https://launchpad.net/ubuntu/+source/snpsift/5.1+dfsg2-2/+build/23594833 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lgw01-amd64-056 5.4.0-109-generic #123-Ubuntu SMP Fri Apr 8 09:10:54 UTC 2022 x86_64 Buildd toolchain package versions: launchpad-buildd_212~550~ubuntu20.04.1 python3-lpbuildd_212~550~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.4 dpkg-dev_1.19.7ubuntu3 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 30 Apr 12:28:15 ntpdate[1809]: adjust time server 10.211.37.1 offset -0.000244 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-23594833 --image-type chroot /home/buildd/filecache-default/4bae5e21afd462667e3742a3b80ddb4ff02f2b5f Creating target for build PACKAGEBUILD-23594833 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-23594833 Starting target for build PACKAGEBUILD-23594833 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-23594833 'deb http://ftpmaster.internal/ubuntu kinetic main universe' 'deb http://ftpmaster.internal/ubuntu kinetic-security main universe' 'deb http://ftpmaster.internal/ubuntu kinetic-updates main universe' 'deb http://ftpmaster.internal/ubuntu kinetic-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-23594833 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-23594833 Updating target for build PACKAGEBUILD-23594833 Get:1 http://ftpmaster.internal/ubuntu kinetic InRelease [224 kB] Get:2 http://ftpmaster.internal/ubuntu kinetic-security InRelease [74.9 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic-updates InRelease [74.9 kB] Get:4 http://ftpmaster.internal/ubuntu kinetic-proposed InRelease [74.9 kB] Get:5 http://ftpmaster.internal/ubuntu kinetic/main amd64 Packages [1396 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic/main Translation-en [510 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/universe amd64 Packages [13.6 MB] Get:8 http://ftpmaster.internal/ubuntu kinetic/universe Translation-en [5652 kB] Get:9 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 Packages [222 kB] Get:10 http://ftpmaster.internal/ubuntu kinetic-proposed/main Translation-en [86.7 kB] Get:11 http://ftpmaster.internal/ubuntu kinetic-proposed/universe amd64 Packages [1174 kB] Get:12 http://ftpmaster.internal/ubuntu kinetic-proposed/universe Translation-en [556 kB] Get:13 http://ftpmaster.internal/ubuntu kinetic-proposed/restricted amd64 Packages [39.6 kB] Get:14 http://ftpmaster.internal/ubuntu kinetic-proposed/restricted Translation-en [6720 B] Get:15 http://ftpmaster.internal/ubuntu kinetic-proposed/multiverse amd64 Packages [1940 B] Get:16 http://ftpmaster.internal/ubuntu kinetic-proposed/multiverse Translation-en [7576 B] Fetched 23.7 MB in 4s (6281 kB/s) Reading package lists... W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Translations (main/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Translations (universe/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Translations (main/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Translations (universe/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: cpp-11 g++-11 gcc-11 gcc-11-base gcc-12-base libasan6 libatomic1 libcc1-0 libgcc-11-dev libgcc-s1 libgnutls30 libgomp1 libgpg-error0 libitm1 libjson-c5 liblsan0 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libpcre3 libpng16-16 libquadmath0 libreadline8 libsqlite3-0 libstdc++-11-dev libstdc++6 libtinfo6 libtsan0 libubsan1 libzstd1 linux-libc-dev lto-disabled-list ncurses-base ncurses-bin pinentry-curses readline-common 41 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 59.3 MB of archives. After this operation, 30.7 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 ncurses-bin amd64 6.3+20220423-1 [184 kB] Get:2 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 ncurses-base all 6.3+20220423-1 [21.4 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libpam0g amd64 1.4.0-13ubuntu1 [60.2 kB] Get:4 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libpam-modules-bin amd64 1.4.0-13ubuntu1 [37.6 kB] Get:5 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libpam-modules amd64 1.4.0-13ubuntu1 [278 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic/main amd64 libatomic1 amd64 12-20220428-1ubuntu1 [10.4 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/main amd64 libubsan1 amd64 12-20220428-1ubuntu1 [976 kB] Get:8 http://ftpmaster.internal/ubuntu kinetic/main amd64 gcc-12-base amd64 12-20220428-1ubuntu1 [18.9 kB] Get:9 http://ftpmaster.internal/ubuntu kinetic/main amd64 libstdc++6 amd64 12-20220428-1ubuntu1 [696 kB] Get:10 http://ftpmaster.internal/ubuntu kinetic/main amd64 libquadmath0 amd64 12-20220428-1ubuntu1 [154 kB] Get:11 http://ftpmaster.internal/ubuntu kinetic/main amd64 liblsan0 amd64 12-20220428-1ubuntu1 [1069 kB] Get:12 http://ftpmaster.internal/ubuntu kinetic/main amd64 libitm1 amd64 12-20220428-1ubuntu1 [30.1 kB] Get:13 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgomp1 amd64 12-20220428-1ubuntu1 [126 kB] Get:14 http://ftpmaster.internal/ubuntu kinetic/main amd64 libcc1-0 amd64 12-20220428-1ubuntu1 [47.4 kB] Get:15 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgcc-s1 amd64 12-20220428-1ubuntu1 [54.3 kB] Get:16 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libgpg-error0 amd64 1.45-2 [69.0 kB] Get:17 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libpam-runtime all 1.4.0-13ubuntu1 [40.2 kB] Get:18 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libpcre2-8-0 amd64 10.40-1 [227 kB] Get:19 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libpcre3 amd64 2:8.39-14 [245 kB] Get:20 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libncursesw6 amd64 6.3+20220423-1 [148 kB] Get:21 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libncurses6 amd64 6.3+20220423-1 [110 kB] Get:22 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libtinfo6 amd64 6.3+20220423-1 [103 kB] Get:23 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libzstd1 amd64 1.5.2+dfsg-1 [270 kB] Get:24 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libp11-kit0 amd64 0.24.1-1 [257 kB] Get:25 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libgnutls30 amd64 3.7.4-2ubuntu1 [972 kB] Get:26 http://ftpmaster.internal/ubuntu kinetic/main amd64 libjson-c5 amd64 0.16-1 [33.7 kB] Get:27 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 readline-common all 8.1.2-1.2 [53.6 kB] Get:28 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libreadline8 amd64 8.1.2-1.2 [153 kB] Get:29 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libsqlite3-0 amd64 3.38.2-1 [648 kB] Get:30 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libpng16-16 amd64 1.6.37-5 [187 kB] Get:31 http://ftpmaster.internal/ubuntu kinetic/main amd64 g++-11 amd64 11.3.0-1ubuntu1 [11.4 MB] Get:32 http://ftpmaster.internal/ubuntu kinetic/main amd64 libstdc++-11-dev amd64 11.3.0-1ubuntu1 [2087 kB] Get:33 http://ftpmaster.internal/ubuntu kinetic/main amd64 libasan6 amd64 11.3.0-1ubuntu1 [2284 kB] Get:34 http://ftpmaster.internal/ubuntu kinetic/main amd64 gcc-11 amd64 11.3.0-1ubuntu1 [20.1 MB] Get:35 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgcc-11-dev amd64 11.3.0-1ubuntu1 [2516 kB] Get:36 http://ftpmaster.internal/ubuntu kinetic/main amd64 libtsan0 amd64 11.3.0-1ubuntu1 [2261 kB] Get:37 http://ftpmaster.internal/ubuntu kinetic/main amd64 cpp-11 amd64 11.3.0-1ubuntu1 [9968 kB] Get:38 http://ftpmaster.internal/ubuntu kinetic/main amd64 gcc-11-base amd64 11.3.0-1ubuntu1 [21.1 kB] Get:39 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 linux-libc-dev amd64 5.15.0-28.29 [1345 kB] Get:40 http://ftpmaster.internal/ubuntu kinetic/main amd64 lto-disabled-list all 25 [12.6 kB] Get:41 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 pinentry-curses amd64 1.2.0-1 [35.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.3 MB in 2s (34.9 MB/s) (Reading database ... 13450 files and directories currently installed.) 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RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-23594833 amd64 kinetic-proposed -c chroot:build-PACKAGEBUILD-23594833 --arch=amd64 --dist=kinetic-proposed --nolog -A snpsift_5.1+dfsg2-2.dsc Initiating build PACKAGEBUILD-23594833 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-109-generic #123-Ubuntu SMP Fri Apr 8 09:10:54 UTC 2022 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lgw01-amd64-056.buildd +==============================================================================+ | snpsift 5.1+dfsg2-2 (amd64) Sat, 30 Apr 2022 12:28:31 +0000 | +==============================================================================+ Package: snpsift Version: 5.1+dfsg2-2 Source Version: 5.1+dfsg2-2 Distribution: kinetic-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-23594833/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/snpsift-VzOHUW/resolver-WhS8lK' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- snpsift_5.1+dfsg2-2.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/snpsift-VzOHUW/snpsift-5.1+dfsg2' with '<>' I: NOTICE: Log filtering will replace 'build/snpsift-VzOHUW' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged 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, build-essential, fakeroot Filtered 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, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [471 B] Get:5 copy:/<>/apt_archive ./ Packages [553 B] Fetched 1981 B in 0s (138 kB/s) Reading package lists... Reading package lists... W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: ant ant-optional antlr4 antlr4-doc autoconf automake autopoint autotools-dev bsdextrautils ca-certificates-java dctrl-tools debhelper debugedit default-jdk-doc default-jdk-headless default-jre-headless devscripts dh-autoreconf dh-strip-nondeterminism dirmngr dwz file fontconfig-config fonts-dejavu-core fonts-mathjax gettext gettext-base gnupg gnupg-l10n gnupg-utils gpg-wks-client gpg-wks-server gpgsm groff-base intltool-debian java-common java-wrappers javahelper junit4 junit5 libactivation-java libantlr3-runtime-java libantlr4-runtime-java libaopalliance-java libapache-pom-java libapfloat-java libapiguardian-java libarchive-zip-perl libargs4j-java libasm-java libasound2 libasound2-data libatinject-jsr330-api-java libavahi-client3 libavahi-common-data libavahi-common3 libb-hooks-op-check-perl libbatik-java libbiojava5-java libbrotli1 libbsh-java libcdi-api-java libcharts4j-java libciftools-java libclass-method-modifiers-perl libclass-xsaccessor-perl libcodemodel-java libcommons-beanutils-java libcommons-cli-java libcommons-codec-java libcommons-collections3-java libcommons-compress-java libcommons-configuration-java libcommons-digester-java libcommons-exec-java libcommons-io-java libcommons-jexl2-java libcommons-lang-java libcommons-lang3-java libcommons-logging-java libcommons-math-java libcommons-math3-java libcommons-math3-java-doc libcommons-parent-java libcommons-text-java libcommons-validator-java libcups2 libdbus-1-3 libdebhelper-perl libdevel-callchecker-perl libdistlib-java libdom4j-java libdoxia-core-java libdoxia-java libdoxia-sitetools-java libdtd-parser-java libdw1 libdynaloader-functions-perl libel-api-java libelf1 libencode-locale-perl libexec-maven-plugin-java libexpat1 libfastinfoset-java libfastutil-java libfile-dirlist-perl libfile-homedir-perl libfile-listing-perl libfile-stripnondeterminism-perl libfile-touch-perl libfile-which-perl libfontbox2-java libfontconfig1 libfop-java libfreemarker-java libfreetype6 libgeronimo-annotation-1.3-spec-java libgeronimo-interceptor-3.0-spec-java libglib2.0-0 libgoogle-gson-java libgraphite2-3 libguava-java libguice-java libhamcrest-java libharfbuzz0b libhawtjni-runtime-java libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhtsjdk-java libhtsjdk-java-doc libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libhttpclient-java libhttpcore-java libicu4j-java libicu71 libimport-into-perl libinchi1 libio-html-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libistack-commons-java libitext1-java libitext5-java libjackson2-annotations-java libjackson2-core-java libjackson2-databind-java libjansi-java libjansi-native-java libjaxb-api-java libjaxb-java libjaxen-java libjaxp1.3-java libjetty9-java libjgrapht-java libjgraphx-java libjheaps-java libjmol-java libjni-inchi-java libjni-inchi-jni libjpeg-turbo8 libjpeg8 libjs-mathjax libjson-simple-java libjsonp-java libjsoup-java libjsp-api-java libjsr305-java libjtidy-java libksba8 liblcms2-2 libldap-2.5-0 liblightcouch-java liblog4j1.2-java liblog4j2-java liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1 libmaven-archiver-java libmaven-artifact-transfer-java libmaven-assembly-plugin-java libmaven-clean-plugin-java libmaven-common-artifact-filters-java libmaven-compiler-plugin-java libmaven-file-management-java libmaven-filtering-java libmaven-invoker-java libmaven-jar-plugin-java libmaven-javadoc-plugin-java libmaven-parent-java libmaven-plugin-tools-java libmaven-reporting-api-java libmaven-reporting-exec-java libmaven-reporting-impl-java libmaven-resolver-java libmaven-resources-plugin-java libmaven-shared-incremental-java libmaven-shared-io-java libmaven-shared-utils-java libmaven-site-plugin-java libmaven3-core-java libmmtf-java libmodule-runtime-perl libmongodb-java libmoo-perl libmpdec3 libmsgpack-java libnaga-java libnet-http-perl libnet-ssleay-perl libngs-java libngs-sdk-dev libngs-sdk2 libnspr4 libnss3 libopentest4j-java liboro-java libparams-classify-perl libparboiled-java libpcsclite1 libpegdown-java libpicocli-java libpipeline1 libplexus-ant-factory-java libplexus-archiver-java libplexus-bsh-factory-java libplexus-build-api-java libplexus-cipher-java libplexus-classworlds-java libplexus-compiler-java libplexus-component-annotations-java libplexus-container-default-java libplexus-container-default1.5-java libplexus-i18n-java libplexus-interactivity-api-java libplexus-interpolation-java libplexus-io-java libplexus-languages-java libplexus-sec-dispatcher-java libplexus-utils2-java libplexus-velocity-java libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib libqdox-java libqdox2-java librelaxng-datatype-java librngom-java librole-tiny-perl libsasl2-2 libsasl2-modules-db libservlet-api-java libsigsegv2 libsisu-inject-java libsisu-plexus-java libslf4j-java libsnappy-java libsnappy-jni libsnappy1v5 libsnpeff-java libsnpeff-java-doc libstax-ex-java libstreambuffer-java libstringtemplate4-java libsub-override-perl libsub-quote-perl libsurefire-java libtimedate-perl libtool libtreelayout-java libtrove3-java libtrove3-java-doc libtry-tiny-perl libtxw2-java libuchardet0 libunivocity-parsers-java liburi-perl libvecmath-java libvelocity-tools-java libwagon-file-java libwagon-http-java libwagon-http-shaded-java libwagon-provider-api-java libwebsocket-api-java libwww-perl libwww-robotrules-perl libxalan2-java libxbean-reflect-java libxerces2-java libxml-commons-external-java libxml-commons-resolver1.1-java libxml2 libxml2-utils libxmlgraphics-commons-java libxsom-java libxz-java m4 man-db maven maven-debian-helper maven-repo-helper media-types netbase openjdk-11-doc openjdk-11-jdk-headless openjdk-11-jre-headless patchutils perl-openssl-defaults po-debconf python3 python3-minimal python3.10 python3.10-minimal sgml-base ucf unzip velocity wdiff Suggested packages: ant-doc antlr javacc junit jython libbcel-java libbsf-java libcommons-net-java libmail-java libjdepend-java libjsch-java libregexp-java autoconf-archive gnu-standards autoconf-doc debtags dh-make default-jdk default-jre adequate at autopkgtest bls-standalone bsd-mailx | mailx check-all-the-things cvs-buildpackage diffoscope disorderfs dose-extra duck elpa-devscripts faketime gnuplot how-can-i-help libauthen-sasl-perl libdbd-pg-perl libfile-desktopentry-perl libnet-smtps-perl libterm-size-perl libyaml-syck-perl mmdebstrap mozilla-devscripts mutt piuparts postgresql-client pristine-lfs quilt ratt reprotest ssh-client svn-buildpackage w3m debian-keyring equivs libsoap-lite-perl pristine-tar dbus-user-session libpam-systemd pinentry-gnome3 tor gettext-doc libasprintf-dev libgettextpo-dev parcimonie xloadimage groff libaopalliance-java-doc libasound2-plugins alsa-utils libatinject-jsr330-api-java-doc librhino-java libbiojava5-java-doc libcommons-beanutils-java-doc libcommons-collections3-java-doc libcommons-jxpath-java libcommons-vfs-java libcommons-digester-java-doc libcommons-io-java-doc libcommons-lang-java-doc libcommons-lang3-java-doc libavalon-framework-java libcommons-logging-java-doc libexcalibur-logkit-java cups-common libdom4j-java-doc libmsv-java libxpp2-java libxpp3-java libdoxia-java-doc libdoxia-sitetools-java-doc libjdom1-java libgoogle-gson-java-doc libcglib-java libdata-dump-perl picard-tools libbcpkix-java libbcprov-java libxml-security-java libitext5-java-doc libjackson2-annotations-java-doc libxom-java jetty9 libjmol-java-doc fonts-mathjax-extras fonts-stix libjs-mathjax-doc libjson-simple-doc libjsonp-java-doc libjsoup-java-doc libjsr305-java-doc libjtidy-java-doc liblcms2-utils liblog4j1.2-java-doc libcommons-csv-java libconversant-disruptor-java libdisruptor-java libgeronimo-jms-1.1-spec-java libjackson2-dataformat-xml-java libjackson2-dataformat-yaml libjctools-java libjeromq-java libwoodstox-java libcrypt-ssleay-perl libmaven-archiver-java-doc libmaven-common-artifact-filters-java-doc libmaven-file-management-java-doc libmaven-reporting-impl-java-doc libmaven-shared-incremental-java-doc libmaven-shared-io-java-doc libmaven-shared-utils-java-doc liblogback-java libmmtf-java-doc