Wed Apr 19 14:53:23 UTC 2023 I: starting to build snpsift/bookworm/arm64 on jenkins on '2023-04-19 14:53' Wed Apr 19 14:53:23 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_20/24325/console.log Wed Apr 19 14:53:23 UTC 2023 I: Downloading source for bookworm/snpsift=5.1+dfsg2-2 --2023-04-19 14:53:24-- http://cdn-fastly.deb.debian.org/debian/pool/main/s/snpsift/snpsift_5.1%2bdfsg2-2.dsc Connecting to 78.137.99.97:3128... 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% 177M=0s 2023-04-19 14:53:24 (177 MB/s) - ‘snpsift_5.1+dfsg2-2.dsc’ saved [2422/2422] Wed Apr 19 14:53:24 UTC 2023 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----- Wed Apr 19 14:53:24 UTC 2023 I: Checking whether the package is not for us Wed Apr 19 14:53:24 UTC 2023 I: Starting 1st build on remote node codethink13-arm64.debian.net. Wed Apr 19 14:53:24 UTC 2023 I: Preparing to do remote build '1' on codethink13-arm64.debian.net. Wed Apr 19 15:16:17 UTC 2023 I: Deleting $TMPDIR on codethink13-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue May 21 09:16:36 -12 2024 I: pbuilder-time-stamp: 1716326196 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [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 01:43:28 2022 -12 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/27516/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='bookworm' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='27516' 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.yHGQte7s/pbuilderrc_GmYx --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.yHGQte7s/b1 --logfile b1/build.log snpsift_5.1+dfsg2-2.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink13-arm64 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 19 04:47 /bin -> usr/bin I: user script /srv/workspace/pbuilder/27516/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: arm64 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 ... 19616 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: ant{a} ant-optional{a} antlr4{a} antlr4-doc{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} dctrl-tools{a} debhelper{a} default-jdk-doc{a} default-jdk-headless{a} default-jre-headless{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{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-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} libasound2{a} libasound2-data{a} libassuan0{a} libatinject-jsr330-api-java{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libb-hooks-op-check-perl{a} libbatik-java{a} libbiojava6-java{a} libbrotli1{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} libcups2{a} libdbus-1-3{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} libelf1{a} libencode-locale-perl{a} liberror-prone-java{a} libexec-maven-plugin-java{a} libexpat1{a} libfastinfoset-java{a} libfastutil-java{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} libfontbox2-java{a} libfontconfig1{a} libfop-java{a} libfreemarker-java{a} libfreetype6{a} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libglib2.0-0{a} libgoogle-gson-java{a} libgraphite2-3{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhtsjdk-java{a} 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} libmagic1{a} libmaven-archiver-java{a} libmaven-artifact-transfer-java{a} libmaven-assembly-plugin-java{a} libmaven-clean-plugin-java{a} libmaven-common-artifact-filters-java{a} libmaven-compiler-plugin-java{a} libmaven-file-management-java{a} libmaven-filtering-java{a} libmaven-invoker-java{a} libmaven-jar-plugin-java{a} libmaven-javadoc-plugin-java{a} libmaven-parent-java{a} libmaven-plugin-tools-java{a} libmaven-reporting-api-java{a} libmaven-reporting-exec-java{a} libmaven-reporting-impl-java{a} libmaven-resolver-java{a} libmaven-resources-plugin-java{a} libmaven-shared-incremental-java{a} libmaven-shared-io-java{a} libmaven-shared-utils-java{a} libmaven-site-plugin-java{a} libmaven3-core-java{a} libmbedcrypto7{a} libmbedtls14{a} libmbedx509-1{a} libmjson-java{a} libmmtf-java{a} libmodule-runtime-perl{a} libmoo-perl{a} libmsgpack-java{a} libnaga-java{a} libncbi-ngs3{a} libncbi-vdb3{a} libnet-http-perl{a} libnet-ssleay-perl{a} libngs-java{a} libngs-jni{a} libnpth0{a} libnspr4{a} libnss3{a} libopentest4j-java{a} libopentest4j-reporting-java{a} liboro-java{a} 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} libpng16-16{a} libproc2-0{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqdox-java{a} libqdox2-java{a} libreadline8{a} libregexp-ipv6-perl{a} librelaxng-datatype-java{a} librhino-java{a} librngom-java{a} librole-tiny-perl{a} libsasl2-2{a} libsasl2-modules-db{a} 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} 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} unzip{a} velocity{a} wdiff{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf curl dbus debian-keyring dput dput-ng dupload equivs icc-profiles-free javascript-common libarchive-cpio-perl libbiojava6-java-doc libdata-dump-perl libdistlib-java-doc libdistro-info-perl libgit-wrapper-perl libgitlab-api-v4-perl libglib2.0-data libhtml-form-perl libhtml-format-perl libhttp-daemon-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 shared-mime-info strace wget xdg-user-dirs 0 packages upgraded, 338 newly installed, 0 to remove and 0 not upgraded. Need to get 472 MB of archives. After unpacking 1269 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-minimal arm64 3.11.2-6 [806 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 python3.11-minimal arm64 3.11.2-6 [1858 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 python3-minimal arm64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 libreadline8 arm64 8.2-1.3 [155 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-stdlib arm64 3.11.2-6 [1747 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 python3.11 arm64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 libpython3-stdlib arm64 3.11.2-1+b1 [9296 B] Get: 11 http://deb.debian.org/debian bookworm/main arm64 python3 arm64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 sgml-base all 1.31 [15.4 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 netbase all 6.4 [12.8 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 libproc2-0 arm64 2:4.0.2-3 [60.1 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 procps arm64 2:4.0.2-3 [698 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 openssl arm64 3.0.8-1 [1373 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 ca-certificates all 20230311 [153 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 21 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 23 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 ca-certificates-java all 20230103 [11.4 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 java-common all 0.74 [6388 B] Get: 30 http://deb.debian.org/debian bookworm/main arm64 libavahi-common-data arm64 0.8-9 [107 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 libavahi-common3 arm64 0.8-9 [40.3 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 libdbus-1-3 arm64 1.14.6-1 [191 kB] Get: 33 http://deb.debian.org/debian bookworm/main arm64 libavahi-client3 arm64 0.8-9 [43.7 kB] Get: 34 http://deb.debian.org/debian bookworm/main arm64 libcups2 arm64 2.4.2-3 [228 kB] Get: 35 http://deb.debian.org/debian bookworm/main arm64 liblcms2-2 arm64 2.14-2 [143 kB] Get: 36 http://deb.debian.org/debian bookworm/main arm64 libjpeg62-turbo arm64 1:2.1.5-2 [171 kB] Get: 37 http://deb.debian.org/debian bookworm/main arm64 libbrotli1 arm64 1.0.9-2+b6 [269 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 libpng16-16 arm64 1.6.39-2 [269 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 libfreetype6 arm64 2.12.1+dfsg-4 [369 kB] Get: 40 http://deb.debian.org/debian bookworm/main arm64 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 41 http://deb.debian.org/debian bookworm/main arm64 fontconfig-config arm64 2.14.1-4 [315 kB] Get: 42 http://deb.debian.org/debian bookworm/main arm64 libfontconfig1 arm64 2.14.1-4 [381 kB] Get: 43 http://deb.debian.org/debian bookworm/main arm64 libnspr4 arm64 2:4.35-1 [105 kB] Get: 44 http://deb.debian.org/debian bookworm/main arm64 libnss3 arm64 2:3.87.1-1 [1218 kB] Get: 45 http://deb.debian.org/debian bookworm/main arm64 libasound2-data all 1.2.8-1 [20.5 kB] Get: 46 http://deb.debian.org/debian bookworm/main arm64 libasound2 arm64 1.2.8-1+b1 [327 kB] Get: 47 http://deb.debian.org/debian bookworm/main arm64 libglib2.0-0 arm64 2.74.6-2 [1310 kB] Get: 48 http://deb.debian.org/debian bookworm/main arm64 libgraphite2-3 arm64 1.3.14-1 [75.6 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 