573 kB] Get: 200 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 201 http://deb.debian.org/debian trixie/main amd64 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 202 http://deb.debian.org/debian trixie/main amd64 libcommons-compress-java all 1.25.0-1 [635 kB] Get: 203 http://deb.debian.org/debian trixie/main amd64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 204 http://deb.debian.org/debian trixie/main amd64 libsnappy1v5 amd64 1.1.10-1+b1 [27.6 kB] Get: 205 http://deb.debian.org/debian trixie/main amd64 libsnappy-jni amd64 1.1.10.5-2 [6396 B] Get: 206 http://deb.debian.org/debian trixie/main amd64 libsnappy-java all 1.1.10.5-2 [87.5 kB] Get: 207 http://deb.debian.org/debian trixie/main amd64 libxz-java all 1.9-1 [143 kB] Get: 208 http://deb.debian.org/debian trixie/main amd64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 209 http://deb.debian.org/debian trixie/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 210 http://deb.debian.org/debian trixie/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 211 http://deb.debian.org/debian trixie/main amd64 libjsoup-java all 1.15.3-1 [431 kB] Get: 212 http://deb.debian.org/debian trixie/main amd64 libwagon-http-java all 3.5.3-1 [49.5 kB] Get: 213 http://deb.debian.org/debian trixie/main amd64 libistack-commons-java all 3.0.6-5 [145 kB] Get: 214 http://deb.debian.org/debian trixie/main amd64 libcodemodel-java all 2.6+jaxb2.3.0.1-10.1 [164 kB] Get: 215 http://deb.debian.org/debian trixie/main amd64 librelaxng-datatype-java all 1.0+ds1-3.1 [11.7 kB] Get: 216 http://deb.debian.org/debian trixie/main amd64 librngom-java all 2.3.0.1-10.1 [290 kB] Get: 217 http://deb.debian.org/debian trixie/main amd64 libxsom-java all 2.3.0.1-10.1 [400 kB] Get: 218 http://deb.debian.org/debian trixie/main amd64 libtxw2-java all 2.3.0.1-10.1 [134 kB] Get: 219 http://deb.debian.org/debian trixie/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 220 http://deb.debian.org/debian trixie/main amd64 libdtd-parser-java all 1.2-1 [64.9 kB] Get: 221 http://deb.debian.org/debian trixie/main amd64 libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 222 http://deb.debian.org/debian trixie/main amd64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB] Get: 223 http://deb.debian.org/debian trixie/main amd64 libfastinfoset-java all 1.2.12-3 [343 kB] Get: 224 http://deb.debian.org/debian trixie/main amd64 libjaxb-java all 2.3.0.1-10.1 [1973 kB] Get: 225 http://deb.debian.org/debian trixie/main amd64 libmaven-archiver-java all 3.6.0-1 [25.1 kB] Get: 226 http://deb.debian.org/debian trixie/main amd64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 227 http://deb.debian.org/debian trixie/main amd64 libcommons-text-java all 1.11.0-1 [217 kB] Get: 228 http://deb.debian.org/debian trixie/main amd64 libfastutil-java all 8.5.12+dfsg-1 [19.6 MB] Get: 229 http://deb.debian.org/debian trixie/main amd64 libjheaps-java all 0.14-2 [144 kB] Get: 230 http://deb.debian.org/debian trixie/main amd64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 231 http://deb.debian.org/debian trixie/main amd64 libjgraphx-java all 2.1.0.7-3 [807 kB] Get: 232 http://deb.debian.org/debian trixie/main amd64 libjgrapht-java all 1.5.2-1 [1610 kB] Get: 233 http://deb.debian.org/debian trixie/main amd64 libinchi1 amd64 1.03+dfsg-4+b2 [436 kB] Get: 234 http://deb.debian.org/debian trixie/main amd64 libjni-inchi-jni amd64 0.8+dfsg-7 [9064 B] Get: 235 http://deb.debian.org/debian trixie/main amd64 libcommons-exec-java all 1.3-2 [48.1 kB] Get: 236 http://deb.debian.org/debian trixie/main amd64 libexec-maven-plugin-java all 3.1.0-2 [66.7 kB] Get: 237 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-incremental-java all 1.1-4 [9924 B] Get: 238 http://deb.debian.org/debian trixie/main amd64 libcommons-lang-java all 2.6-10 [273 kB] Get: 239 http://deb.debian.org/debian trixie/main amd64 libxbean-reflect-java all 4.5-8 [133 kB] Get: 240 http://deb.debian.org/debian trixie/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 241 http://deb.debian.org/debian trixie/main amd64 libplexus-compiler-java all 2.12.1-2 [99.0 kB] Get: 242 http://deb.debian.org/debian trixie/main amd64 libqdox2-java all 2.0.3-1 [296 kB] Get: 243 http://deb.debian.org/debian trixie/main amd64 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 244 http://deb.debian.org/debian trixie/main amd64 libmaven-compiler-plugin-java all 3.10.1-2 [59.0 kB] Get: 245 http://deb.debian.org/debian trixie/main amd64 liblog4j1.2-java all 1.2.17-11 [444 kB] Get: 246 http://deb.debian.org/debian trixie/main amd64 libjni-inchi-java all 0.8+dfsg-7 [33.2 kB] Get: 247 http://deb.debian.org/debian trixie/main amd64 libnaga-java all 3.0+svn80-5 [43.5 kB] Get: 248 http://deb.debian.org/debian trixie/main amd64 libjmol-java all 14.32.83+dfsg-3 [8698 kB] Get: 249 http://deb.debian.org/debian trixie/main amd64 libjson-simple-java all 2.3.0-1 [63.8 kB] Get: 250 http://deb.debian.org/debian trixie/main amd64 libmsgpack-java all 0.9.6-1 [161 kB] Get: 251 http://deb.debian.org/debian trixie/main amd64 libmmtf-java all 1.0.11-1 [187 kB] Get: 252 http://deb.debian.org/debian trixie/main amd64 libvecmath-java all 1.5.2-7 [97.0 kB] Get: 253 http://deb.debian.org/debian trixie/main amd64 libbiojava6-java all 6.1.0+dfsg-4 [5367 kB] Get: 254 http://deb.debian.org/debian trixie/main amd64 libbsh-java all 2.0b4-20 [291 kB] Get: 255 http://deb.debian.org/debian trixie/main amd64 libcharts4j-java all 1.3-4 [162 kB] Get: 256 http://deb.debian.org/debian trixie/main amd64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 257 http://deb.debian.org/debian trixie/main amd64 libcommons-beanutils-java all 1.9.4-2 [233 kB] Get: 258 http://deb.debian.org/debian trixie/main amd64 libcommons-configuration-java all 1.10-6 [347 kB] Get: 259 http://deb.debian.org/debian trixie/main amd64 libcommons-digester-java all 1.8.1-6 [137 kB] Get: 260 http://deb.debian.org/debian trixie/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get: 261 http://deb.debian.org/debian trixie/main amd64 libcommons-math3-java all 3.6.1-3 [2018 kB] Get: 262 http://deb.debian.org/debian trixie/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 263 http://deb.debian.org/debian trixie/main amd64 libcommons-math3-java-doc all 3.6.1-3 [1560 kB] Get: 264 http://deb.debian.org/debian trixie/main amd64 libcommons-validator-java all 1:1.7-1 [181 kB] Get: 265 http://deb.debian.org/debian trixie/main amd64 libdistlib-java all 1.0-4 [72.1 kB] Get: 266 http://deb.debian.org/debian trixie/main amd64 libdoxia-core-java all 1.12.0-1 [213 kB] Get: 267 http://deb.debian.org/debian trixie/main amd64 libfontbox2-java all 2.0.29-1 [1510 kB] Get: 268 http://deb.debian.org/debian trixie/main amd64 libqdox-java all 1.12.1-3 [172 kB] Get: 269 http://deb.debian.org/debian trixie/main amd64 libfop-java all 1:2.8-3 [10.1 MB] Get: 270 http://deb.debian.org/debian trixie/main amd64 libitext1-java all 1.4-7 [1257 kB] Get: 271 http://deb.debian.org/debian trixie/main amd64 libdoxia-java all 1.12.0-1 [459 kB] Get: 272 http://deb.debian.org/debian trixie/main amd64 libmaven-reporting-api-java all 3.1.1-1 [7240 B] Get: 273 http://deb.debian.org/debian trixie/main amd64 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB] Get: 274 http://deb.debian.org/debian trixie/main amd64 velocity all 1.7-7 [431 kB] Get: 275 http://deb.debian.org/debian trixie/main amd64 libplexus-velocity-java all 1.2-3.1 [10.5 kB] Get: 276 http://deb.debian.org/debian trixie/main amd64 liboro-java all 2.0.8a-14 [70.5 kB] Get: 277 http://deb.debian.org/debian trixie/main amd64 libvelocity-tools-java all 2.0-9 [311 kB] Get: 278 http://deb.debian.org/debian trixie/main amd64 libxalan2-java all 2.7.2-4 [3419 kB] Get: 279 http://deb.debian.org/debian trixie/main amd64 libdoxia-sitetools-java all 1.11.1-1 [202 kB] Get: 280 http://deb.debian.org/debian trixie/main amd64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 281 http://deb.debian.org/debian trixie/main amd64 libfreemarker-java all 2.3.32-2 [1546 kB] Get: 282 http://deb.debian.org/debian trixie/main amd64 libmjson-java all 1.4.0-3 [60.4 kB] Get: 283 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB] Get: 284 http://deb.debian.org/debian trixie/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB] Get: 285 http://deb.debian.org/debian trixie/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB] Get: 286 http://deb.debian.org/debian trixie/main amd64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB] Get: 287 http://deb.debian.org/debian trixie/main amd64 libncbi-vdb3 amd64 3.0.2+dfsg-2+b1 [1049 kB] Get: 288 http://deb.debian.org/debian trixie/main amd64 libncbi-ngs3 amd64 3.0.3+dfsg-6 [154 kB] Get: 289 http://deb.debian.org/debian trixie/main amd64 libngs-jni amd64 3.0.3+dfsg-6 [23.4 kB] Get: 290 http://deb.debian.org/debian trixie/main amd64 libngs-java amd64 3.0.3+dfsg-6 [110 kB] Get: 291 http://deb.debian.org/debian trixie/main amd64 librhino-java all 1.7.14-2.1 [1357 kB] Get: 292 http://deb.debian.org/debian