libscalar-number-perl pcscd libplexus-classworlds-java-doc libeclipse-jdt-core-java libplexus-interactivity-api-java-doc libplexus-sec-dispatcher-java-doc libplexus-utils2-java-doc libplexus-velocity-java-doc libqdox-java-doc libqdox2-java-doc testng libtool-doc gfortran | fortran95-compiler gcj-jdk libsub-name-perl libbusiness-isbn-perl libauthen-ntlm-perl libxalan2-java-doc libxsltc-java libxerces2-java-doc libxml-commons-resolver1.1-java-doc libxmlgraphics-commons-java-doc m4-doc apparmor less www-browser apt-file licensecheck subversion openjdk-11-jdk openjdk-11-demo openjdk-11-source libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic libmail-box-perl python3-doc python3-tk python3-venv python3.10-venv python3.10-doc binfmt-support sgml-base-doc zip velocity-doc wdiff-doc Recommended packages: dput | dupload libdistro-info-perl libgit-wrapper-perl libgitlab-api-v4-perl liblist-compare-perl libstring-shellquote-perl licensecheck lintian python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg strace wget | curl curl | wget | lynx alsa-ucm-conf alsa-topology-conf dbus libdistlib-java-doc libarchive-cpio-perl icc-profiles-free libsaxon-java libglib2.0-data shared-mime-info xdg-user-dirs libhtml-format-perl libclone-perl libldap-common libnamespace-clean-perl libsasl2-modules libbiojava5-java-doc libcommons-codec-java-doc libcommons-io-java-doc libfreemarker-java-doc libltdl-dev libdata-dump-perl libhtml-form-perl libhttp-daemon-perl libmailtools-perl libmail-sendmail-perl The following NEW packages will be installed: ant ant-optional antlr4 antlr4-doc autoconf automake autopoint autotools-dev bsdextrautils ca-certificates-java dctrl-tools debhelper debugedit default-jdk-doc default-jdk-headless default-jre-headless devscripts dh-autoreconf dh-strip-nondeterminism dirmngr dwz file fontconfig-config fonts-dejavu-core fonts-mathjax gettext gettext-base gnupg gnupg-l10n gnupg-utils gpg-wks-client gpg-wks-server gpgsm groff-base intltool-debian java-common java-wrappers javahelper junit4 junit5 libactivation-java libantlr3-runtime-java libantlr4-runtime-java libaopalliance-java libapache-pom-java libapfloat-java libapiguardian-java libarchive-zip-perl libargs4j-java libasm-java libasound2 libasound2-data libatinject-jsr330-api-java libavahi-client3 libavahi-common-data libavahi-common3 libb-hooks-op-check-perl libbatik-java libbiojava5-java libbrotli1 libbsh-java libcdi-api-java libcharts4j-java libciftools-java libclass-method-modifiers-perl libclass-xsaccessor-perl libcodemodel-java libcommons-beanutils-java libcommons-cli-java libcommons-codec-java libcommons-collections3-java libcommons-compress-java libcommons-configuration-java libcommons-digester-java libcommons-exec-java libcommons-io-java libcommons-jexl2-java libcommons-lang-java libcommons-lang3-java libcommons-logging-java libcommons-math-java libcommons-math3-java libcommons-math3-java-doc libcommons-parent-java libcommons-text-java libcommons-validator-java libcups2 libdbus-1-3 libdebhelper-perl libdevel-callchecker-perl libdistlib-java libdom4j-java libdoxia-core-java libdoxia-java libdoxia-sitetools-java libdtd-parser-java libdw1 libdynaloader-functions-perl libel-api-java libelf1 libencode-locale-perl libexec-maven-plugin-java libexpat1 libfastinfoset-java libfastutil-java libfile-dirlist-perl libfile-homedir-perl libfile-listing-perl libfile-stripnondeterminism-perl libfile-touch-perl libfile-which-perl libfontbox2-java libfontconfig1 libfop-java libfreemarker-java libfreetype6 libgeronimo-annotation-1.3-spec-java libgeronimo-interceptor-3.0-spec-java libglib2.0-0 libgoogle-gson-java libgraphite2-3 libguava-java libguice-java libhamcrest-java libharfbuzz0b libhawtjni-runtime-java libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhtsjdk-java libhtsjdk-java-doc libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libhttpclient-java libhttpcore-java libicu4j-java libicu71 libimport-into-perl libinchi1 libio-html-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libistack-commons-java libitext1-java libitext5-java libjackson2-annotations-java libjackson2-core-java libjackson2-databind-java libjansi-java libjansi-native-java libjaxb-api-java libjaxb-java libjaxen-java libjaxp1.3-java libjetty9-java libjgrapht-java libjgraphx-java libjheaps-java libjmol-java libjni-inchi-java libjni-inchi-jni libjpeg-turbo8 libjpeg8 libjs-mathjax libjson-simple-java libjsonp-java libjsoup-java libjsp-api-java libjsr305-java libjtidy-java libksba8 liblcms2-2 libldap-2.5-0 liblightcouch-java liblog4j1.2-java liblog4j2-java liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1 libmaven-archiver-java libmaven-artifact-transfer-java libmaven-assembly-plugin-java libmaven-clean-plugin-java libmaven-common-artifact-filters-java libmaven-compiler-plugin-java libmaven-file-management-java libmaven-filtering-java libmaven-invoker-java libmaven-jar-plugin-java libmaven-javadoc-plugin-java libmaven-parent-java libmaven-plugin-tools-java libmaven-reporting-api-java libmaven-reporting-exec-java libmaven-reporting-impl-java libmaven-resolver-java libmaven-resources-plugin-java libmaven-shared-incremental-java libmaven-shared-io-java libmaven-shared-utils-java libmaven-site-plugin-java libmaven3-core-java libmmtf-java libmodule-runtime-perl libmongodb-java libmoo-perl libmpdec3 libmsgpack-java libnaga-java libnet-http-perl libnet-ssleay-perl libngs-java libngs-sdk-dev libngs-sdk2 libnspr4 libnss3 libopentest4j-java liboro-java libparams-classify-perl libparboiled-java libpcsclite1 libpegdown-java libpicocli-java libpipeline1 libplexus-ant-factory-java libplexus-archiver-java libplexus-bsh-factory-java libplexus-build-api-java libplexus-cipher-java libplexus-classworlds-java libplexus-compiler-java libplexus-component-annotations-java libplexus-container-default-java libplexus-container-default1.5-java