libharfbuzz0b arm64 6.0.0+dfsg-3 [1914 kB] Get: 50 http://deb.debian.org/debian bookworm/main arm64 libpcsclite1 arm64 1.9.9-2 [49.3 kB] Get: 51 http://deb.debian.org/debian bookworm/main arm64 openjdk-17-jre-headless arm64 17.0.6+10-1 [42.5 MB] Get: 52 http://deb.debian.org/debian bookworm/main arm64 default-jre-headless arm64 2:1.17-74 [2932 B] Get: 53 http://deb.debian.org/debian bookworm/main arm64 ant all 1.10.13-1 [2161 kB] Get: 54 http://deb.debian.org/debian bookworm/main arm64 ant-optional all 1.10.13-1 [449 kB] Get: 55 http://deb.debian.org/debian bookworm/main arm64 libantlr4-runtime-java all 4.7.2-5 [315 kB] Get: 56 http://deb.debian.org/debian bookworm/main arm64 libantlr3-runtime-java all 3.5.3-1 [165 kB] Get: 57 http://deb.debian.org/debian bookworm/main arm64 libicu4j-java all 72.1-1 [16.3 MB] Get: 58 http://deb.debian.org/debian bookworm/main arm64 libjsonp-java all 1.1.2-3 [127 kB] Get: 59 http://deb.debian.org/debian bookworm/main arm64 libstringtemplate4-java all 4.0.8-2.1 [241 kB] Get: 60 http://deb.debian.org/debian bookworm/main arm64 libtreelayout-java all 1.0.3-2 [27.0 kB] Get: 61 http://deb.debian.org/debian bookworm/main arm64 antlr4 all 4.7.2-5 [1345 kB] Get: 62 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 63 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 64 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery-ui-theme-base all 1.12.1+dfsg-1.1 [44.3 kB] Get: 65 http://deb.debian.org/debian bookworm/main arm64 openjdk-17-doc all 17.0.6+10-1 [12.8 MB] Get: 66 http://deb.debian.org/debian bookworm/main arm64 default-jdk-doc arm64 2:1.17-74 [3020 B] Get: 67 http://deb.debian.org/debian bookworm/main arm64 antlr4-doc all 4.7.2-5 [1093 kB] Get: 68 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 69 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 70 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 71 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 72 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 73 http://deb.debian.org/debian bookworm/main arm64 dctrl-tools arm64 2.24-3 [101 kB] Get: 74 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 75 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 76 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 77 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 78 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 79 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 80 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 81 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 82 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 83 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 84 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.1+b3 [619 kB] Get: 85 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 86 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 87 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 88 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 89 http://deb.debian.org/debian bookworm/main arm64 openjdk-17-jdk-headless arm64 17.0.6+10-1 [219 MB] Get: 90 http://deb.debian.org/debian bookworm/main arm64 default-jdk-headless arm64 2:1.17-74 [1108 B] Get: 91 http://deb.debian.org/debian bookworm/main arm64 libassuan0 arm64 2.5.5-5 [45.9 kB] Get: 92 http://deb.debian.org/debian bookworm/main arm64 gpgconf arm64 2.2.40-1.1 [557 kB] Get: 93 http://deb.debian.org/debian bookworm/main arm64 libksba8 arm64 1.6.3-2 [119 kB] Get: 94 http://deb.debian.org/debian bookworm/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg-10 [20.8 kB] Get: 95 http://deb.debian.org/debian bookworm/main arm64 libsasl2-2 arm64 2.1.28+dfsg-10 [58.0 kB] Get: 96 http://deb.debian.org/debian bookworm/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5 [171 kB] Get: 97 http://deb.debian.org/debian bookworm/main arm64 libnpth0 arm64 1.6-3 [18.6 kB] Get: 98 http://deb.debian.org/debian bookworm/main arm64 dirmngr arm64 2.2.40-1.1 [770 kB] Get: 99 http://deb.debian.org/debian bookworm/main arm64 gnupg-l10n all 2.2.40-1.1 [1093 kB] Get: 100 http://deb.debian.org/debian bookworm/main arm64 gnupg-utils arm64 2.2.40-1.1 [880 kB] Get: 101 http://deb.debian.org/debian bookworm/main arm64 gpg arm64 2.2.40-1.1 [903 kB] Get: 102 http://deb.debian.org/debian bookworm/main arm64 pinentry-curses arm64 1.2.1-1 [75.2 kB] Get: 103 http://deb.debian.org/debian bookworm/main arm64 gpg-agent arm64 2.2.40-1.1 [673 kB] Get: 104 http://deb.debian.org/debian bookworm/main arm64 gpg-wks-client arm64 2.2.40-1.1 [532 kB] Get: 105 http://deb.debian.org/debian bookworm/main arm64 gpg-wks-server arm64 2.2.40-1.1 [524 kB] Get: 106 http://deb.debian.org/debian bookworm/main arm64 gpgsm arm64 2.2.40-1.1 [651 kB] Get: 107 http://deb.debian.org/debian bookworm/main arm64 gnupg all 2.2.40-1.1 [846 kB] Get: 108 http://deb.debian.org/debian bookworm/main arm64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 109 http://deb.debian.org/debian bookworm/main arm64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 110 http://deb.debian.org/debian bookworm/main arm64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 111 http://deb.debian.org/debian bookworm/main arm64 libfile-touch-perl all 0.12-2 [8816 B] Get: 112 http://deb.debian.org/debian bookworm/main arm64 libio-pty-perl arm64 1:1.17-1 [34.5 kB] Get: 113 http://deb.debian.org/debian bookworm/main arm64 libipc-run-perl all 20220807.0-1 [104 kB] Get: 114 http://deb.debian.org/debian bookworm/main arm64 libclass-method-modifiers-perl all 2.14-1 [18.1 kB] Get: 115 http://deb.debian.org/debian bookworm/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b1 [35.3 kB] Get: 116 http://deb.debian.org/debian bookworm/main arm64 libb-hooks-op-check-perl arm64 0.22-2+b1 [10.4 kB] Get: 117 http://deb.debian.org/debian bookworm/main arm64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 118 http://deb.debian.org/debian bookworm/main arm64 libdevel-callchecker-perl arm64 0.008-2 [15.9 kB] Get: 119 http://deb.debian.org/debian bookworm/main arm64 libparams-classify-perl arm64 0.015-2+b1 [22.9 kB] Get: 120 http://deb.debian.org/debian bookworm/main arm64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 121 http://deb.debian.org/debian bookworm/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 122 http://deb.debian.org/debian bookworm/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 123 http://deb.debian.org/debian bookworm/main arm64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 124 http://deb.debian.org/debian bookworm/main arm64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 125 http://deb.debian.org/debian bookworm/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 126 http://deb.debian.org/debian bookworm/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 127 http://deb.debian.org/debian bookworm/main arm64 libhttp-date-perl all 6.05-2 [10.5 kB] Get: 128 http://deb.debian.org/debian bookworm/main arm64 libfile-listing-perl all 6.15-1 [12.6 kB] Get: 129 http://deb.debian.org/debian bookworm/main arm64 libhtml-tagset-perl all 3.20-6 [11.7 kB] Get: 130 http://deb.debian.org/debian bookworm/main arm64 libregexp-ipv6-perl all 0.03-3 [5212 B] Get: 131 http://deb.debian.org/debian bookworm/main arm64 liburi-perl all 5.17-1 [90.4 kB] Get: 132 http://deb.debian.org/debian bookworm/main arm64 libhtml-parser-perl arm64 3.81-1 [98.6 kB] Get: 133 http://deb.debian.org/debian bookworm/main arm64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 134 http://deb.debian.org/debian bookworm/main arm64 libclone-perl arm64 0.46-1 [13.5 kB] Get: 135 http://deb.debian.org/debian bookworm/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get: 136 http://deb.debian.org/debian bookworm/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 137 http://deb.debian.org/debian bookworm/main arm64 libhttp-message-perl all 6.44-1 [81.7 kB] Get: 138 http://deb.debian.org/debian bookworm/main arm64 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get: 139 http://deb.debian.org/debian bookworm/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 140 http://deb.debian.org/debian bookworm/main arm64 perl-openssl-defaults arm64 7+b1 [7924 B] Get: 141 http://deb.debian.org/debian bookworm/main arm64 libnet-ssleay-perl arm64 1.92-2+b1 [308 kB] Get: 142 http://deb.debian.org/debian bookworm/main arm64 libio-socket-ssl-perl all 2.081-2 [219 kB] Get: 143 http://deb.debian.org/debian bookworm/main arm64 libnet-http-perl all 6.22-1 [25.3 kB] Get: 144 http://deb.debian.org/debian bookworm/main arm64 liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get: 145 