trixie/main amd64 libhtsjdk-java all 4.1.0+dfsg-1 [1833 kB] Get: 293 http://deb.debian.org/debian trixie/main amd64 libhtsjdk-java-doc all 4.1.0+dfsg-1 [1044 kB] Get: 294 http://deb.debian.org/debian trixie/main amd64 libjansi-java all 2.4.1-2 [100 kB] Get: 295 http://deb.debian.org/debian trixie/main amd64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 296 http://deb.debian.org/debian trixie/main amd64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 297 http://deb.debian.org/debian trixie/main amd64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 298 http://deb.debian.org/debian trixie/main amd64 libjetty9-java all 9.4.54-1 [2980 kB] Get: 299 http://deb.debian.org/debian trixie/main amd64 libjtidy-java all 7+svn20110807-5 [250 kB] Get: 300 http://deb.debian.org/debian trixie/main amd64 libmaven-common-artifact-filters-java all 3.3.2-1 [48.2 kB] Get: 301 http://deb.debian.org/debian trixie/main amd64 libmaven-artifact-transfer-java all 0.13.1-2 [158 kB] Get: 302 http://deb.debian.org/debian trixie/main amd64 libplexus-build-api-java all 0.0.7-4 [10.3 kB] Get: 303 http://deb.debian.org/debian trixie/main amd64 libmaven-filtering-java all 3.3.0-1 [50.2 kB] Get: 304 http://deb.debian.org/debian trixie/main amd64 libmaven-assembly-plugin-java all 3.4.2-1 [242 kB] Get: 305 http://deb.debian.org/debian trixie/main amd64 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB] Get: 306 http://deb.debian.org/debian trixie/main amd64 libmaven-invoker-java all 3.2.0-1 [28.1 kB] Get: 307 http://deb.debian.org/debian trixie/main amd64 libplexus-interactivity-api-java all 1.1-2 [11.0 kB] Get: 308 http://deb.debian.org/debian trixie/main amd64 libmaven-javadoc-plugin-java all 3.4.1-3 [454 kB] Get: 309 http://deb.debian.org/debian trixie/main amd64 libmaven-reporting-impl-java all 3.2.0-2 [15.2 kB] Get: 310 http://deb.debian.org/debian trixie/main amd64 libplexus-container-default1.5-java all 2.1.1-1 [4476 B] Get: 311 http://deb.debian.org/debian trixie/main amd64 libplexus-ant-factory-java all 1.0~alpha2.1-4 [11.4 kB] Get: 312 http://deb.debian.org/debian trixie/main amd64 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B] Get: 313 http://deb.debian.org/debian trixie/main amd64 libmaven-plugin-tools-java all 3.7.1-1 [265 kB] Get: 314 http://deb.debian.org/debian trixie/main amd64 libmaven-reporting-exec-java all 1.6.0-1 [26.8 kB] Get: 315 http://deb.debian.org/debian trixie/main amd64 libmaven-resources-plugin-java all 3.3.0-1 [28.4 kB] Get: 316 http://deb.debian.org/debian trixie/main amd64 libmaven-site-plugin-java all 3.12.1-2 [107 kB] Get: 317 http://deb.debian.org/debian trixie/main amd64 libtrove3-java all 3.0.3-5 [2146 kB] Get: 318 http://deb.debian.org/debian trixie/main amd64 libsnpeff-java all 5.2.b+dfsg-1 [1656 kB] Get: 319 http://deb.debian.org/debian trixie/main amd64 libsnpeff-java-doc all 5.2.b+dfsg-1 [656 kB] Get: 320 http://deb.debian.org/debian trixie/main amd64 libsurefire-java all 2.22.3-2 [1169 kB] Get: 321 http://deb.debian.org/debian trixie/main amd64 libtrove3-java-doc all 3.0.3-5 [823 kB] Get: 322 http://deb.debian.org/debian trixie/main amd64 libwagon-file-java all 3.5.3-1 [8388 B] Get: 323 http://deb.debian.org/debian trixie/main amd64 libwagon-http-shaded-java all 3.5.3-1 [1341 kB] Get: 324 http://deb.debian.org/debian trixie/main amd64 libxml2-utils amd64 2.9.14+dfsg-1.3+b3 [99.0 kB] Get: 325 http://deb.debian.org/debian trixie/main amd64 maven all 3.8.7-2 [19.3 kB] Get: 326 http://deb.debian.org/debian trixie/main amd64 maven-repo-helper all 1.11 [142 kB] Get: 327 http://deb.debian.org/debian trixie/main amd64 maven-debian-helper all 2.6.4 [108 kB] Fetched 324 MB in 17s (18.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libdb5.3:amd64: dependency problems, but removing anyway as you requested: libperl5.38:amd64 depends on libdb5.3. libpam-modules:amd64 depends on libdb5.3. (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 ... 19699 files and directories currently installed.) Removing libdb5.3:amd64 (5.3.28+dfsg2-4+b1) ... Selecting previously unselected package libdb5.3t64:amd64. (Reading database ... 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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 ... 19698 files and directories currently installed.) Removing libssl3:amd64 (3.1.5-1) ... Selecting previously unselected package libssl3t64: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 ... 19685 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.2.1-3_amd64.deb ... Unpacking libssl3t64:amd64 (3.2.1-3) ... Setting up libssl3t64:amd64 (3.2.1-3) ... Selecting previously unselected package libpipeline1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19700 files and directories currently installed.) Preparing to unpack .../libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package binfmt-support. Preparing to unpack .../binfmt-support_2.2.2-7_amd64.deb ... Unpacking binfmt-support (2.2.2-7) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20039 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-3_all.deb ... Unpacking tzdata (2024a-3) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../5-libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... 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 ... 21031 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../002-libproc2-0_2%3a4.0.4-4_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-4) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.4-4_amd64.deb ... Unpacking procps (2:4.0.4-4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package openssl. Preparing to unpack .../005-openssl_3.2.1-3_amd64.deb ... Unpacking openssl (3.2.1-3) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../006-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../007-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../008-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../009-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../010-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../011-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../012-groff-base_1.23.0-3+b1_amd64.deb ... Unpacking groff-base (1.23.0-3+b1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../013-bsdextrautils_2.40-8_amd64.deb ... Unpacking bsdextrautils (2.40-8) ... 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Setting up libmaven-parent-java (35-1) ... Setting up libcommons-parent-java (56-1) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libnet-http-perl (6.23-1) ... Setting up libsisu-inject-java (0.3.4-2) ... Setting up libnss3:amd64 (2:3.99-1) ... Setting up libciftools-java (6.0.0-1) ... Setting up libdevel-callchecker-perl:amd64 (0.008-2+b1) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5+b3) ... Setting up libjackson2-databind-java (2.14.0-1) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up patchutils (0.4.2-1) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.4-3) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libxalan2-java (2.7.2-4) ... Setting up libstreambuffer-java (1.5.4-1.1) ... Setting up libcommons-lang3-java (3.14.0-1) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up librngom-java (2.3.0.1-10.1) ... Setting up libjni-inchi-jni (0.8+dfsg-7) ... Setting up libmaven-common-artifact-filters-java (3.3.2-1) ... Setting up libjgraphx-java (2.1.0.7-3) ... Setting up libmbedtls14t64:amd64 (2.28.8-1) ... Setting up groff-base (1.23.0-3+b1) ... Setting up libhtml-parser-perl:amd64 (3.81-1+b1) ... Setting up gpgconf (2.2.40-1.1+b1) ... Setting up openjdk-17-doc (17.0.11+9-1) ... Setting up libcommons-beanutils-java (1.9.4-2) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libsnappy-java (1.1.10.5-2) ... Setting up libxsom-java (2.3.0.1-10.1) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libcommons-configuration-java (1.10-6) ... Setting up libwagon-file-java (3.5.3-1) ... Setting up libxml2-utils (2.9.14+dfsg-1.3+b3) ... Setting up libcommons-codec-java (1.16.0-1) ... Setting up libio-socket-ssl-perl (2.085-1) ... Setting up gpg (2.2.40-1.1+b1) ... Setting up gnupg-utils (2.2.40-1.1+b1) ... Setting up libhttp-message-perl (6.45-1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up velocity (1.7-7) ... Setting up gpg-agent (2.2.40-1.1+b1) ... Setting up libcommons-compress-java (1.25.0-1) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up libcommons-io-java (2.16.1-1) ... Setting up libcommons-digester-java (1.8.1-6) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up libdistlib-java (1.0-4) ... Setting up libparams-classify-perl:amd64 (0.015-2+b2) ... Setting up gpgsm (2.2.40-1.1+b1) ... Setting up libncbi-vdb3:amd64 (3.0.2+dfsg-2+b1) ... Setting up libxmlgraphics-commons-java (2.8-2) ... Setting up default-jdk-doc (2:1.17-75) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up dirmngr (2.2.40-1.1+b1) ... Setting up libmaven-filtering-java (3.3.0-1) ... Setting up libmaven-resolver-java (1.6.3-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up antlr4-doc (4.9.2-2) ... Setting up openjdk-17-jre-headless:amd64 (17.