libplexus-i18n-java libplexus-interactivity-api-java libplexus-interpolation-java libplexus-io-java libplexus-languages-java libplexus-sec-dispatcher-java libplexus-utils2-java libplexus-velocity-java libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib libqdox-java libqdox2-java librelaxng-datatype-java librngom-java librole-tiny-perl libsasl2-2 libsasl2-modules-db libservlet-api-java libsigsegv2 libsisu-inject-java libsisu-plexus-java libslf4j-java libsnappy-java libsnappy-jni libsnappy1v5 libsnpeff-java libsnpeff-java-doc libstax-ex-java libstreambuffer-java libstringtemplate4-java libsub-override-perl libsub-quote-perl libsurefire-java libtimedate-perl libtool libtreelayout-java libtrove3-java libtrove3-java-doc libtry-tiny-perl libtxw2-java libuchardet0 libunivocity-parsers-java liburi-perl libvecmath-java libvelocity-tools-java libwagon-file-java libwagon-http-java libwagon-http-shaded-java libwagon-provider-api-java libwebsocket-api-java libwww-perl libwww-robotrules-perl libxalan2-java libxbean-reflect-java libxerces2-java libxml-commons-external-java libxml-commons-resolver1.1-java libxml2 libxml2-utils libxmlgraphics-commons-java libxsom-java libxz-java m4 man-db maven maven-debian-helper maven-repo-helper media-types netbase openjdk-11-doc openjdk-11-jdk-headless openjdk-11-jre-headless patchutils perl-openssl-defaults po-debconf python3 python3-minimal python3.10 python3.10-minimal sbuild-build-depends-main-dummy sgml-base ucf unzip velocity wdiff 0 upgraded, 324 newly installed, 0 to remove and 0 not upgraded. Need to get 451 MB of archives. After this operation, 1194 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [776 B] Get:2 http://ftpmaster.internal/ubuntu kinetic/main amd64 libpython3.10-minimal amd64 3.10.4-3 [809 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libexpat1 amd64 2.4.8-1 [90.6 kB] Get:4 http://ftpmaster.internal/ubuntu kinetic/main amd64 python3.10-minimal amd64 3.10.4-3 [2246 kB] Get:5 http://ftpmaster.internal/ubuntu kinetic/main amd64 python3-minimal amd64 3.10.4-0ubuntu2 [24.4 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic/main amd64 media-types all 7.1.0 [25.6 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/main amd64 libmpdec3 amd64 2.5.1-2build2 [86.8 kB] Get:8 http://ftpmaster.internal/ubuntu kinetic/main amd64 libpython3.10-stdlib amd64 3.10.4-3 [1830 kB] Get:9 http://ftpmaster.internal/ubuntu kinetic/main amd64 python3.10 amd64 3.10.4-3 [488 kB] Get:10 http://ftpmaster.internal/ubuntu kinetic/main amd64 libpython3-stdlib amd64 3.10.4-0ubuntu2 [6990 B] Get:11 http://ftpmaster.internal/ubuntu kinetic/main amd64 python3 amd64 3.10.4-0ubuntu2 [22.8 kB] Get:12 http://ftpmaster.internal/ubuntu kinetic/main amd64 sgml-base all 1.30 [12.5 kB] Get:13 http://ftpmaster.internal/ubuntu kinetic/main amd64 libdbus-1-3 amd64 1.12.20-2ubuntu4 [188 kB] Get:14 http://ftpmaster.internal/ubuntu kinetic/main amd64 libelf1 amd64 0.186-1build1 [51.0 kB] Get:15 http://ftpmaster.internal/ubuntu kinetic/main amd64 libglib2.0-0 amd64 2.72.1-1 [1460 kB] Get:16 http://ftpmaster.internal/ubuntu kinetic/main amd64 libicu71 amd64 71.1-2 [10.8 MB] Get:17 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libxml2 amd64 2.9.13+dfsg-1build2 [762 kB] Get:18 http://ftpmaster.internal/ubuntu kinetic/main amd64 netbase all 6.3 [12.9 kB] Get:19 http://ftpmaster.internal/ubuntu kinetic/main amd64 ucf all 3.0043 [56.1 kB] Get:20 http://ftpmaster.internal/ubuntu kinetic/main amd64 bsdextrautils amd64 2.37.2-4ubuntu3 [71.1 kB] Get:21 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libmagic-mgc amd64 1:5.41-4 [257 kB] Get:22 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libmagic1 amd64 1:5.41-4 [87.3 kB] Get:23 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 file amd64 1:5.41-4 [21.5 kB] Get:24 http://ftpmaster.internal/ubuntu kinetic/main amd64 gettext-base amd64 0.21-4ubuntu4 [37.8 kB] Get:25 http://ftpmaster.internal/ubuntu kinetic/main amd64 libuchardet0 amd64 0.0.7-1build2 [76.9 kB] Get:26 http://ftpmaster.internal/ubuntu kinetic/main amd64 groff-base amd64 1.22.4-8build1 [955 kB] Get:27 http://ftpmaster.internal/ubuntu kinetic/main amd64 libpipeline1 amd64 1.5.5-1 [23.5 kB] Get:28 http://ftpmaster.internal/ubuntu kinetic/main amd64 man-db amd64 2.10.2-1 [1187 kB] Get:29 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libnspr4 amd64 2:4.33-1 [119 kB] Get:30 http://ftpmaster.internal/ubuntu kinetic/main amd64 libnss3 amd64 2:3.68.2-0ubuntu1 [1279 kB] Get:31 http://ftpmaster.internal/ubuntu kinetic/main amd64 ca-certificates-java all 20190909 [12.1 kB] Get:32 http://ftpmaster.internal/ubuntu kinetic/main amd64 java-common all 0.72build2 [6782 B] Get:33 http://ftpmaster.internal/ubuntu kinetic/main amd64 libavahi-common-data amd64 0.8-5ubuntu5 [23.9 kB] Get:34 http://ftpmaster.internal/ubuntu kinetic/main amd64 libavahi-common3 amd64 0.8-5ubuntu5 [23.7 kB] Get:35 http://ftpmaster.internal/ubuntu kinetic/main amd64 libavahi-client3 amd64 0.8-5ubuntu5 [28.1 kB] Get:36 http://ftpmaster.internal/ubuntu kinetic/main amd64 libcups2 amd64 2.4.1op1-1ubuntu4 [264 kB] Get:37 http://ftpmaster.internal/ubuntu kinetic/main amd64 liblcms2-2 amd64 2.12~rc1-2build2 [159 kB] Get:38 http://ftpmaster.internal/ubuntu kinetic/main amd64 libjpeg-turbo8 amd64 2.1.2-0ubuntu1 [134 kB] Get:39 http://ftpmaster.internal/ubuntu kinetic/main amd64 libjpeg8 amd64 8c-2ubuntu10 [2264 B] Get:40 http://ftpmaster.internal/ubuntu kinetic/main amd64 libbrotli1 amd64 1.0.9-2build6 [315 kB] Get:41 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libfreetype6 amd64 2.11.1+dfsg-2 [389 kB] Get:42 http://ftpmaster.internal/ubuntu kinetic/main amd64 fonts-dejavu-core all 2.37-2build1 [1041 kB] Get:43 http://ftpmaster.internal/ubuntu kinetic/main amd64 fontconfig-config all 2.13.1-4.2ubuntu5 [29.1 