http://deb.debian.org/debian bookworm/main arm64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 146 http://deb.debian.org/debian bookworm/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 147 http://deb.debian.org/debian bookworm/main arm64 libwww-perl all 6.68-1 [186 kB] Get: 148 http://deb.debian.org/debian bookworm/main arm64 patchutils arm64 0.4.2-1 [73.5 kB] Get: 149 http://deb.debian.org/debian bookworm/main arm64 wdiff arm64 1.2.2-5 [119 kB] Get: 150 http://deb.debian.org/debian bookworm/main arm64 devscripts arm64 2.23.3 [1073 kB] Get: 151 http://deb.debian.org/debian bookworm/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 152 http://deb.debian.org/debian bookworm/main arm64 unzip arm64 6.0-28 [157 kB] Get: 153 http://deb.debian.org/debian bookworm/main arm64 java-wrappers all 0.4 [8916 B] Get: 154 http://deb.debian.org/debian bookworm/main arm64 javahelper all 0.78 [97.2 kB] Get: 155 http://deb.debian.org/debian bookworm/main arm64 libhamcrest-java all 2.2-1 [121 kB] Get: 156 http://deb.debian.org/debian bookworm/main arm64 junit4 all 4.13.2-3 [348 kB] Get: 157 http://deb.debian.org/debian bookworm/main arm64 libapiguardian-java all 1.1.2-1 [4656 B] Get: 158 http://deb.debian.org/debian bookworm/main arm64 libopentest4j-java all 1.2.0-4 [9516 B] Get: 159 http://deb.debian.org/debian bookworm/main arm64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 160 http://deb.debian.org/debian bookworm/main arm64 libpicocli-java all 4.6.2-2 [390 kB] Get: 161 http://deb.debian.org/debian bookworm/main arm64 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 162 http://deb.debian.org/debian bookworm/main arm64 junit5 all 5.9.2-1 [2398 kB] Get: 163 http://deb.debian.org/debian bookworm/main arm64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 164 http://deb.debian.org/debian bookworm/main arm64 libaopalliance-java all 20070526-7 [8572 B] Get: 165 http://deb.debian.org/debian bookworm/main arm64 libapache-pom-java all 29-2 [5276 B] Get: 166 http://deb.debian.org/debian bookworm/main arm64 libapfloat-java all 1.10.1-2 [620 kB] Get: 167 http://deb.debian.org/debian bookworm/main arm64 libargs4j-java all 2.33-2 [138 kB] Get: 168 http://deb.debian.org/debian bookworm/main arm64 libasm-java all 9.4-1 [389 kB] Get: 169 http://deb.debian.org/debian bookworm/main arm64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 170 http://deb.debian.org/debian bookworm/main arm64 libjaxp1.3-java all 1.3.05-6 [227 kB] Get: 171 http://deb.debian.org/debian bookworm/main arm64 libxml-commons-external-java all 1.4.01-5 [240 kB] Get: 172 http://deb.debian.org/debian bookworm/main arm64 libcommons-parent-java all 56-1 [10.8 kB] Get: 173 http://deb.debian.org/debian bookworm/main arm64 libcommons-io-java all 2.11.0-2 [319 kB] Get: 174 http://deb.debian.org/debian bookworm/main arm64 libcommons-logging-java all 1.2-3 [62.4 kB] Get: 175 http://deb.debian.org/debian bookworm/main arm64 libxmlgraphics-commons-java all 2.8-2 [623 kB] Get: 176 http://deb.debian.org/debian bookworm/main arm64 libbatik-java all 1.16+dfsg-1 [3908 kB] Get: 177 http://deb.debian.org/debian bookworm/main arm64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 178 http://deb.debian.org/debian bookworm/main arm64 libgoogle-gson-java all 2.10-1 [261 kB] Get: 179 http://deb.debian.org/debian bookworm/main arm64 libciftools-java all 4.0.5-1 [2139 kB] Get: 180 http://deb.debian.org/debian bookworm/main arm64 libcommons-codec-java all 1.15-1 [292 kB] Get: 181 http://deb.debian.org/debian bookworm/main arm64 libcommons-math-java all 2.2-8 [926 kB] Get: 182 http://deb.debian.org/debian bookworm/main arm64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 183 http://deb.debian.org/debian bookworm/main arm64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 184 http://deb.debian.org/debian bookworm/main arm64 libguava-java all 31.1-1 [2613 kB] Get: 185 http://deb.debian.org/debian bookworm/main arm64 libitext5-java all 5.5.13.3-2 [2665 kB] Get: 186 http://deb.debian.org/debian bookworm/main arm64 libjackson2-annotations-java all 2.14.0-1 [68.8 kB] Get: 187 http://deb.debian.org/debian bookworm/main arm64 libjackson2-core-java all 2.14.1-1 [447 kB] Get: 188 http://deb.debian.org/debian bookworm/main arm64 libjackson2-databind-java all 2.14.0-1 [1584 kB] Get: 189 http://deb.debian.org/debian bookworm/main arm64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 190 http://deb.debian.org/debian bookworm/main arm64 libjaxen-java all 1.1.6-4 [214 kB] Get: 191 http://deb.debian.org/debian bookworm/main arm64 libdom4j-java all 2.1.3-2 [310 kB] Get: 192 http://deb.debian.org/debian bookworm/main arm64 libmaven-shared-utils-java all 3.3.4-1 [138 kB] Get: 193 http://deb.debian.org/debian bookworm/main arm64 libcommons-cli-java all 1.5.0-1 [60.0 kB] Get: 194 http://deb.debian.org/debian bookworm/main arm64 libcommons-lang3-java all 3.12.0-2 [561 kB] Get: 195 http://deb.debian.org/debian bookworm/main arm64 libguice-java all 4.2.3-2 [1435 kB] Get: 196 http://deb.debian.org/debian bookworm/main arm64 libmaven-parent-java all 35-1 [6140 B] Get: 197 http://deb.debian.org/debian bookworm/main arm64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 198 http://deb.debian.org/debian bookworm/main arm64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 199 http://deb.debian.org/debian bookworm/main arm64 libmaven-resolver-java all 1.6.3-1 [548 kB] Get: 200 http://deb.debian.org/debian bookworm/main arm64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 201 http://deb.debian.org/debian bookworm/main arm64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 202 http://deb.debian.org/debian bookworm/main arm64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 203 http://deb.debian.org/debian bookworm/main arm64 libplexus-interpolation-java all 1.26-1 [76.8 kB] Get: 204 http://deb.debian.org/debian bookworm/main arm64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 205 http://deb.debian.org/debian bookworm/main arm64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 206 http://deb.debian.org/debian bookworm/main arm64 libcdi-api-java all 1.2-3 [54.3 kB] Get: 207 http://deb.debian.org/debian bookworm/main arm64 libslf4j-java all 1.7.32-1 [144 kB] Get: 208 http://deb.debian.org/debian bookworm/main arm64 libsisu-inject-java all 0.3.4-2 [347 kB] Get: 209 http://deb.debian.org/debian bookworm/main arm64 libsisu-plexus-java all 0.3.4-3 [181 kB] Get: 210 http://deb.debian.org/debian bookworm/main arm64 libmaven3-core-java all 3.8.7-1 [1572 kB] Get: 211 http://deb.debian.org/debian bookworm/main arm64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 212 http://deb.debian.org/debian bookworm/main arm64 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 213 http://deb.debian.org/debian bookworm/main arm64 libcommons-compress-java all 1.22-1 [615 kB] Get: 214 http://deb.debian.org/debian bookworm/main arm64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 215 http://deb.debian.org/debian bookworm/main arm64 libsnappy1v5 arm64 1.1.9-3 [25.4 kB] Get: 216 http://deb.debian.org/debian bookworm/main arm64 libsnappy-jni arm64 1.1.8.3-1 [7056 B] Get: 217 http://deb.debian.org/debian bookworm/main arm64 libsnappy-java all 1.1.8.3-1 [98.9 kB] Get: 218 http://deb.debian.org/debian bookworm/main arm64 libxz-java all 1.9-1 [143 kB] Get: 219 http://deb.debian.org/debian bookworm/main arm64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 220 http://deb.debian.org/debian bookworm/main arm64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 221 http://deb.debian.org/debian bookworm/main arm64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 222 http://deb.debian.org/debian bookworm/main arm64 libjsoup-java all 1.15.3-1 [431 kB] Get: 223 http://deb.debian.org/debian bookworm/main arm64 libwagon-http-java all 3.5.3-1 [49.5 kB] Get: 224 http://deb.debian.org/debian bookworm/main arm64 libistack-commons-java all 3.0.6-5 [145 kB] Get: 225 http://deb.debian.org/debian bookworm/main arm64 libcodemodel-java all 2.6+jaxb2.3.0.1-10.1 [164 kB] Get: 226 http://deb.debian.org/debian bookworm/main arm64 librelaxng-datatype-java all 1.0+ds1-3.1 [11.7 kB] Get: 227 http://deb.debian.org/debian bookworm/main arm64 librngom-java all 2.3.0.1-10.1 [290 kB] Get: 228 http://deb.debian.org/debian bookworm/main arm64 libxsom-java all 2.3.0.1-10.1 [400 kB] Get: 229 http://deb.debian.org/debian bookworm/main arm64 libtxw2-java all 2.3.0.1-10.1 [134 kB] Get: 230 http://deb.debian.org/debian bookworm/main arm64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 231 http://deb.debian.org/debian