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up gpg-wks-server (2.2.40-1.1+b1) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up libwagon-http-java (3.5.3-1) ... Setting up libmaven-shared-utils-java (3.3.4-1) ... Setting up libfastinfoset-java (1.2.12-3) ... Setting up libmaven-resources-plugin-java (3.3.0-1) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up libncbi-ngs3:amd64 (3.0.3+dfsg-6) ... Setting up python3.11 (3.11.9-1) ... Setting up libngs-jni:amd64 (3.0.3+dfsg-6) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up gpg-wks-client (2.2.40-1.1+b1) ... Setting up libcommons-validator-java (1:1.7-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libbatik-java (1.17+dfsg-1) ... Setting up libmoo-perl (2.005005-1) ... Setting up libmaven-invoker-java (3.2.0-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up libmaven-clean-plugin-java (3.2.0-2) ... Setting up gnupg (2.2.40-1.1) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libngs-java:amd64 (3.0.3+dfsg-6) ... Setting up libhtsjdk-java (4.1.0+dfsg-1) ... Setting up libfop-java (1:2.8-3) ... Setting up libmaven-archiver-java (3.6.0-1) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libwww-perl (6.77-1) ... Setting up devscripts (2.23.7) ... Setting up libguava-java (32.0.1-1) ... Setting up javahelper (0.79) ... Setting up libplexus-container-default-java (2.1.1-1) ... Setting up libguice-java (4.2.3-2) ... Setting up libplexus-i18n-java (1.0-beta-10-6) ... Setting up libplexus-container-default1.5-java (2.1.1-1) ... Setting up libplexus-interactivity-api-java (1.1-2) ... Setting up libplexus-velocity-java (1.2-3.1) ... Setting up libmaven3-core-java (3.8.7-2) ... Setting up libmaven-shared-incremental-java (1.1-4) ... Setting up libmaven-shared-io-java (3.0.0-4) ... Setting up libplexus-bsh-factory-java (1.0~alpha7-5) ... Setting up libplexus-compiler-java (2.12.1-2) ... Setting up libmaven-compiler-plugin-java (3.10.1-2) ... Setting up libjni-inchi-java (0.8+dfsg-7) ... Setting up libmaven-artifact-transfer-java (0.13.1-2) ... Setting up libmaven-file-management-java (3.0.0-1) ... Setting up libjmol-java (14.32.83+dfsg-3) ... Setting up libmaven-jar-plugin-java (3.3.0-2) ... Setting up libmaven-assembly-plugin-java (3.4.2-1) ... Setting up libcommons-text-java (1.11.0-1) ... Setting up 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 (1.12.0-1) ... Setting up libdoxia-java (1.12.0-1) ... Setting up libmaven-reporting-api-java (3.1.1-1) ... Setting up libmaven-reporting-exec-java (1.6.0-1) ... Processing triggers for libc-bin (2.37-18) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up maven-repo-helper (1.11) ... Setting up maven (3.8.7-2) ... update-alternatives: using /usr/share/maven/bin/mvn to provide /usr/bin/mvn (mvn) in auto mode Setting up openjdk-17-jdk-headless:amd64 (17.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up ant (1.10.14-1) ... Setting up junit4 (4.13.2-4) ... Setting up default-jre-headless (2:1.17-75) ... Setting up antlr4 (4.9.2-2) ... Setting up libplexus-ant-factory-java (1.0~alpha2.1-4) ... Setting up ant-optional (1.10.14-1) ... Setting up default-jdk-headless (2:1.17-75) ... Setting up junit5 (5.10.1-1) ... Setting up libistack-commons-java (3.0.6-5) ... Setting up libcodemodel-java (2.6+jaxb2.3.0.1-10.1) ... Setting up libtxw2-java (2.3.0.1-10.1) ... Setting up libjaxb-java (2.3.0.1-10.1) ... Setting up libbiojava6-java (6.1.0+dfsg-4) ... Setting up libsnpeff-java (5.2.b+dfsg-1) ... Processing triggers for sgml-base (1.31) ... Setting up libvelocity-tools-java (2.0-9) ... Setting up libdoxia-sitetools-java (1.11.1-1) ... Setting up libmaven-site-plugin-java (3.12.1-2) ... Setting up libmaven-javadoc-plugin-java (3.4.1-3) ... Setting up libmaven-reporting-impl-java (3.2.0-2) ... Setting up libmaven-plugin-tools-java (3.7.1-1) ... Setting up libsurefire-java (2.22.3-2) ... Setting up maven-debian-helper (2.6.4) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/snpsift-5.1+dfsg2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../snpsift_5.1+dfsg2-2_source.changes dpkg-buildpackage: info: source package snpsift dpkg-buildpackage: info: source version 5.1+dfsg2-2 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/snpsift-5.1+dfsg2' 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 -plibsnpsift-java # Removing the unit tests we copied into a subdirectory of src/test. if [ -e src/test/java/org ]; then \ rm -f -rf src/test/java/org; \ fi make[1]: Leaving directory '/build/reproducible-path/snpsift-5.1+dfsg2' jh_clean dh_clean debian/rules binary dh binary --with javahelper dh_update_autotools_config dh_autoreconf dh_auto_configure mh_patchpoms -plibsnpsift-java --debian-build --keep-pom-version --maven-repo=/build/reproducible-path/snpsift-5.1\+dfsg2/debian/maven-repo Failed to parse /build/reproducible-path/snpsift-5.1+dfsg2/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/snpsift-5.1+dfsg2/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) 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/snpsift-5.1\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/snpsift-5.1\+dfsg2/debian -Dmaven.repo.local=/build/reproducible-path/snpsift-5.1\+dfsg2/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.snpsift:snpsift >------------------------- [INFO] Building SnpSift 5.1 [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The artifact org.apache.maven.plugins:maven-surefire-plugin:jar:2.12.4 has been relocated to org.apache.maven.plugins:maven-surefire-plugin:jar:2.22.3 [WARNING] The artifact org.apache.maven.plugins:maven-jar-plugin:jar:2.4 has been relocated to org.apache.maven.plugins:maven-jar-plugin:jar:3.3.0 [WARNING] The POM for org.biojava:biojava-structure:jar:6.x is invalid, transitive dependencies (if any) will not be available, enable debug logging for more details [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ snpsift --- [INFO] skip non existing resourceDirectory /build/reproducible-path/snpsift-5.1+dfsg2/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ snpsift --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 112 source files to /build/reproducible-path/snpsift-5.1+dfsg2/target/classes [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/lang/LangFactory.java:[112,25] org.antlr.v4.runtime.ANTLRInputStream in org.antlr.v4.runtime has been deprecated [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/lang/LangFactory.java:[112,54] org.antlr.v4.runtime.ANTLRInputStream in org.antlr.v4.runtime has been deprecated [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/hwe/VcfHwe.java:[116,45] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/hwe/VcfHwe.java:[116,80] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/hwe/VcfHwe.java:[116,116] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/hwe/VcfHwe.java:[116,152] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/hwe/VcfHwe.java:[117,45] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/hwe/VcfHwe.java:[117,84] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/hwe/VcfHwe.java:[117,119] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ snpsift --- [INFO] skip non existing resourceDirectory /build/reproducible-path/snpsift-5.1+dfsg2/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ snpsift --- [INFO] Changes detected - recompiling the module! [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ snpsift --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ snpsift --- [INFO] Building jar: /build/reproducible-path/snpsift-5.1+dfsg2/target/snpsift-5.1.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ snpsift --- [INFO] Adding the --ignore-source-errors option [INFO] No previous run data found, generating javadoc. [WARNING] Javadoc Warnings [WARNING] Loading source files for package org.snpsift.lang.expression... [WARNING] Loading source files for package org.snpsift.lang... [WARNING] Loading source files for package org.snpsift.lang.function... [WARNING] Loading source files for package org.snpsift... [WARNING] Loading source files for package org.snpsift.testCases.unit... [WARNING] Loading source files for package org.snpsift.testCases... [WARNING] Loading source files for package org.snpsift.phatsCons... [WARNING] Loading source files for package org.snpsift.util... [WARNING] Loading source files for package org.snpsift.fileIterator... [WARNING] Loading source files for package org.snpsift.hwe... [WARNING] Loading source files for package org.snpsift.gwasCatalog... [WARNING] Loading source files for package org.snpsift.pedigree... [WARNING] Loading source files for package org.snpsift.annotate... [WARNING] Loading source files for package org.snpsift.antlr... [WARNING] Loading source files for package org.snpsift.caseControl... [WARNING] Constructing Javadoc information... [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:16: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:15: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:9: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:9: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:10: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:10: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilter.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilter.java:17: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIntervals.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGwasCatalog.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGwasCatalog.java:13: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGwasCatalog.java:13: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:12: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:12: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGt.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGt.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGt.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVcfCheck.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterChrPos.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterChrPos.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:15: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:15: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGeneSets.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGeneSets.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGeneSets.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:12: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertFalse; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:12: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertFalse; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:13: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:13: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:13: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:13: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:14: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:14: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterGt.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterGt.java:12: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterGt.java:12: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotateTabix.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:7: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:7: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesLd.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesLd.java:6: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesLd.java:6: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:10: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:10: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesConcordance.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesConcordance.java:9: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesConcordance.java:9: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:3: error: package org.junit.platform.suite.api does not exist [WARNING] import org.junit.platform.suite.api.SelectPackages; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:4: error: package org.junit.platform.suite.api does not exist [WARNING] import org.junit.platform.suite.api.Suite; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:5: error: package org.junit.platform.suite.api does not exist [WARNING] import org.junit.platform.suite.api.SuiteDisplayName; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:13: error: cannot find symbol [WARNING] @Suite [WARNING] ^ [WARNING] symbol: class Suite [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:14: error: cannot find symbol [WARNING] @SuiteDisplayName("Unit test cases") [WARNING] ^ [WARNING] symbol: class SuiteDisplayName [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:15: error: cannot find symbol [WARNING] @SelectPackages({"org.snpsift.testCases.unit"}) [WARNING] ^ [WARNING] symbol: class SelectPackages [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestCasesZzz.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestCasesZzz.java:13: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:143: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:151: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:159: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:167: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:179: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:190: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:215: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:230: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:243: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:271: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:298: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:318: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:338: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:354: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:370: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:388: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:413: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:426: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:437: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:451: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:477: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:489: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:507: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:537: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:566: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:578: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] 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[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/antlr/package-use.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/caseControl/package-use.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/fileIterator/package-use.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/gwasCatalog/package-use.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/hwe/package-use.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/package-use.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/package-use.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/function/package-use.html... 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[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/allclasses-index.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/index-all.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/help-doc.html... [WARNING] 100 warnings [INFO] Building jar: /build/reproducible-path/snpsift-5.1+dfsg2/target/snpsift-5.1-javadoc.jar [INFO] [INFO] ------------------------< org.snpsift:snpsift >------------------------- [INFO] Building SnpSift 5.1 [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] >>> maven-javadoc-plugin:3.4.1:aggregate (default-cli) > compile @ snpsift >>> [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ snpsift --- [INFO] skip non existing resourceDirectory /build/reproducible-path/snpsift-5.1+dfsg2/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ snpsift --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 112 source files to /build/reproducible-path/snpsift-5.1+dfsg2/target/classes [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/lang/LangFactory.java:[112,25] org.antlr.v4.runtime.ANTLRInputStream in org.antlr.v4.runtime has been deprecated [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/lang/LangFactory.java:[112,54] org.antlr.v4.runtime.ANTLRInputStream in org.antlr.v4.runtime has been deprecated [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/hwe/VcfHwe.java:[116,45] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/hwe/VcfHwe.java:[116,80] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/hwe/VcfHwe.java:[116,116] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/hwe/VcfHwe.java:[116,152] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/hwe/VcfHwe.java:[117,45] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/hwe/VcfHwe.java:[117,84] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/hwe/VcfHwe.java:[117,119] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [INFO] [INFO] <<< maven-javadoc-plugin:3.4.1:aggregate (default-cli) < compile @ snpsift <<< [INFO] [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:aggregate (default-cli) @ snpsift --- [INFO] Adding the --ignore-source-errors option [INFO] Configuration changed, re-generating javadoc. [WARNING] Javadoc Warnings [WARNING] Loading source files for package org.snpsift.lang.expression... [WARNING] Loading source files for package org.snpsift.lang... [WARNING] Loading source files for package org.snpsift.lang.function... [WARNING] Loading source files for package org.snpsift... [WARNING] Loading source files for package org.snpsift.testCases.unit... [WARNING] Loading source files for package org.snpsift.testCases... [WARNING] Loading source files for package org.snpsift.phatsCons... [WARNING] Loading source files for package org.snpsift.util... [WARNING] Loading source files for package org.snpsift.fileIterator... [WARNING] Loading source files for package org.snpsift.hwe... [WARNING] Loading source files for package org.snpsift.gwasCatalog... [WARNING] Loading source files for package org.snpsift.pedigree... [WARNING] Loading source files for package org.snpsift.annotate... [WARNING] Loading source files for package org.snpsift.antlr... [WARNING] Loading source files for package org.snpsift.caseControl... [WARNING] Constructing Javadoc information... [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:16: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:15: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:9: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:9: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:10: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:10: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilter.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilter.java:17: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIntervals.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGwasCatalog.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGwasCatalog.java:13: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGwasCatalog.java:13: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:12: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:12: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGt.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGt.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGt.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVcfCheck.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterChrPos.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterChrPos.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:15: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:15: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGeneSets.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGeneSets.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGeneSets.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:12: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertFalse; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:12: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertFalse; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:13: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:13: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:13: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:13: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:14: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:14: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterGt.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterGt.java:12: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterGt.java:12: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotateTabix.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:7: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:7: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesLd.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesLd.java:6: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesLd.java:6: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:10: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:10: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesConcordance.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesConcordance.java:9: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesConcordance.java:9: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:3: error: package org.junit.platform.suite.api does not exist [WARNING] import org.junit.platform.suite.api.SelectPackages; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:4: error: package org.junit.platform.suite.api does not exist [WARNING] import org.junit.platform.suite.api.Suite; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:5: error: package org.junit.platform.suite.api does not exist [WARNING] import org.junit.platform.suite.api.SuiteDisplayName; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:13: error: cannot find symbol [WARNING] @Suite [WARNING] ^ [WARNING] symbol: class Suite [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:14: error: cannot find symbol [WARNING] @SuiteDisplayName("Unit test cases") [WARNING] ^ [WARNING] symbol: class SuiteDisplayName [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:15: error: cannot find symbol [WARNING] @SelectPackages({"org.snpsift.testCases.unit"}) [WARNING] ^ [WARNING] symbol: class SelectPackages [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestCasesZzz.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestCasesZzz.java:13: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:143: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:151: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:159: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:167: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:179: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:190: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:215: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:230: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:243: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:271: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:298: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:318: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:338: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:354: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:370: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:388: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:413: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:426: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:437: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:451: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:477: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:489: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:507: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:537: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:566: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:578: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] 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[WARNING] 100 warnings [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 11.279 s [INFO] Finished at: 2025-06-04T01:20:11-12:00 [INFO] ------------------------------------------------------------------------ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/snpsift-5.1+dfsg2' # Moving the unit tests into a subdir of src/test so that Maven sees them. mkdir -p src/test/java/org/snpsift/testCases cp -a src/main/java/org/snpsift/testCases/unit src/test/java/org/snpsift/testCases dh_auto_test /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/snpsift-5.1\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/snpsift-5.1\+dfsg2/debian -Dmaven.repo.local=/build/reproducible-path/snpsift-5.1\+dfsg2/debian/maven-repo --batch-mode test OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release. [INFO] Scanning for projects... [INFO] [INFO] ------------------------< org.snpsift:snpsift >------------------------- [INFO] Building SnpSift 5.1 [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The artifact org.apache.maven.plugins:maven-surefire-plugin:jar:2.12.4 has been relocated to org.apache.maven.plugins:maven-surefire-plugin:jar:2.22.3 [WARNING] The POM for org.biojava:biojava-structure:jar:6.x is invalid, transitive dependencies (if any) will not be available, enable debug logging for more details [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ snpsift --- [INFO] skip non existing resourceDirectory /build/reproducible-path/snpsift-5.1+dfsg2/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ snpsift --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ snpsift --- [INFO] skip non existing resourceDirectory /build/reproducible-path/snpsift-5.1+dfsg2/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ snpsift --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 26 source files to /build/reproducible-path/snpsift-5.1+dfsg2/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ snpsift --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.snpsift.testCases.unit.TestCasesGt TestCasesGt.test_01(25): Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.213 s - in org.snpsift.testCases.unit.TestCasesGt [INFO] Running org.snpsift.testCases.unit.TestCasesFilterChrPos Annotate: ./test/filterChrPos_01.txt ./test/filterChrPos_01.vcf Annotate: ./test/filterChrPos_02.txt ./test/filterChrPos_02.vcf Annotate: ./test/filterChrPos_03.txt ./test/filterChrPos_03.vcf [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpsift.testCases.unit.TestCasesFilterChrPos [INFO] Running org.snpsift.testCases.unit.TestCasesFilterGt TestCasesFilterGt.test_01(28): Test TestCasesFilterGt.test_02(62): Test [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.064 s - in org.snpsift.testCases.unit.TestCasesFilterGt [INFO] Running org.snpsift.testCases.unit.TestCasesHwe [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.snpsift.testCases.unit.TestCasesHwe [INFO] Running org.snpsift.testCases.unit.TestCasesFilterALL [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.073 s - in org.snpsift.testCases.unit.TestCasesFilterALL [INFO] Running org.snpsift.testCases.unit.TestCasesLd [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpsift.testCases.unit.TestCasesLd [INFO] Running org.snpsift.testCases.unit.TestCasesAnnotateUseIndex TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test TestCasesAnnotate.test_29_repeated_IDs(618): Test TestCasesAnnotate.test_01(145): Test TestCasesAnnotate.test_02(153): Test TestCasesAnnotate.test_03(161): Test TestCasesAnnotate.test_04(169): Test TestCasesAnnotate.test_05(181): Test TestCasesAnnotate.test_06(192): Test TestCasesAnnotate.test_07(217): Test TestCasesAnnotate.test_08(232): Test TestCasesAnnotate.test_09(245): Test TestCasesAnnotate.test_11(273): Test TestCasesAnnotate.test_12(300): Test TestCasesAnnotate.test_13(320): Test TestCasesAnnotate.test_14(340): Test TestCasesAnnotate.test_15(356): Test TestCasesAnnotate.test_16(372): Test TestCasesAnnotate.test_17(390): Test TestCasesAnnotate.test_18(415): Test TestCasesAnnotate.test_19(428): Test TestCasesAnnotate.test_20(439): Test TestCasesAnnotate.test_21(453): Test TestCasesAnnotate.test_22(479): Test TestCasesAnnotate.test_24(509): Test TestCasesAnnotate.test_25(539): Test TestCasesAnnotate.test_35(693): Test TestCasesAnnotate.test_36(711): Test TestCasesAnnotate.test_38(732): Test TestCasesAnnotate.test_39(743): Test TestCasesAnnotate.test_40(762): Test TestCasesAnnotate.test_41(770): Test TestCasesAnnotate.test_42(781): Test TestCasesAnnotate.test_43(809): Test TestCasesAnnotate.test_44(835): Test TestCasesAnnotate.test_45(861): Test TestCasesAnnotate.test_33_empty_db(665): Test TestCasesAnnotate.test_26_repeat_db_entry(568): Test TestCasesAnnotate.test_32_annotate_minimal_representation_input(654): Test TestCasesAnnotate.test_28_exists(596): Test TestCasesAnnotate.test_34_dbStartsOnDifferentChromo(676): Test TestCasesAnnotate.test_23_allele_specific_annotation_missing_R(491): Test TestCasesAnnotate.test_27_repeat_db_entry(580): Test [INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.65 s - in org.snpsift.testCases.unit.TestCasesAnnotateUseIndex [INFO] Running org.snpsift.testCases.unit.TestCasesConcordance TestCasesConcordance.test_01(68): Test TestCasesConcordance.test_02(74): Test TestCasesConcordance.test_03(80): Test TestCasesConcordance.test_04(91): Test TestCasesConcordance.test_05(102): Test TestCasesConcordance.test_06(113): Test TestCasesConcordance.test_07(125): Test TestCasesConcordance.test_08(131): Test TestCasesConcordance.test_09(142): Test TestCasesConcordance.test_10(153): Test TestCasesConcordance.test_11(164): Test TestCasesConcordance.test_12(181): Test [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 s - in org.snpsift.testCases.unit.TestCasesConcordance [INFO] Running org.snpsift.testCases.unit.TestCasesVarType TestCasesVarType.test_05_multiple(82): Test TestCasesVarType.test_01_SNP(58): Test TestCasesVarType.test_02_MNP(64): Test TestCasesVarType.test_03_INS(70): Test TestCasesVarType.test_04_DEL(76): Test [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.snpsift.testCases.unit.TestCasesVarType [INFO] Running org.snpsift.testCases.unit.TestCasesExtractFields TestCasesExtractFields.test_31_ann(291): Test TestCasesExtractFields.test_00(71): Test TestCasesExtractFields.test_01(98): Test TestCasesExtractFields.test_02(104): Test TestCasesExtractFields.test_03(110): Test TestCasesExtractFields.test_04(116): Test TestCasesExtractFields.test_05(122): Test TestCasesExtractFields.test_06(128): Test TestCasesExtractFields.test_07(134): Test TestCasesExtractFields.test_08(140): Test TestCasesExtractFields.test_09(146): Test TestCasesExtractFields.test_10(152): Test TestCasesExtractFields.test_11(158): Test TestCasesExtractFields.test_12(164): Test TestCasesExtractFields.test_13(170): Test TestCasesExtractFields.test_14(176): Test TestCasesExtractFields.test_15(182): Test TestCasesExtractFields.test_16(188): Test TestCasesExtractFields.test_17(194): Test TestCasesExtractFields.test_18(200): Test TestCasesExtractFields.test_19(206): Test TestCasesExtractFields.test_20(212): Test TestCasesExtractFields.test_23(218): Test TestCasesExtractFields.test_24(224): Test TestCasesExtractFields.test_25(230): Test TestCasesExtractFields.test_26(236): Test TestCasesExtractFields.test_27(242): Test TestCasesExtractFields.test_28(253): Test TestCasesExtractFields.test_29(262): Test TestCasesExtractFields.test_30(273): Test TestCasesExtractFields.test_31(282): Test TestCasesExtractFields.test_32(300): Test TestCasesExtractFields.test_33(312): Test TestCasesExtractFields.test_34(323): Test TestCasesExtractFields.test_35(340): Test [INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.06 s - in org.snpsift.testCases.unit.TestCasesExtractFields [INFO] Running org.snpsift.testCases.unit.TestCasesAnnotateCreateIndex TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test TestCasesAnnotate.test_29_repeated_IDs(618): Test TestCasesAnnotate.test_01(145): Test TestCasesAnnotate.test_02(153): Test TestCasesAnnotate.test_03(161): Test TestCasesAnnotate.test_04(169): Test TestCasesAnnotate.test_05(181): Test TestCasesAnnotate.test_06(192): Test TestCasesAnnotate.test_07(217): Test TestCasesAnnotate.test_08(232): Test TestCasesAnnotate.test_09(245): Test TestCasesAnnotate.test_11(273): Test TestCasesAnnotate.test_12(300): Test TestCasesAnnotate.test_13(320): Test TestCasesAnnotate.test_14(340): Test TestCasesAnnotate.test_15(356): Test TestCasesAnnotate.test_16(372): Test TestCasesAnnotate.test_17(390): Test TestCasesAnnotate.test_18(415): Test TestCasesAnnotate.test_19(428): Test TestCasesAnnotate.test_20(439): Test TestCasesAnnotate.test_21(453): Test TestCasesAnnotate.test_22(479): Test TestCasesAnnotate.test_24(509): Test TestCasesAnnotate.test_25(539): Test TestCasesAnnotate.test_35(693): Test TestCasesAnnotate.test_36(711): Test TestCasesAnnotate.test_38(732): Test TestCasesAnnotate.test_39(743): Test TestCasesAnnotate.test_40(762): Test TestCasesAnnotate.test_41(770): Test TestCasesAnnotate.test_42(781): Test TestCasesAnnotate.test_43(809): Test TestCasesAnnotate.test_44(835): Test TestCasesAnnotate.test_45(861): Test TestCasesAnnotate.test_33_empty_db(665): Test TestCasesAnnotate.test_26_repeat_db_entry(568): Test TestCasesAnnotate.test_32_annotate_minimal_representation_input(654): Test TestCasesAnnotate.test_28_exists(596): Test TestCasesAnnotate.test_34_dbStartsOnDifferentChromo(676): Test TestCasesAnnotate.test_23_allele_specific_annotation_missing_R(491): Test TestCasesAnnotate.test_27_repeat_db_entry(580): Test [INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.538 s - in org.snpsift.testCases.unit.TestCasesAnnotateCreateIndex [INFO] Running org.snpsift.testCases.unit.TestCasesSort TestCasesSort.test_01(30): Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpsift.testCases.unit.TestCasesSort [INFO] Running org.snpsift.testCases.unit.TestCasesCaseControl TestCasesCaseControl.test_01(53): Test TestCasesCaseControl.test_02(65): Test TestCasesCaseControl.test_03(83): Test TestCasesCaseControl.test_04(107): Test TestCasesCaseControl.test_05(119): Test TestCasesCaseControl.test_06(125): Test TestCasesCaseControl.test_07(131): Test TestCasesCaseControl.test_08(137): Test TestCasesCaseControl.test_09(146): Test TestCasesCaseControl.test_10(222): Test TestCasesCaseControl.test_02_Str2(77): Test TestCasesCaseControl.test_03_Str2(95): Test TestCasesCaseControl.test_03_Str3(101): Test TestCasesCaseControl.test_01_Str(59): Test TestCasesCaseControl.test_02_Str(71): Test TestCasesCaseControl.test_03_Str(89): Test TestCasesCaseControl.test_04_Str(113): Test [INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.25 s - in org.snpsift.testCases.unit.TestCasesCaseControl [INFO] Running org.snpsift.testCases.unit.TestCasesAnnotateMem TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test TestCasesAnnotate.test_29_repeated_IDs(618): Test TestCasesAnnotate.test_01(145): Test TestCasesAnnotate.test_02(153): Test TestCasesAnnotate.test_03(161): Test TestCasesAnnotate.test_04(169): Test TestCasesAnnotate.test_05(181): Test TestCasesAnnotate.test_06(192): Test TestCasesAnnotate.test_07(217): Test TestCasesAnnotate.test_08(232): Test TestCasesAnnotate.test_09(245): Test TestCasesAnnotate.test_11(273): Test TestCasesAnnotate.test_12(300): Test TestCasesAnnotate.test_13(320): Test TestCasesAnnotate.test_14(340): Test TestCasesAnnotate.test_15(356): Test TestCasesAnnotate.test_16(372): Test TestCasesAnnotate.test_17(390): Test TestCasesAnnotate.test_18(415): Test TestCasesAnnotate.test_19(428): Test TestCasesAnnotate.test_20(439): Test TestCasesAnnotate.test_21(453): Test TestCasesAnnotate.test_22(479): Test TestCasesAnnotate.test_24(509): Test