kB] Get:44 http://ftpmaster.internal/ubuntu kinetic/main amd64 libfontconfig1 amd64 2.13.1-4.2ubuntu5 [131 kB] Get:45 http://ftpmaster.internal/ubuntu kinetic/main amd64 libasound2-data all 1.2.6.1-1ubuntu1 [19.1 kB] Get:46 http://ftpmaster.internal/ubuntu kinetic/main amd64 libasound2 amd64 1.2.6.1-1ubuntu1 [390 kB] Get:47 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgraphite2-3 amd64 1.3.14-1build2 [71.3 kB] Get:48 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libharfbuzz0b amd64 2.7.4-1ubuntu4 [352 kB] Get:49 http://ftpmaster.internal/ubuntu kinetic/main amd64 libpcsclite1 amd64 1.9.5-3 [19.9 kB] Get:50 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 openjdk-11-jre-headless amd64 11.0.15+10-0ubuntu0.22.04.1 [41.5 MB] Get:51 http://ftpmaster.internal/ubuntu kinetic/main amd64 default-jre-headless amd64 2:1.11-72build2 [3042 B] Get:52 http://ftpmaster.internal/ubuntu kinetic/universe amd64 ant all 1.10.12-1 [2100 kB] Get:53 http://ftpmaster.internal/ubuntu kinetic/universe amd64 ant-optional all 1.10.12-1 [368 kB] Get:54 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libantlr4-runtime-java all 4.7.2-5 [307 kB] Get:55 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libantlr3-runtime-java all 3.5.2-9 [164 kB] Get:56 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libicu4j-java all 68.2-2 [15.2 MB] Get:57 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libjsonp-java all 1.1.2-3 [127 kB] Get:58 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libstringtemplate4-java all 4.0.8-2.1 [234 kB] Get:59 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libtreelayout-java all 1.0.3-2 [26.1 kB] Get:60 http://ftpmaster.internal/ubuntu kinetic/universe amd64 antlr4 all 4.7.2-5 [1337 kB] Get:61 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 openjdk-11-doc all 11.0.15+10-0ubuntu0.22.04.1 [12.4 MB] Get:62 http://ftpmaster.internal/ubuntu kinetic/main amd64 default-jdk-doc amd64 2:1.11-72build2 [3126 B] Get:63 http://ftpmaster.internal/ubuntu kinetic/universe amd64 antlr4-doc all 4.7.2-5 [1086 kB] Get:64 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsigsegv2 amd64 2.13-1ubuntu3 [14.6 kB] Get:65 http://ftpmaster.internal/ubuntu kinetic/main amd64 m4 amd64 1.4.18-5ubuntu2 [199 kB] Get:66 http://ftpmaster.internal/ubuntu kinetic/main amd64 autoconf all 2.71-2 [338 kB] Get:67 http://ftpmaster.internal/ubuntu kinetic/main amd64 autotools-dev all 20220109.1 [44.9 kB] Get:68 http://ftpmaster.internal/ubuntu kinetic/main amd64 automake all 1:1.16.5-1.3 [558 kB] Get:69 http://ftpmaster.internal/ubuntu kinetic/main amd64 autopoint all 0.21-4ubuntu4 [422 kB] Get:70 http://ftpmaster.internal/ubuntu kinetic/main amd64 dctrl-tools amd64 2.24-3build2 [66.9 kB] Get:71 http://ftpmaster.internal/ubuntu kinetic/main amd64 libdebhelper-perl all 13.6ubuntu1 [67.2 kB] Get:72 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libtool all 2.4.7-3 [166 kB] Get:73 http://ftpmaster.internal/ubuntu kinetic/main amd64 dh-autoreconf all 20 [16.1 kB] Get:74 http://ftpmaster.internal/ubuntu kinetic/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:75 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsub-override-perl all 0.09-2 [9532 B] Get:76 http://ftpmaster.internal/ubuntu kinetic/main amd64 libfile-stripnondeterminism-perl all 1.13.0-1 [18.1 kB] Get:77 http://ftpmaster.internal/ubuntu kinetic/main amd64 dh-strip-nondeterminism all 1.13.0-1 [5344 B] Get:78 http://ftpmaster.internal/ubuntu kinetic/main amd64 libdw1 amd64 0.186-1build1 [250 kB] Get:79 http://ftpmaster.internal/ubuntu kinetic/main amd64 debugedit amd64 1:5.0-4build1 [47.2 kB] Get:80 http://ftpmaster.internal/ubuntu kinetic/main amd64 dwz amd64 0.14-1build2 [105 kB] Get:81 http://ftpmaster.internal/ubuntu kinetic/main amd64 gettext amd64 0.21-4ubuntu4 [868 kB] Get:82 http://ftpmaster.internal/ubuntu kinetic/main amd64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:83 http://ftpmaster.internal/ubuntu kinetic/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] Get:84 http://ftpmaster.internal/ubuntu kinetic/main amd64 debhelper all 13.6ubuntu1 [923 kB] Get:85 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 openjdk-11-jdk-headless amd64 11.0.15+10-0ubuntu0.22.04.1 [214 MB] Get:86 http://ftpmaster.internal/ubuntu kinetic/main amd64 default-jdk-headless amd64 2:1.11-72build2 [942 B] Get:87 http://ftpmaster.internal/ubuntu kinetic/main amd64 libksba8 amd64 1.6.0-2build1 [119 kB] Get:88 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg2-3ubuntu1 [20.8 kB] Get:89 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsasl2-2 amd64 2.1.27+dfsg2-3ubuntu1 [53.9 kB] Get:90 http://ftpmaster.internal/ubuntu kinetic/main amd64 libldap-2.5-0 amd64 2.5.11+dfsg-1~exp1ubuntu3 [184 kB] Get:91 http://ftpmaster.internal/ubuntu kinetic/main amd64 dirmngr amd64 2.2.27-3ubuntu2 [293 kB] Get:92 http://ftpmaster.internal/ubuntu kinetic/main amd64 gnupg-l10n all 2.2.27-3ubuntu2 [54.3 kB] Get:93 http://ftpmaster.internal/ubuntu kinetic/main amd64 gnupg-utils amd64 2.2.27-3ubuntu2 [308 kB] Get:94 http://ftpmaster.internal/ubuntu kinetic/main amd64 gpg-wks-client amd64 2.2.27-3ubuntu2 [62.7 kB] Get:95 http://ftpmaster.internal/ubuntu kinetic/main amd64 gpg-wks-server amd64 2.2.27-3ubuntu2 [57.5 kB] Get:96 http://ftpmaster.internal/ubuntu kinetic/main amd64 gpgsm amd64 2.2.27-3ubuntu2 [198 kB] Get:97 http://ftpmaster.internal/ubuntu kinetic/main amd64 gnupg all 2.2.27-3ubuntu2 [315 kB] Get:98 http://ftpmaster.internal/ubuntu kinetic/main amd64 libfile-dirlist-perl all 0.05-2 [7100 B] Get:99 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libfile-which-perl all 1.27-1 [14.3 kB] Get:100 http://ftpmaster.internal/ubuntu kinetic/main amd64 libfile-homedir-perl all 1.006-1 [38.3 kB] Get:101 http://ftpmaster.internal/ubuntu kinetic/main amd64 libfile-touch-perl all 