bookworm/main arm64 libdtd-parser-java all 1.2-1 [64.9 kB] Get: 232 http://deb.debian.org/debian bookworm/main arm64 libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 233 http://deb.debian.org/debian bookworm/main arm64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB] Get: 234 http://deb.debian.org/debian bookworm/main arm64 libfastinfoset-java all 1.2.12-3 [343 kB] Get: 235 http://deb.debian.org/debian bookworm/main arm64 libjaxb-java all 2.3.0.1-10.1 [1973 kB] Get: 236 http://deb.debian.org/debian bookworm/main arm64 libmaven-archiver-java all 3.6.0-1 [25.1 kB] Get: 237 http://deb.debian.org/debian bookworm/main arm64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 238 http://deb.debian.org/debian bookworm/main arm64 libcommons-text-java all 1.10.0-1 [211 kB] Get: 239 http://deb.debian.org/debian bookworm/main arm64 libfastutil-java all 8.5.11+dfsg-1 [19.6 MB] Get: 240 http://deb.debian.org/debian bookworm/main arm64 libjheaps-java all 0.14-2 [144 kB] Get: 241 http://deb.debian.org/debian bookworm/main arm64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 242 http://deb.debian.org/debian bookworm/main arm64 libjgraphx-java all 2.1.0.7-3 [807 kB] Get: 243 http://deb.debian.org/debian bookworm/main arm64 libjgrapht-java all 1.5.1-3 [1584 kB] Get: 244 http://deb.debian.org/debian bookworm/main arm64 libinchi1 arm64 1.03+dfsg-4 [387 kB] Get: 245 http://deb.debian.org/debian bookworm/main arm64 libjni-inchi-jni arm64 0.8+dfsg-7 [9312 B] Get: 246 http://deb.debian.org/debian bookworm/main arm64 libcommons-exec-java all 1.3-2 [48.1 kB] Get: 247 http://deb.debian.org/debian bookworm/main arm64 libexec-maven-plugin-java all 3.1.0-1 [66.2 kB] Get: 248 http://deb.debian.org/debian bookworm/main arm64 libmaven-shared-incremental-java all 1.1-3 [9524 B] Get: 249 http://deb.debian.org/debian bookworm/main arm64 libcommons-lang-java all 2.6-10 [273 kB] Get: 250 http://deb.debian.org/debian bookworm/main arm64 libxbean-reflect-java all 4.5-8 [133 kB] Get: 251 http://deb.debian.org/debian bookworm/main arm64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 252 http://deb.debian.org/debian bookworm/main arm64 libplexus-compiler-java all 2.12.1-1 [99.8 kB] Get: 253 http://deb.debian.org/debian bookworm/main arm64 libqdox2-java all 2.0.3-1 [296 kB] Get: 254 http://deb.debian.org/debian bookworm/main arm64 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 255 http://deb.debian.org/debian bookworm/main arm64 libmaven-compiler-plugin-java all 3.10.1-2 [59.0 kB] Get: 256 http://deb.debian.org/debian bookworm/main arm64 liblog4j1.2-java all 1.2.17-11 [444 kB] Get: 257 http://deb.debian.org/debian bookworm/main arm64 libjni-inchi-java all 0.8+dfsg-7 [33.2 kB] Get: 258 http://deb.debian.org/debian bookworm/main arm64 libnaga-java all 3.0+svn80-5 [43.5 kB] Get: 259 http://deb.debian.org/debian bookworm/main arm64 libjmol-java all 14.32.83+dfsg-1 [8698 kB] Get: 260 http://deb.debian.org/debian bookworm/main arm64 libjson-simple-java all 2.3.0-1 [63.8 kB] Get: 261 http://deb.debian.org/debian bookworm/main arm64 libmsgpack-java all 0.9.3-1 [155 kB] Get: 262 http://deb.debian.org/debian bookworm/main arm64 libmmtf-java all 1.0.11-1 [187 kB] Get: 263 http://deb.debian.org/debian bookworm/main arm64 libvecmath-java all 1.5.2-7 [97.0 kB] Get: 264 http://deb.debian.org/debian bookworm/main arm64 libbiojava6-java all 6.1.0+dfsg-4 [5367 kB] Get: 265 http://deb.debian.org/debian bookworm/main arm64 libbsh-java all 2.0b4-20 [291 kB] Get: 266 http://deb.debian.org/debian bookworm/main arm64 libcharts4j-java all 1.3-4 [162 kB] Get: 267 http://deb.debian.org/debian bookworm/main arm64 libcommons-collections3-java all 3.2.2-2 [526 kB] Get: 268 http://deb.debian.org/debian bookworm/main arm64 libcommons-beanutils-java all 1.9.4-1 [232 kB] Get: 269 http://deb.debian.org/debian bookworm/main arm64 libcommons-configuration-java all 1.10-6 [347 kB] Get: 270 http://deb.debian.org/debian bookworm/main arm64 libcommons-digester-java all 1.8.1-5 [168 kB] Get: 271 http://deb.debian.org/debian bookworm/main arm64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get: 272 http://deb.debian.org/debian bookworm/main arm64 libcommons-math3-java all 3.6.1-3 [2018 kB] Get: 273 http://deb.debian.org/debian bookworm/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 274 http://deb.debian.org/debian bookworm/main arm64 libcommons-math3-java-doc all 3.6.1-3 [1560 kB] Get: 275 http://deb.debian.org/debian bookworm/main arm64 libcommons-validator-java all 1:1.7-1 [181 kB] Get: 276 http://deb.debian.org/debian bookworm/main arm64 libdistlib-java all 1.0-4 [72.1 kB] Get: 277 http://deb.debian.org/debian bookworm/main arm64 libdoxia-core-java all 1.12.0-1 [213 kB] Get: 278 http://deb.debian.org/debian bookworm/main arm64 libfontbox2-java all 2.0.27-2 [1510 kB] Get: 279 http://deb.debian.org/debian bookworm/main arm64 libqdox-java all 1.12.1-3 [172 kB] Get: 280 http://deb.debian.org/debian bookworm/main arm64 libfop-java all 1:2.8-2 [10.1 MB] Get: 281 http://deb.debian.org/debian bookworm/main arm64 libitext1-java all 1.4-7 [1257 kB] Get: 282 http://deb.debian.org/debian bookworm/main arm64 libdoxia-java all 1.12.0-1 [459 kB] Get: 283 http://deb.debian.org/debian bookworm/main arm64 libmaven-reporting-api-java all 3.1.1-1 [7240 B] Get: 284 http://deb.debian.org/debian bookworm/main arm64 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB] Get: 285 http://deb.debian.org/debian bookworm/main arm64 velocity all 1.7-6 [429 kB] Get: 286 http://deb.debian.org/debian bookworm/main arm64 libplexus-velocity-java all 1.2-3.1 [10.5 kB] Get: 287 http://deb.debian.org/debian bookworm/main arm64 liboro-java all 2.0.8a-14 [70.5 kB] Get: 288 http://deb.debian.org/debian bookworm/main arm64 libvelocity-tools-java all 2.0-8 [308 kB] Get: 289 http://deb.debian.org/debian bookworm/main arm64 libxalan2-java all 2.7.2-4 [3419 kB] Get: 290 http://deb.debian.org/debian bookworm/main arm64 libdoxia-sitetools-java all 1.11.1-1 [202 kB] Get: 291 http://deb.debian.org/debian bookworm/main arm64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 292 http://deb.debian.org/debian bookworm/main arm64 libfreemarker-java all 2.3.31-2 [1528 kB] Get: 293 http://deb.debian.org/debian bookworm/main arm64 libmjson-java all 1.4.0-3 [60.4 kB] Get: 294 http://deb.debian.org/debian bookworm/main arm64 libmbedcrypto7 arm64 2.28.3-1 [263 kB] Get: 295 http://deb.debian.org/debian bookworm/main arm64 libmbedx509-1 arm64 2.28.3-1 [127 kB] Get: 296 http://deb.debian.org/debian bookworm/main arm64 libmbedtls14 arm64 2.28.3-1 [156 kB] Get: 297 http://deb.debian.org/debian bookworm/main arm64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB] Get: 298 http://deb.debian.org/debian bookworm/main arm64 libncbi-vdb3 arm64 3.0.2+dfsg-2 [977 kB] Get: 299 http://deb.debian.org/debian bookworm/main arm64 libncbi-ngs3 arm64 3.0.3+dfsg-5 [141 kB] Get: 300 http://deb.debian.org/debian bookworm/main arm64 libngs-jni arm64 3.0.3+dfsg-5 [23.4 kB] Get: 301 http://deb.debian.org/debian bookworm/main arm64 libngs-java arm64 3.0.3+dfsg-5 [110 kB] Get: 302 http://deb.debian.org/debian bookworm/main arm64 librhino-java all 1.7.7.2-3 [1200 kB] Get: 303 http://deb.debian.org/debian bookworm/main arm64 libhtsjdk-java all 3.0.4+dfsg-2 [1813 kB] Get: 304 http://deb.debian.org/debian bookworm/main arm64 libhtsjdk-java-doc all 3.0.4+dfsg-2 [1039 kB] Get: 305 http://deb.debian.org/debian bookworm/main arm64 libjansi-java all 2.4.0-2 [105 kB] Get: 306 http://deb.debian.org/debian bookworm/main arm64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 307 http://deb.debian.org/debian bookworm/main arm64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 308 http://deb.debian.org/debian bookworm/main arm64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 309 http://deb.debian.org/debian bookworm/main arm64 libjetty9-java all 9.4.50-3 [2962 kB] Get: 310 http://deb.debian.org/debian bookworm/main arm64 libjtidy-java all 7+svn20110807-5 [250 kB] Get: 311 http://deb.debian.org/debian bookworm/main arm64 libmaven-common-artifact-filters-java all 3.3.2-1 [48.2 kB] Get: 312 http://deb.debian.org/debian bookworm/main arm64 libmaven-artifact-transfer-java all 0.13.1-2 [158 kB] Get: 313 http://deb.debian.org/debian bookworm/main arm64 libplexus-build-api-java all 0.0.7-4 [10.3 kB] Get: 314 http://deb.debian.org/debian bookworm/main arm64 libmaven-filtering-java all 3.3.0-1 [50.2 kB] Get: 315 http://deb.debian.org/debian bookworm/main arm64 libmaven-assembly-plugin-java all 3.4.2-1 [242 kB] Get: 316 http://deb.debian.org/debian