TestCasesAnnotate.test_25(539): Test TestCasesAnnotate.test_35(693): Test TestCasesAnnotate.test_36(711): Test TestCasesAnnotate.test_38(732): Test TestCasesAnnotate.test_39(743): Test TestCasesAnnotate.test_40(762): Test TestCasesAnnotate.test_41(770): Test TestCasesAnnotate.test_42(781): Test TestCasesAnnotate.test_43(809): Test TestCasesAnnotate.test_44(835): Test TestCasesAnnotate.test_45(861): Test TestCasesAnnotate.test_33_empty_db(665): Test TestCasesAnnotate.test_26_repeat_db_entry(568): Test TestCasesAnnotate.test_32_annotate_minimal_representation_input(654): Test TestCasesAnnotate.test_28_exists(596): Test TestCasesAnnotate.test_34_dbStartsOnDifferentChromo(676): Test TestCasesAnnotate.test_23_allele_specific_annotation_missing_R(491): Test TestCasesAnnotate.test_27_repeat_db_entry(580): Test [INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.388 s - in org.snpsift.testCases.unit.TestCasesAnnotateMem [INFO] Running org.snpsift.testCases.unit.TestCasesPrivate TestCasesPrivate.test_01(48): Test TestCasesPrivate.test_02(59): Test TestCasesPrivate.test_03(70): Test TestCasesPrivate.test_04(81): Test TestCasesPrivate.test_05(89): Test TestCasesPrivate.test_06(95): Test TestCasesPrivate.test_07(101): Test TestCasesPrivate.test_08(107): Test [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.snpsift.testCases.unit.TestCasesPrivate [INFO] Running org.snpsift.testCases.unit.TestCasesIntervals TestCasesIntervals.test_01(25): Test TestCasesIntervals.test_02(50): Test [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.snpsift.testCases.unit.TestCasesIntervals [INFO] Running org.snpsift.testCases.unit.TestCasesDbNsfp TestCasesDbNsfp.test_01(113): Test TestCasesDbNsfp.test_02(138): Test TestCasesDbNsfp.test_03(160): Test TestCasesDbNsfp.test_04(179): Test TestCasesDbNsfp.test_05(200): Test TestCasesDbNsfp.test_06(223): Test [INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.492 s - in org.snpsift.testCases.unit.TestCasesDbNsfp [INFO] Running org.snpsift.testCases.unit.TestCasesDbNsfpDeleteCache TestCasesDbNsfp.test_01(113): Test TestCasesDbNsfp.test_02(138): Test TestCasesDbNsfp.test_03(160): Test TestCasesDbNsfp.test_04(179): Test TestCasesDbNsfp.test_05(200): Test TestCasesDbNsfp.test_06(223): Test [INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.09 s - in org.snpsift.testCases.unit.TestCasesDbNsfpDeleteCache [INFO] Running org.snpsift.testCases.unit.TestCasesFilter TestCasesFilter.test_57_short_circuit_AND_OR_operators(1724): Test TestCasesFilter.test_32_ann(988): Test TestCasesFilter.test_33_ann(1049): Test TestCasesFilter.test_34_ann(1108): Test TestCasesFilter.test_35_ann(1167): Test TestCasesFilter.test_01(40): Test TestCasesFilter.test_02(64): Test TestCasesFilter.test_03(86): Test TestCasesFilter.test_04(110): Test TestCasesFilter.test_05(134): Test TestCasesFilter.test_06(158): Test TestCasesFilter.test_07(182): Test TestCasesFilter.test_08(208): Test TestCasesFilter.test_09(236): Test TestCasesFilter.test_10(258): Test TestCasesFilter.test_11(281): Test TestCasesFilter.test_12(303): Test TestCasesFilter.test_13(326): Test TestCasesFilter.test_14(348): Test TestCasesFilter.test_15(381): Test TestCasesFilter.test_16(407): Test TestCasesFilter.test_17(435): Test TestCasesFilter.test_18(459): Test TestCasesFilter.test_19(483): Test TestCasesFilter.test_20(507): Test TestCasesFilter.test_21(532): Test TestCasesFilter.test_22(559): Test TestCasesFilter.test_23(615): Test TestCasesFilter.test_24(642): Test TestCasesFilter.test_25(669): Test TestCasesFilter.test_26(697): Test TestCasesFilter.test_27(748): Test TestCasesFilter.test_28(846): Test TestCasesFilter.test_29(875): Test TestCasesFilter.test_30(903): Test TestCasesFilter.test_31(932): Test TestCasesFilter.test_32(960): Test TestCasesFilter.test_33(1021): Test TestCasesFilter.test_34(1081): Test TestCasesFilter.test_35(1140): Test TestCasesFilter.test_36(1198): Test TestCasesFilter.test_37(1222): Test TestCasesFilter.test_38(1247): Test TestCasesFilter.test_39(1272): Test TestCasesFilter.test_40(1295): Test TestCasesFilter.test_41(1320): Test TestCasesFilter.test_42(1356): Test TestCasesFilter.test_43(1374): Test TestCasesFilter.test_44(1392): Test TestCasesFilter.test_45(1410): Test TestCasesFilter.test_46(1437): Test TestCasesFilter.test_47(1448): Test TestCasesFilter.test_48(1459): Test TestCasesFilter.test_49(1475): Test TestCasesFilter.test_50(1494): Test TestCasesFilter.test_51(1526): Test TestCasesFilter.test_52(1560): Test TestCasesFilter.test_53(1583): Test TestCasesFilter.test_54(1605): Test TestCasesFilter.test_55(1627): Test TestCasesFilter.test_22_3(589): Test TestCasesFilter.test_55_2(1647): Test TestCasesFilter.test_55_3(1667): Test TestCasesFilter.test_56_empty_vcf(1687): Test TestCasesFilter.test_58_rmFilter_info_field(1747): Test TestCasesFilter.test_27_ann2(812): Test TestCasesFilter.test_26_ann(721): Test TestCasesFilter.test_27_ann(778): Test [INFO] Tests run: 68, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.271 s - in org.snpsift.testCases.unit.TestCasesFilter [INFO] Running org.snpsift.testCases.unit.TestCasesGeneSets TestCasesGeneSets.test_01(25): Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s - in org.snpsift.testCases.unit.TestCasesGeneSets [INFO] Running org.snpsift.testCases.unit.TestCasesAnnotateTabix TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test TestCasesAnnotate.test_29_repeated_IDs(618): Test TestCasesAnnotate.test_01(145): Test TestCasesAnnotate.test_02(153): Test TestCasesAnnotate.test_03(161): Test TestCasesAnnotate.test_04(169): Test TestCasesAnnotate.test_05(181): Test TestCasesAnnotate.test_06(192): Test TestCasesAnnotate.test_07(217): Test TestCasesAnnotate.test_08(232): Test TestCasesAnnotate.test_09(245): Test TestCasesAnnotate.test_11(273): Test TestCasesAnnotate.test_12(300): Test TestCasesAnnotate.test_13(320): Test TestCasesAnnotate.test_14(340): Test TestCasesAnnotate.test_15(356): Test TestCasesAnnotate.test_16(372): Test TestCasesAnnotate.test_17(390): Test TestCasesAnnotate.test_18(415): Test TestCasesAnnotate.test_19(428): Test TestCasesAnnotate.test_20(439): Test TestCasesAnnotate.test_21(453): Test TestCasesAnnotate.test_22(479): Test TestCasesAnnotate.test_24(509): Test TestCasesAnnotate.test_25(539): Test TestCasesAnnotate.test_35(693): Test TestCasesAnnotate.test_36(711): Test TestCasesAnnotate.test_38(732): Test TestCasesAnnotate.test_39(743): Test TestCasesAnnotate.test_40(762): Test TestCasesAnnotate.test_41(770): Test TestCasesAnnotate.test_42(781): Test TestCasesAnnotate.test_43(809): Test TestCasesAnnotate.test_44(835): Test TestCasesAnnotate.test_45(861): Test TestCasesAnnotate.test_33_empty_db(665): Test TestCasesAnnotate.test_26_repeat_db_entry(568): Test TestCasesAnnotate.test_32_annotate_minimal_representation_input(654): Test TestCasesAnnotate.test_28_exists(596): Test TestCasesAnnotate.test_34_dbStartsOnDifferentChromo(676): Test TestCasesAnnotate.test_23_allele_specific_annotation_missing_R(491): Test TestCasesAnnotate.test_27_repeat_db_entry(580): Test [INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.657 s - in org.snpsift.testCases.unit.TestCasesAnnotateTabix [INFO] Running org.snpsift.testCases.unit.TestCasesVcfCheck TestCasesVcfCheck.test_01(18): Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.snpsift.testCases.unit.TestCasesVcfCheck [INFO] Running org.snpsift.testCases.unit.TestCasesSplit TestCasesSplit.test_01(28): Test TestCasesSplit.test_02(58): Test TestCasesSplit.test_03(84): Test [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.snpsift.testCases.unit.TestCasesSplit [INFO] Running org.snpsift.testCases.unit.TestCasesIndex TestCasesIndex.test_01(32): Test TestCasesIndex.test_02(84): Test [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.832 s - in org.snpsift.testCases.unit.TestCasesIndex [INFO] Running org.snpsift.testCases.unit.TestCasesGwasCatalog TestCasesGwasCatalog.test_01(34): Test WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '19:16185558' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs8109288' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '19:46172277' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs11671664' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '11:116648916' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs964184' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '6:161010117' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs10455872' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '1:67705957' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs11209026' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '19:45412078' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs7412' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '2:169763147' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs560887' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: Too many 'WARNING_DUPLICATE_PRIMARY_KEY' warnings, no further warnings will be shown. TestCasesGwasCatalog.test_02(50): Test [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.46 s - in org.snpsift.testCases.unit.TestCasesGwasCatalog [INFO] Running org.snpsift.testCases.unit.TestCasesAnnotate TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test TestCasesAnnotate.test_29_repeated_IDs(618): Test TestCasesAnnotate.test_01(145): Test TestCasesAnnotate.test_02(153): Test TestCasesAnnotate.test_03(161): Test TestCasesAnnotate.test_04(169): Test TestCasesAnnotate.test_05(181): Test TestCasesAnnotate.test_06(192): Test TestCasesAnnotate.test_07(217): Test TestCasesAnnotate.test_08(232): Test TestCasesAnnotate.test_09(245): Test TestCasesAnnotate.test_11(273): Test TestCasesAnnotate.test_12(300): Test TestCasesAnnotate.test_13(320): Test TestCasesAnnotate.test_14(340): Test TestCasesAnnotate.test_15(356): Test TestCasesAnnotate.test_16(372): Test TestCasesAnnotate.test_17(390): Test TestCasesAnnotate.test_18(415): Test TestCasesAnnotate.test_19(428): Test TestCasesAnnotate.test_20(439): Test TestCasesAnnotate.test_21(453): Test TestCasesAnnotate.test_22(479): Test TestCasesAnnotate.test_24(509): Test TestCasesAnnotate.test_25(539): Test TestCasesAnnotate.test_35(693): Test TestCasesAnnotate.test_36(711): Test TestCasesAnnotate.test_38(732): Test TestCasesAnnotate.test_39(743): Test TestCasesAnnotate.test_40(762): Test TestCasesAnnotate.test_41(770): Test TestCasesAnnotate.test_42(781): Test TestCasesAnnotate.test_43(809): Test TestCasesAnnotate.test_44(835): Test TestCasesAnnotate.test_45(861): Test TestCasesAnnotate.test_33_empty_db(665): Test TestCasesAnnotate.test_26_repeat_db_entry(568): Test TestCasesAnnotate.test_32_annotate_minimal_representation_input(654): Test TestCasesAnnotate.test_28_exists(596): Test TestCasesAnnotate.test_34_dbStartsOnDifferentChromo(676): Test TestCasesAnnotate.test_23_allele_specific_annotation_missing_R(491): Test TestCasesAnnotate.test_27_repeat_db_entry(580): Test [INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.814 s - in org.snpsift.testCases.unit.TestCasesAnnotate [INFO] [INFO] Results: [INFO] [INFO] Tests run: 403, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:11 min [INFO] Finished at: 2025-06-04T01:21:25-12:00 [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/reproducible-path/snpsift-5.1+dfsg2' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/snpsift-5.1\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/snpsift-5.1\+dfsg2/debian -Dmaven.repo.local=/build/reproducible-path/snpsift-5.1\+dfsg2/debian/maven-repo --batch-mode -Ddebian.dir=/build/reproducible-path/snpsift-5.1\+dfsg2/debian -Ddebian.package=libsnpsift-java -Dmaven.repo.local=/build/reproducible-path/snpsift-5.1\+dfsg2/debian/maven-repo -Dinstall.to.usj=true org.debian.maven:debian-maven-plugin:2.6:install OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release. [INFO] Scanning for projects... [INFO] [INFO] ------------------------< org.snpsift:snpsift >------------------------- [INFO] Building SnpSift 5.1 [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ snpsift --- [INFO] Cleaning pom file: /build/reproducible-path/snpsift-5.1+dfsg2/pom.xml.save with options: [INFO] --keep-pom-version --package=libsnpsift-java [INFO] --rules=/build/reproducible-path/snpsift-5.1+dfsg2/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/snpsift-5.1+dfsg2/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/snpsift-5.1+dfsg2/debian/maven.publishedRules [INFO] Install jar for snpsift into /usr/share/java [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.436 s [INFO] Finished at: 2025-06-04T01:21:26-12:00 [INFO] ------------------------------------------------------------------------ mh_resolve_dependencies --non-interactive --offline --build -plibsnpsift-java --javadoc --base-directory=/build/reproducible-path/snpsift-5.1\+dfsg2 --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... Checking dependencies for documentation packages... > dpkg --search /usr/share/doc/antlr4/api/index.html Found antlr4-doc > dpkg --search /usr/share/doc/libcommons-math3-java/api/index.html Found libcommons-math3-java-doc > dpkg --search /usr/share/doc/libhtsjdk-java/api/index.html Found libhtsjdk-java-doc > dpkg --search /usr/share/doc/libsnpeff-java/api/index.html Found libsnpeff-java-doc > dpkg --search /usr/share/doc/libtrove3-java/api/index.html Found libtrove3-java-doc bash -c "rm -f target/apidocs/*.sh target/apidocs/options" mh_unpatchpoms -plibsnpsift-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 libsnpsift-java: substitution variable ${java:Depends} unused, but is defined dpkg-gencontrol: warning: package libsnpsift-java: substitution variable ${maven:CompileDepends} unused, but is defined dpkg-gencontrol: warning: package libsnpsift-java: substitution variable ${maven:DocDepends} unused, but is defined dpkg-gencontrol: warning: package libsnpsift-java-doc: substitution variable ${maven:CompileDepends} unused, but is defined dpkg-gencontrol: warning: package libsnpsift-java-doc: substitution variable ${maven:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'libsnpsift-java' in '../libsnpsift-java_5.1+dfsg2-2_all.deb'. dpkg-deb: building package 'snpsift' in '../snpsift_5.1+dfsg2-2_all.deb'. dpkg-deb: building package 'libsnpsift-java-doc' in '../libsnpsift-java-doc_5.1+dfsg2-2_all.deb'. dpkg-genbuildinfo --build=binary -O../snpsift_5.1+dfsg2-2_amd64.buildinfo dpkg-genchanges --build=binary -O../snpsift_5.1+dfsg2-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1402880 and its subdirectories I: Current time: Wed Jun 4 01:22:01 -12 2025 I: pbuilder-time-stamp: 1749043321 Thu May 2 06:59:03 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Thu May 2 06:59:03 UTC 2024 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Thu May 2 07:13:49 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Thu May 2 07:13:49 UTC 2024 I: snpsift_5.1+dfsg2-2_amd64.changes: Format: 1.8 Date: Sun, 27 Feb 2022 14:17:09 +0100 Source: snpsift Binary: libsnpsift-java libsnpsift-java-doc snpsift Architecture: all Version: 5.1+dfsg2-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Pierre Gruet Description: libsnpsift-java - tool to annotate and manipulate genome variants - lib libsnpsift-java-doc - Documentation for SnpSift snpsift - tool to annotate and manipulate genome variants - tool Changes: snpsift (5.1+dfsg2-2) unstable; urgency=medium . * Source-only upload Checksums-Sha1: 1d557a0cd1d3bc9f37d993cd7fc7dc0a82b2267d 215728 libsnpsift-java-doc_5.1+dfsg2-2_all.deb a3ff60e8d3eff162f644727f010c66dca695d569 311476 libsnpsift-java_5.1+dfsg2-2_all.deb e3a649232d00477fa0db9753d5cc3ed8f77cfedd 4400 snpsift_5.1+dfsg2-2_all.deb 273ac626604cc6bac82c541cc7a87f231a6b345f 15798 snpsift_5.1+dfsg2-2_amd64.buildinfo Checksums-Sha256: d0c418ddc46fc97cbb970cd14cae834ca96af4d6f647fed68169a966c42eab83 215728 libsnpsift-java-doc_5.1+dfsg2-2_all.deb 9f09e50483e497b9f73b5e4a91f2c0866cba2562bbbd14898c84a7a16952b7ab 311476 libsnpsift-java_5.1+dfsg2-2_all.deb 44a620dac28d7a206b1f91f050189589dce45802662657d98673073a10c35dff 4400 snpsift_5.1+dfsg2-2_all.deb 71cab578c1088af13cde86fdb23e98087ba11c78fd96ddeaae1c6060664b1c6f 15798 snpsift_5.1+dfsg2-2_amd64.buildinfo Files: 72b64804ebb38f3a3ec50ca65d5f3339 215728 doc optional libsnpsift-java-doc_5.1+dfsg2-2_all.deb c9897e51c734691b513605a4c00200f1 311476 java optional libsnpsift-java_5.1+dfsg2-2_all.deb 2f25f078e01d730117ece5ec15cff742 4400 java optional snpsift_5.1+dfsg2-2_all.deb 3af76f66e9fe1dba95246a73788ef2ff 15798 java optional snpsift_5.1+dfsg2-2_amd64.buildinfo Thu May 2 07:13:51 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_24-18959.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.DuYiYMto/snpsift_5.1+dfsg2-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.DuYiYMto/snpsift_5.1+dfsg2-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.DuYiYMto/snpsift_5.1+dfsg2-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.DuYiYMto/b1/snpsift_5.1+dfsg2-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.DuYiYMto/b2/snpsift_5.1+dfsg2-2_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.397s) 0.397s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.022s) 0.022s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 741ms CPU time consumed: 718ms Thu May 2 07:13:52 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Thu May 2 07:13:52 UTC 2024 I: snpsift from trixie built successfully and reproducibly on amd64. Thu May 2 07:13:53 UTC 2024 I: Submitting .buildinfo files to external archives: Thu May 2 07:13:54 UTC 2024 I: Submitting 20K b1/snpsift_5.1+dfsg2-2_amd64.buildinfo.asc Thu May 2 07:13:54 UTC 2024 I: Submitting 20K b2/snpsift_5.1+dfsg2-2_amd64.buildinfo.asc Thu May 2 07:13:55 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu May 2 07:13:55 UTC 2024 I: Done submitting .buildinfo files. Thu May 2 07:13:55 UTC 2024 I: Removing signed snpsift_5.1+dfsg2-2_amd64.buildinfo.asc files: removed './b1/snpsift_5.1+dfsg2-2_amd64.buildinfo.asc' removed './b2/snpsift_5.1+dfsg2-2_amd64.buildinfo.asc'