0.12-1 [9024 B] Get:102 http://ftpmaster.internal/ubuntu kinetic/main amd64 libio-pty-perl amd64 1:1.15-2build2 [35.1 kB] Get:103 http://ftpmaster.internal/ubuntu kinetic/main amd64 libipc-run-perl all 20200505.0-1 [89.8 kB] Get:104 http://ftpmaster.internal/ubuntu kinetic/main amd64 libclass-method-modifiers-perl all 2.13-1 [16.2 kB] Get:105 http://ftpmaster.internal/ubuntu kinetic/main amd64 libclass-xsaccessor-perl amd64 1.19-3build9 [34.1 kB] Get:106 http://ftpmaster.internal/ubuntu kinetic/main amd64 libb-hooks-op-check-perl amd64 0.22-1build5 [10.3 kB] Get:107 http://ftpmaster.internal/ubuntu kinetic/main amd64 libdynaloader-functions-perl all 0.003-1.1 [12.1 kB] Get:108 http://ftpmaster.internal/ubuntu kinetic/main amd64 libdevel-callchecker-perl amd64 0.008-1ubuntu4 [14.9 kB] Get:109 http://ftpmaster.internal/ubuntu kinetic/main amd64 libparams-classify-perl amd64 0.015-1build5 [22.0 kB] Get:110 http://ftpmaster.internal/ubuntu kinetic/main amd64 libmodule-runtime-perl all 0.016-1 [16.2 kB] Get:111 http://ftpmaster.internal/ubuntu kinetic/main amd64 libimport-into-perl all 1.002005-1 [11.0 kB] Get:112 http://ftpmaster.internal/ubuntu kinetic/main amd64 librole-tiny-perl all 2.002004-1 [16.3 kB] Get:113 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsub-quote-perl all 2.006006-1 [19.5 kB] Get:114 http://ftpmaster.internal/ubuntu kinetic/main amd64 libmoo-perl all 2.005004-3 [48.0 kB] Get:115 http://ftpmaster.internal/ubuntu kinetic/main amd64 libencode-locale-perl all 1.05-1.1 [11.8 kB] Get:116 http://ftpmaster.internal/ubuntu kinetic/main amd64 libtimedate-perl all 2.3300-2 [34.0 kB] Get:117 http://ftpmaster.internal/ubuntu kinetic/main amd64 libhttp-date-perl all 6.05-1 [9920 B] Get:118 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libfile-listing-perl all 6.15-1 [11.5 kB] Get:119 http://ftpmaster.internal/ubuntu kinetic/main amd64 libhtml-tagset-perl all 3.20-4 [12.5 kB] Get:120 http://ftpmaster.internal/ubuntu kinetic/main amd64 liburi-perl all 5.10-1 [78.8 kB] Get:121 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libhtml-parser-perl amd64 3.78-1 [88.3 kB] Get:122 http://ftpmaster.internal/ubuntu kinetic/main amd64 libhtml-tree-perl all 5.07-2 [200 kB] Get:123 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libio-html-perl all 1.004-3 [15.9 kB] Get:124 http://ftpmaster.internal/ubuntu kinetic/main amd64 liblwp-mediatypes-perl all 6.04-1 [19.5 kB] Get:125 http://ftpmaster.internal/ubuntu kinetic/main amd64 libhttp-message-perl all 6.36-1 [76.8 kB] Get:126 http://ftpmaster.internal/ubuntu kinetic/main amd64 libhttp-cookies-perl all 6.10-1 [18.4 kB] Get:127 http://ftpmaster.internal/ubuntu kinetic/main amd64 libhttp-negotiate-perl all 6.01-1 [12.5 kB] Get:128 http://ftpmaster.internal/ubuntu kinetic/main amd64 perl-openssl-defaults amd64 5build2 [7542 B] Get:129 http://ftpmaster.internal/ubuntu kinetic/main amd64 libnet-ssleay-perl amd64 1.92-1build2 [327 kB] Get:130 http://ftpmaster.internal/ubuntu kinetic/main amd64 libio-socket-ssl-perl all 2.074-2 [192 kB] Get:131 http://ftpmaster.internal/ubuntu kinetic/main amd64 libnet-http-perl all 6.22-1 [23.2 kB] Get:132 http://ftpmaster.internal/ubuntu kinetic/main amd64 liblwp-protocol-https-perl all 6.10-1 [10.9 kB] Get:133 http://ftpmaster.internal/ubuntu kinetic/main amd64 libtry-tiny-perl all 0.31-1 [21.8 kB] Get:134 http://ftpmaster.internal/ubuntu kinetic/main amd64 libwww-robotrules-perl all 6.02-1 [12.6 kB] Get:135 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libwww-perl all 6.64-1 [142 kB] Get:136 http://ftpmaster.internal/ubuntu kinetic/main amd64 patchutils amd64 0.4.2-1build2 [77.8 kB] Get:137 http://ftpmaster.internal/ubuntu kinetic/main amd64 wdiff amd64 1.2.2-2build3 [29.6 kB] Get:138 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 devscripts amd64 2.22.1ubuntu2 [1055 kB] Get:139 http://ftpmaster.internal/ubuntu kinetic/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] Get:140 http://ftpmaster.internal/ubuntu kinetic/main amd64 unzip amd64 6.0-26ubuntu3 [174 kB] Get:141 http://ftpmaster.internal/ubuntu kinetic/universe amd64 java-wrappers all 0.3 [9560 B] Get:142 http://ftpmaster.internal/ubuntu kinetic/universe amd64 javahelper all 0.78 [86.2 kB] Get:143 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libhamcrest-java all 1.3-9 [386 kB] Get:144 http://ftpmaster.internal/ubuntu kinetic/universe amd64 junit4 all 4.13.2-1 [344 kB] Get:145 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libapiguardian-java all 1.1.0-3 [4148 B] Get:146 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libopentest4j-java all 1.2.0-3 [9250 B] Get:147 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libpicocli-java all 3.9.6-3 [258 kB] Get:148 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libapache-pom-java all 18-1 [4720 B] Get:149 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libcommons-parent-java all 43-1 [10.8 kB] Get:150 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libcommons-io-java all 2.11.0-2 [297 kB] Get:151 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libcommons-lang3-java all 3.11-1 [526 kB] Get:152 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libcommons-collections3-java all 3.2.2-2 [525 kB] Get:153 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libcommons-lang-java all 2.6-9 [272 kB] Get:154 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libcommons-codec-java all 1.15-1 [291 kB] Get:155 http://ftpmaster.internal/ubuntu kinetic-proposed/universe amd64 libcommons-logging-java all 1.2-3 [59.9 kB] Get:156 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libhttpcore-java all 4.4.14-2 [606 kB] Get:157 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libhttpclient-java all 4.5.13-3 [1226 kB] Get:158 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libplexus-utils2-java