bookworm/main arm64 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB] Get: 317 http://deb.debian.org/debian bookworm/main arm64 libmaven-invoker-java all 3.2.0-1 [28.1 kB] Get: 318 http://deb.debian.org/debian bookworm/main arm64 libplexus-interactivity-api-java all 1.1-2 [11.0 kB] Get: 319 http://deb.debian.org/debian bookworm/main arm64 libmaven-javadoc-plugin-java all 3.4.1-2 [454 kB] Get: 320 http://deb.debian.org/debian bookworm/main arm64 libmaven-reporting-impl-java all 3.2.0-2 [15.2 kB] Get: 321 http://deb.debian.org/debian bookworm/main arm64 libplexus-container-default1.5-java all 2.1.1-1 [4476 B] Get: 322 http://deb.debian.org/debian bookworm/main arm64 libplexus-ant-factory-java all 1.0~alpha2.1-4 [11.4 kB] Get: 323 http://deb.debian.org/debian bookworm/main arm64 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B] Get: 324 http://deb.debian.org/debian bookworm/main arm64 libmaven-plugin-tools-java all 3.7.1-1 [265 kB] Get: 325 http://deb.debian.org/debian bookworm/main arm64 libmaven-reporting-exec-java all 1.6.0-1 [26.8 kB] Get: 326 http://deb.debian.org/debian bookworm/main arm64 libmaven-resources-plugin-java all 3.3.0-1 [28.4 kB] Get: 327 http://deb.debian.org/debian bookworm/main arm64 libmaven-site-plugin-java all 3.12.1-2 [107 kB] Get: 328 http://deb.debian.org/debian bookworm/main arm64 libtrove3-java all 3.0.3-5 [2146 kB] Get: 329 http://deb.debian.org/debian bookworm/main arm64 libsnpeff-java all 5.1+d+dfsg-3 [2150 kB] Get: 330 http://deb.debian.org/debian bookworm/main arm64 libsnpeff-java-doc all 5.1+d+dfsg-3 [760 kB] Get: 331 http://deb.debian.org/debian bookworm/main arm64 libsurefire-java all 2.22.3-2 [1169 kB] Get: 332 http://deb.debian.org/debian bookworm/main arm64 libtrove3-java-doc all 3.0.3-5 [823 kB] Get: 333 http://deb.debian.org/debian bookworm/main arm64 libwagon-file-java all 3.5.3-1 [8388 B] Get: 334 http://deb.debian.org/debian bookworm/main arm64 libwagon-http-shaded-java all 3.5.3-1 [1341 kB] Get: 335 http://deb.debian.org/debian bookworm/main arm64 libxml2-utils arm64 2.9.14+dfsg-1.1+b3 [97.2 kB] Get: 336 http://deb.debian.org/debian bookworm/main arm64 maven all 3.8.7-1 [18.9 kB] Get: 337 http://deb.debian.org/debian bookworm/main arm64 maven-repo-helper all 1.11 [142 kB] Get: 338 http://deb.debian.org/debian bookworm/main arm64 maven-debian-helper all 2.6.2 [108 kB] Fetched 472 MB in 46s (10.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (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 ... 19616 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.2-6) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.5.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_arm64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:arm64 (3.11.2-6) ... Setting up libexpat1:arm64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... 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 ... 19932 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_arm64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../3-libreadline8_8.2-1.3_arm64.deb ... Unpacking libreadline8:arm64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_arm64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20366 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_arm64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package netbase. Preparing to unpack .../002-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../003-libproc2-0_2%3a4.0.2-3_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../004-procps_2%3a4.0.2-3_arm64.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../005-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package openssl. Preparing to unpack .../006-openssl_3.0.8-1_arm64.deb ... Unpacking openssl (3.0.8-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../007-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../008-libmagic-mgc_1%3a5.44-3_arm64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../009-libmagic1_1%3a5.44-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../010-file_1%3a5.44-3_arm64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../011-gettext-base_0.21-12_arm64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../012-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../013-groff-base_1.22.4-10_arm64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../014-bsdextrautils_2.38.1-5+b1_arm64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../015-libpipeline1_1.5.7-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../016-man-db_2.11.2-2_arm64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package ca-certificates-java. Preparing to unpack .../017-ca-certificates-java_20230103_all.deb ... Unpacking ca-certificates-java (20230103) ... Selecting previously unselected package java-common. Preparing to unpack .../018-java-common_0.74_all.deb ... Unpacking java-common (0.74) ... Selecting previously unselected package libavahi-common-data:arm64. Preparing to unpack .../019-libavahi-common-data_0.8-9_arm64.deb ... Unpacking libavahi-common-data:arm64 (0.8-9) ... Selecting previously unselected package libavahi-common3:arm64. Preparing to unpack .../020-libavahi-common3_0.8-9_arm64.deb ... 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Setting up libxerces2-java (2.12.2-1) ... Setting up libfile-dirlist-perl (0.05-3) ... Setting up libjaxp1.3-java (1.3.05-6) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up librelaxng-datatype-java (1.0+ds1-3.1) ... Setting up openssl (3.0.8-1) ... Setting up libjsonp-java (1.1.2-3) ... Setting up libcdi-api-java (1.2-3) ... Setting up libelf1:arm64 (0.188-2.1) ... Setting up libsnappy-jni (1.1.8.3-1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.1+b3) ... Setting up liburi-perl (5.17-1) ... Setting up libargs4j-java (2.33-2) ... Setting up libfile-touch-perl (0.12-2) ... Setting up dctrl-tools (2.24-3) ... Setting up libinchi1 (1.03+dfsg-4) ... Setting up libnaga-java (3.0+svn80-5) ... Setting up libnet-ssleay-perl:arm64 (1.92-2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up pinentry-curses (1.2.1-1) ... Setting up libdom4j-java (2.1.3-2) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libwagon-provider-api-java (3.5.3-1) ... Setting up libhttp-date-perl (6.05-2) ... Setting up gettext (0.21-12) ... Setting up libjetty9-java (9.4.50-3) ... Setting up java-wrappers (0.4) ... Setting up libfile-listing-perl (6.15-1) ... Setting up libmbedx509-1:arm64 (2.28.3-1) ... Setting up libstringtemplate4-java (4.0.8-2.1) ... Setting up libplexus-languages-java (1.1.1-2) ... Setting up libmbedtls14:arm64 (2.28.3-1) ... Setting up libtool (2.4.7-5) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libstax-ex-java (1.7.8-3) ... Setting up libmaven-parent-java (35-1) ... Setting up libreadline8:arm64 (8.2-1.3) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:arm64 (0.8-9) ... Setting up libncbi-vdb3:arm64 (3.0.2+dfsg-2) ... Setting up libcommons-logging-java (1.2-3) ... Setting up libnet-http-perl (6.22-1) ... Setting up libsisu-inject-java (0.3.4-2) ... Setting up libnss3:arm64 (2:3.87.1-1) ... Setting up libciftools-java (4.0.5-1) ... Setting up libdevel-callchecker-perl:arm64 (0.008-2) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libldap-2.5-0:arm64 (2.5.13+dfsg-5) ... Setting up libjackson2-databind-java (2.14.0-1) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up patchutils (0.4.2-1) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.4-3) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:arm64 (2.12.1+dfsg-4) ... Setting up libxalan2-java (2.7.2-4) ... Setting up libstreambuffer-java (1.5.4-1.1) ... Setting up libcommons-lang3-java (3.12.0-2) ... 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 dwz (0.15-1) ... Setting up libmaven-common-artifact-filters-java (3.3.2-1) ... Setting up libjgraphx-java (2.1.0.7-3) ... Setting up groff-base (1.22.4-10) ... Setting up libhtml-parser-perl:arm64 (3.81-1) ... Setting up gpgconf (2.2.40-1.1) ... Setting up openjdk-17-doc (17.0.6+10-1) ... Setting up libcommons-beanutils-java (1.9.4-1) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libharfbuzz0b:arm64 (6.0.0+dfsg-3) ... Setting up libsnappy-java (1.1.8.3-1) ... Setting up libfontconfig1:arm64 (2.14.1-4) ... Setting up libxsom-java (2.3.0.1-10.1) ... 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-1.1+b3) ... Setting up libcommons-codec-java (1.15-1) ... Setting up libavahi-client3:arm64 (0.8-9) ... Setting up libio-socket-ssl-perl (2.081-2) ... Setting up gpg (2.2.40-1.1) ... Setting up gnupg-utils (2.2.40-1.1) ... Setting up libhttp-message-perl (6.44-1) ... Setting up libncbi-ngs3:arm64 (3.0.3+dfsg-5) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up velocity (1.7-6) ... Setting up libngs-jni:arm64 (3.0.3+dfsg-5) ... Setting up gpg-agent (2.2.40-1.1) ... Setting up libcommons-compress-java (1.22-1) ... Setting up libhttp-cookies-perl (6.10-1) ... Setting up libcommons-io-java (2.11.0-2) ... Setting up libcommons-digester-java (1.8.1-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libpython3.11-stdlib:arm64 (3.11.2-6) ... Setting up libdistlib-java (1.0-4) ... Setting up libparams-classify-perl:arm64 (0.015-2+b1) ... Setting up gpgsm (2.2.40-1.1) ... Setting up libxmlgraphics-commons-java (2.8-2) ... Setting up default-jdk-doc (2:1.17-74) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dirmngr (2.2.40-1.1) ... Setting up libmaven-filtering-java (3.3.0-1) ... Setting up libmaven-resolver-java (1.6.3-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up antlr4-doc (4.7.2-5) ... Setting up gpg-wks-server (2.2.40-1.1) ... Setting up libcups2:arm64 (2.4.2-3) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up libwagon-http-java (3.5.3-1) ... Setting up libmaven-shared-utils-java (3.3.4-1) ... Setting up libfastinfoset-java (1.2.12-3) ... Setting up libngs-java:arm64 (3.0.3+dfsg-5) ... Setting up libmaven-resources-plugin-java (3.3.0-1) ... Setting up libhtsjdk-java (3.0.4+dfsg-2) ... Setting up libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up gpg-wks-client (2.2.40-1.1) ... Setting up libcommons-validator-java (1:1.7-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libbatik-java (1.16+dfsg-1) ... Setting up libmoo-perl (2.005005-1) ... Setting up libmaven-invoker-java (3.2.0-1) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up 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 libfop-java (1:2.8-2) ... Setting up libmaven-archiver-java (3.6.0-1) ... Setting up openjdk-17-jre-headless:arm64 (17.0.6+10-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up ca-certificates-java (20230103) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068_2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:E-Tugra_Global_Root_CA_ECC_v3.pem Adding debian:E-Tugra_Global_Root_CA_RSA_v3.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up junit4 (4.13.2-3) ... Setting up liblwp-protocol-https-perl (6.10-1) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up default-jre-headless (2:1.17-74) ... Setting up libwww-perl (6.68-1) ... Setting up antlr4 (4.7.2-5) ... Setting up maven-repo-helper (1.11) ... Setting up devscripts (2.23.3) ... Setting up libguava-java (31.1-1) ... Setting up openjdk-17-jdk-headless:arm64 (17.0.6+10-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up ant (1.10.13-1) ... Setting up javahelper (0.78) ... Setting up junit5 (5.9.2-1) ... Setting up libplexus-container-default-java (2.1.1-1) ... Setting up libguice-java (4.2.3-2) ... Setting up ant-optional (1.10.13-1) ... Setting up default-jdk-headless (2:1.17-74) ... Setting up libplexus-i18n-java (1.0-beta-10-6) ... Setting up libplexus-container-default1.5-java (2.1.1-1) ... Setting up libplexus-interactivity-api-java (1.1-2) ... Setting up libplexus-velocity-java (1.2-3.1) ... Setting up libmaven3-core-java (3.8.7-1) ... Setting up libmaven-shared-incremental-java (1.1-3) ... Setting up libmaven-shared-io-java (3.0.0-4) ... Setting up libplexus-bsh-factory-java (1.0~alpha7-5) ... Setting up maven (3.8.7-1) ... update-alternatives: using /usr/share/maven/bin/mvn to provide /usr/bin/mvn (mvn) in auto mode Setting up libplexus-ant-factory-java (1.0~alpha2.1-4) ... Setting up libplexus-compiler-java (2.12.1-1) ... Setting up libmaven-compiler-plugin-java (3.10.1-2) ... Setting up libjni-inchi-java (0.8+dfsg-7) ... Setting up libmaven-artifact-transfer-java (0.13.1-2) ... Setting up libmaven-file-management-java (3.0.0-1) ... Setting up libjmol-java (14.32.83+dfsg-1) ... Setting up libistack-commons-java (3.0.6-5) ... Setting up libmaven-jar-plugin-java (3.3.0-2) ... Setting up libmaven-assembly-plugin-java (3.4.2-1) ... Setting up libcommons-text-java (1.10.0-1) ... Setting up libcodemodel-java (2.6+jaxb2.3.0.1-10.1) ... Setting up libmsgpack-java (0.9.3-1) ... Setting up libtxw2-java (2.3.0.1-10.1) ... Setting up libjaxb-java (2.3.0.1-10.1) ... Setting up libmmtf-java (1.0.11-1) ... Setting up libjgrapht-java (1.5.1-3) ... Setting up libdoxia-core-java (1.12.0-1) ... Setting up libdoxia-java (1.12.0-1) ... Setting up libmaven-reporting-api-java (3.1.1-1) ... Setting up libmaven-reporting-exec-java (1.6.0-1) ... Setting up libbiojava6-java (6.1.0+dfsg-4) ... Setting up libsnpeff-java (5.1+d+dfsg-3) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for sgml-base (1.31) ... Setting up libvelocity-tools-java (2.0-8) ... Setting up libdoxia-sitetools-java (1.11.1-1) ... Setting up libmaven-site-plugin-java (3.12.1-2) ... Setting up libmaven-javadoc-plugin-java (3.4.1-2) ... Setting up libmaven-reporting-impl-java (3.2.0-2) ... Setting up libmaven-plugin-tools-java (3.7.1-1) ... Setting up libsurefire-java (2.22.3-2) ... Setting up maven-debian-helper (2.6.2) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20230103) ... 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/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 arm64 debian/rules clean dh clean --with javahelper debian/rules override_dh_auto_clean make[1]: Entering directory '/build/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/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/snpsift-5.1\+dfsg2/debian/maven-repo Failed to parse /build/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/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/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/snpsift-5.1\+dfsg2/debian -Dmaven.repo.local=/build/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/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/snpsift-5.1+dfsg2/target/classes [WARNING] /build/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/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/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/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/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/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/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/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/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/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/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... [WARNING] Loading source files for package org.snpsift.util... [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.pedigree... [WARNING] Loading source files for package org.snpsift.lang.function... [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.hwe... [WARNING] Loading source files for package org.snpsift.gwasCatalog... [WARNING] Loading source files for package org.snpsift.fileIterator... [WARNING] Loading source files for package org.snpsift.caseControl... [WARNING] Loading source files for package org.snpsift.antlr... [WARNING] Loading source files for package org.snpsift.annotate... [WARNING] Constructing Javadoc information... [WARNING] /build/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVcfCheck.java:16: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesVcfCheck [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:56: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesVarType [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:62: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesVarType [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:68: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesVarType [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:74: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesVarType [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:80: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesVarType [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:26: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesSplit [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:56: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesSplit [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:82: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesSplit [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:28: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesSort [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:46: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:57: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:68: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:79: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:87: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:93: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:99: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:105: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesLd.java:22: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesLd [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIntervals.java:23: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesIntervals [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIntervals.java:48: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesIntervals [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:30: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesIndex [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:82: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesIndex [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:21: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesHwe [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:33: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesHwe [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:45: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesHwe [WARNING] Building index for all the packages and classes... 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[WARNING] Generating /build/snpsift-5.1+dfsg2/target/apidocs/overview-summary.html... [WARNING] Generating /build/snpsift-5.1+dfsg2/target/apidocs/help-doc.html... [WARNING] 100 warnings [INFO] Building jar: /build/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/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/snpsift-5.1+dfsg2/target/classes [WARNING] /build/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/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/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/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/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/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/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/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/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... [WARNING] Loading source files for package org.snpsift.util... [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.pedigree... [WARNING] Loading source files for package org.snpsift.lang.function... [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.hwe... [WARNING] Loading source files for package org.snpsift.gwasCatalog... [WARNING] Loading source files for package org.snpsift.fileIterator... [WARNING] Loading source files for package org.snpsift.caseControl... [WARNING] Loading source files for package org.snpsift.antlr... [WARNING] Loading source files for package org.snpsift.annotate... [WARNING] Constructing Javadoc information... [WARNING] /build/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVcfCheck.java:16: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesVcfCheck [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:56: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesVarType [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:62: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesVarType [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:68: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesVarType [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:74: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesVarType [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:80: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesVarType [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:26: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesSplit [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:56: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesSplit [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:82: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesSplit [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:28: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesSort [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:46: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:57: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:68: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:79: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:87: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:93: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:99: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:105: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesLd.java:22: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesLd [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIntervals.java:23: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesIntervals [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIntervals.java:48: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesIntervals [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:30: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesIndex [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:82: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesIndex [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:21: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesHwe [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:33: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesHwe [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:45: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesHwe [WARNING] Building index for all the packages and classes... 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[WARNING] 100 warnings [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 05:37 min [INFO] Finished at: 2024-05-21T09:25:38-12:00 [INFO] ------------------------------------------------------------------------  debian/rules override_dh_auto_test make[1]: Entering directory '/build/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/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/snpsift-5.1\+dfsg2/debian -Dmaven.repo.local=/build/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/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/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/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.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: 1.91 s - in org.snpsift.testCases.unit.TestCasesFilterChrPos [INFO] Running org.snpsift.testCases.unit.TestCasesGt TestCasesGt.test_01(25): Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.014 s - in org.snpsift.testCases.unit.TestCasesGt [INFO] Running org.snpsift.testCases.unit.TestCasesGeneSets TestCasesGeneSets.test_01(25): Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.5 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: 140.834 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: 0.143 s - in org.snpsift.testCases.unit.TestCasesVcfCheck [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: 115.692 s - in org.snpsift.testCases.unit.TestCasesAnnotateUseIndex [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.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: 0.025 s - in org.snpsift.testCases.unit.TestCasesSplit [INFO] Running org.snpsift.testCases.unit.TestCasesHwe [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.23 s - in org.snpsift.testCases.unit.TestCasesHwe [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: 85.856 s - in org.snpsift.testCases.unit.TestCasesAnnotateCreateIndex [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: 7.574 s - in org.snpsift.testCases.unit.TestCasesGwasCatalog [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: 5.649 s - in org.snpsift.testCases.unit.TestCasesCaseControl [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: 0.301 s - in org.snpsift.testCases.unit.TestCasesVarType [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: 1.054 s - in org.snpsift.testCases.unit.TestCasesConcordance [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: 88.191 s - in org.snpsift.testCases.unit.TestCasesAnnotateMem [INFO] Running org.snpsift.testCases.unit.TestCasesFilterGt TestCasesFilterGt.test_01(28): Test ANTLR Tool version 4.9.3 used for code generation does not match the current runtime version 4.7.2ANTLR Tool version 4.9.3 used for code generation does not match the current runtime version 4.7.2TestCasesFilterGt.test_02(62): Test [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.987 s - in org.snpsift.testCases.unit.TestCasesFilterGt [INFO] Running org.snpsift.testCases.unit.TestCasesSort TestCasesSort.test_01(30): Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 s - in org.snpsift.testCases.unit.TestCasesSort [INFO] Running org.snpsift.testCases.unit.TestCasesFilterALL [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.513 s - in org.snpsift.testCases.unit.TestCasesFilterALL [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: 1.762 s - in org.snpsift.testCases.unit.TestCasesExtractFields [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: 28.75 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: 63.871 s - in org.snpsift.testCases.unit.TestCasesDbNsfpDeleteCache [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: 0.027 s - in org.snpsift.testCases.unit.TestCasesPrivate [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: 73.679 s - in org.snpsift.testCases.unit.TestCasesAnnotate [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: 17.731 s - in org.snpsift.testCases.unit.TestCasesIndex [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: 0.02 s - in org.snpsift.testCases.unit.TestCasesIntervals [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: 19.96 s - in org.snpsift.testCases.unit.TestCasesFilter [INFO] [INFO] Results: [INFO] [INFO] Tests run: 403, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 12:06 min [INFO] Finished at: 2024-05-21T09:38:00-12:00 [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/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/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/snpsift-5.1\+dfsg2/debian -Dmaven.repo.local=/build/snpsift-5.1\+dfsg2/debian/maven-repo --batch-mode -Ddebian.dir=/build/snpsift-5.1\+dfsg2/debian -Ddebian.package=libsnpsift-java -Dmaven.repo.local=/build/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/snpsift-5.1+dfsg2/pom.xml.save with options: [INFO] --keep-pom-version --package=libsnpsift-java [INFO] --rules=/build/snpsift-5.1+dfsg2/debian/maven.rules [INFO] --ignore-rules=/build/snpsift-5.1+dfsg2/debian/maven.ignoreRules [INFO] --published-rules=/build/snpsift-5.1+dfsg2/debian/maven.publishedRules [INFO] Install jar for snpsift into /usr/share/java [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 4.213 s [INFO] Finished at: 2024-05-21T09:38:15-12:00 [INFO] ------------------------------------------------------------------------  mh_resolve_dependencies --non-interactive --offline --build -plibsnpsift-java --javadoc --base-directory=/build/snpsift-5.1\+dfsg2 --non-explore Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) at org.debian.maven.repo.POMReader.readPom(POMReader.java:82) at org.debian.maven.repo.POMReader.readPom(POMReader.java:57) at org.debian.maven.repo.Repository.scan(Repository.java:397) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:201) at org.debian.maven.repo.Repository.scanOnce(Repository.java:196) at org.debian.maven.repo.POMTransformer.usePluginVersionsFromRepository(POMTransformer.java:107) at org.debian.maven.packager.DependenciesSolver.main(DependenciesSolver.java:907) Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) at org.debian.maven.repo.POMReader.readPom(POMReader.java:82) at org.debian.maven.repo.POMReader.readPom(POMReader.java:57) at org.debian.maven.repo.Repository.scan(Repository.java:397) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:201) at org.debian.maven.repo.Repository.scanOnce(Repository.java:196) at org.debian.maven.repo.POMTransformer.usePluginVersionsFromRepository(POMTransformer.java:107) at org.debian.maven.packager.DependenciesSolver.main(DependenciesSolver.java:907) Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) at org.debian.maven.repo.POMReader.readPom(POMReader.java:82) at org.debian.maven.repo.POMReader.readPom(POMReader.java:57) at org.debian.maven.repo.Repository.scan(Repository.java:397) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:201) at org.debian.maven.packager.DependenciesSolver.getRepository(DependenciesSolver.java:231) at org.debian.maven.packager.DependenciesSolver.solveDependencies(DependenciesSolver.java:237) at org.debian.maven.packager.DependenciesSolver.main(DependenciesSolver.java:922) Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) at org.debian.maven.repo.POMReader.readPom(POMReader.java:82) at org.debian.maven.repo.POMReader.readPom(POMReader.java:57) at org.debian.maven.repo.Repository.scan(Repository.java:397) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:201) at org.debian.maven.packager.DependenciesSolver.getRepository(DependenciesSolver.java:231) at org.debian.maven.packager.DependenciesSolver.solveDependencies(DependenciesSolver.java:237) at org.debian.maven.packager.DependenciesSolver.main(DependenciesSolver.java:922) Analysing pom.xml... 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-doc: substitution variable ${maven:CompileDepends} unused, but is defined dpkg-gencontrol: warning: package libsnpsift-java-doc: substitution variable ${maven:Depends} unused, but is defined 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 dh_md5sums dh_builddeb dpkg-deb: building package 'libsnpsift-java-doc' in '../libsnpsift-java-doc_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' in '../libsnpsift-java_5.1+dfsg2-2_all.deb'. dpkg-genbuildinfo --build=binary -O../snpsift_5.1+dfsg2-2_arm64.buildinfo dpkg-genchanges --build=binary -O../snpsift_5.1+dfsg2-2_arm64.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/27516 and its subdirectories I: Current time: Tue May 21 09:39:15 -12 2024 I: pbuilder-time-stamp: 1716327555 Wed Apr 19 15:16:18 UTC 2023 I: 1st build successful. Starting 2nd build on remote node codethink16-arm64.debian.net. Wed Apr 19 15:16:18 UTC 2023 I: Preparing to do remote build '2' on codethink16-arm64.debian.net. Wed Apr 19 15:33:41 UTC 2023 I: Deleting $TMPDIR on codethink16-arm64.debian.net. Wed Apr 19 15:33:42 UTC 2023 I: snpsift_5.1+dfsg2-2_arm64.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: ce8469287b96849184a78e9efd54817cb243c798 215700 libsnpsift-java-doc_5.1+dfsg2-2_all.deb 1e0993b6a6423ecaed5e1e17e08de3cbfa3bda49 311484 libsnpsift-java_5.1+dfsg2-2_all.deb e3a649232d00477fa0db9753d5cc3ed8f77cfedd 4400 snpsift_5.1+dfsg2-2_all.deb 5c6571ad6c30706755d47a837bf8408cd19290f8 16136 snpsift_5.1+dfsg2-2_arm64.buildinfo Checksums-Sha256: 7cd0a90f3831d5dd50490fbcc95ac3506326529cf779213e70296f205f037aaa 215700 libsnpsift-java-doc_5.1+dfsg2-2_all.deb 094c0fcc160af8946656a28fb52ba8145630b4df585cbeb8d1be34a2f981287f 311484 libsnpsift-java_5.1+dfsg2-2_all.deb 44a620dac28d7a206b1f91f050189589dce45802662657d98673073a10c35dff 4400 snpsift_5.1+dfsg2-2_all.deb a2d3f034d789ec129a8fbc473b21c45f93d42bfd219baf7c4bcf834139e697c5 16136 snpsift_5.1+dfsg2-2_arm64.buildinfo Files: e1d6fd43ef66a1036a5e58f5ea306e6a 215700 doc optional libsnpsift-java-doc_5.1+dfsg2-2_all.deb 158d28adc1493fb996ab5dc1fba739e6 311484 java optional libsnpsift-java_5.1+dfsg2-2_all.deb 2f25f078e01d730117ece5ec15cff742 4400 java optional snpsift_5.1+dfsg2-2_all.deb 8814b61fb6173ad58f171e8e45045ac9 16136 java optional snpsift_5.1+dfsg2-2_arm64.buildinfo Wed Apr 19 15:33:43 UTC 2023 I: diffoscope 240 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.yHGQte7s/snpsift_5.1+dfsg2-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.yHGQte7s/snpsift_5.1+dfsg2-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.yHGQte7s/snpsift_5.1+dfsg2-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.yHGQte7s/b1/snpsift_5.1+dfsg2-2_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.yHGQte7s/b2/snpsift_5.1+dfsg2-2_arm64.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: 0.341s) 0.341s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.024s) 0.023s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.001s) 0.001s 1 call specialize Wed Apr 19 15:33:44 UTC 2023 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists. Wed Apr 19 15:33:44 UTC 2023 I: snpsift from bookworm built successfully and reproducibly on arm64. Wed Apr 19 15:33:45 UTC 2023 I: Submitting .buildinfo files to external archives: Wed Apr 19 15:33:45 UTC 2023 I: Submitting 20K b1/snpsift_5.1+dfsg2-2_arm64.buildinfo.asc Wed Apr 19 15:33:46 UTC 2023 I: Submitting 20K b2/snpsift_5.1+dfsg2-2_arm64.buildinfo.asc Wed Apr 19 15:33:47 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Apr 19 15:33:47 UTC 2023 I: Done submitting .buildinfo files. Wed Apr 19 15:33:47 UTC 2023 I: Removing signed snpsift_5.1+dfsg2-2_arm64.buildinfo.asc files: removed './b1/snpsift_5.1+dfsg2-2_arm64.buildinfo.asc' removed './b2/snpsift_5.1+dfsg2-2_arm64.buildinfo.asc'