all 3.3.0-1 [250 kB] Get:159 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libmaven-parent-java all 31-2 [5140 B] Get:160 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libdoxia-core-java all 1.7-2 [168 kB] Get:161 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libcommons-configuration-java all 1.10-5 [328 kB] Get:162 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libjaxp1.3-java all 1.3.05-6 [227 kB] Get:163 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libxml-commons-external-java all 1.4.01-5 [240 kB] Get:164 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libxml-commons-resolver1.1-java all 1.2-11 [97.6 kB] Get:165 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libxerces2-java all 2.12.1-1 [1437 kB] Get:166 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libxalan2-java all 2.7.2-4 [3416 kB] Get:167 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libxmlgraphics-commons-java all 2.6-1 [612 kB] Get:168 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libbatik-java all 1.14-1 [3866 kB] Get:169 http://ftpmaster.internal/ubuntu kinetic-proposed/universe amd64 libfontbox2-java all 2.0.26-1 [1503 kB] Get:170 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libqdox-java all 1.12.1-3 [172 kB] Get:171 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libfop-java all 1:2.6-2 [10.1 MB] Get:172 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libitext1-java all 1.4-7 [1257 kB] Get:173 http://ftpmaster.internal/ubuntu kinetic/universe amd64 liblog4j1.2-java all 1.2.17-11 [439 kB] Get:174 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libasm-java all 9.2-1 [375 kB] Get:175 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libparboiled-java all 1.1.7-2.1 [272 kB] Get:176 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libpegdown-java all 1.6.0-1.1 [73.9 kB] Get:177 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libplexus-component-annotations-java all 2.1.0-1 [6564 B] Get:178 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5348 B] Get:179 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libjsr305-java all 0.1~+svn49-11 [27.0 kB] Get:180 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libguava-java all 29.0-6 [2418 kB] Get:181 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libplexus-classworlds-java all 2.6.0-1 [49.4 kB] Get:182 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libxbean-reflect-java all 4.5-8 [132 kB] Get:183 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libplexus-container-default-java all 2.1.0-1 [192 kB] Get:184 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libdoxia-java all 1.7-2 [442 kB] Get:185 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libmaven-reporting-api-java all 3.0-1.1 [6828 B] Get:186 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libcommons-cli-java all 1.4-2 [55.8 kB] Get:187 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.2 kB] Get:188 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libaopalliance-java all 20070526-6 [9084 B] Get:189 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libguice-java all 4.2.3-2 [1434 kB] Get:190 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libwagon-provider-api-java all 3.3.4-1 [48.5 kB] Get:191 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libmaven-resolver-java all 1.4.2-3build1 [555 kB] Get:192 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libmaven-shared-utils-java all 3.3.0-1 [149 kB] Get:193 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libplexus-cipher-java all 1.8-2 [15.1 kB] Get:194 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libplexus-interpolation-java all 1.26-1 [76.8 kB] Get:195 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libplexus-sec-dispatcher-java all 1.4-4 [28.1 kB] Get:196 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4fakesync [8616 B] Get:197 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libcdi-api-java all 1.2-3 [54.3 kB] Get:198 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libslf4j-java all 1.7.32-1 [141 kB] Get:199 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libsisu-inject-java all 0.3.4-2 [347 kB] Get:200 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libsisu-plexus-java all 0.3.4-3 [181 kB] Get:201 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libmaven3-core-java all 3.6.3-5 [1535 kB] Get:202 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libplexus-i18n-java all 1.0-beta-10-5 [14.0 kB] Get:203 http://ftpmaster.internal/ubuntu kinetic/universe amd64 velocity all 1.7-6 [428 kB] Get:204 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libplexus-velocity-java all 1.2-3.1 [10.5 kB] Get:205 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libcommons-beanutils-java all 1.9.4-1 [226 kB] Get:206 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libcommons-digester-java all 1.8.1-5 [167 kB] Get:207 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libcommons-validator-java all 1:1.6-2 [174 kB] Get:208 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libjaxen-java all 1.1.6-4 [214 kB] Get:209 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libdom4j-java all 2.1.3-1 [309 kB] Get:210 http://ftpmaster.internal/ubuntu kinetic/universe amd64 liboro-java all 2.0.8a-14 [65.0 kB] Get:211 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libvelocity-tools-java all 2.0-8 [308 kB] Get:212 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libdoxia-sitetools-java all 1.7.5-2 [199 kB] Get:213 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libmaven-common-artifact-filters-java all 3.1.1-1 [44.0 kB] Get:214 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libbsh-java all 2.0b4-20 [289 kB] Get:215 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libjtidy-java all 7+svn20110807-5 [250 kB] Get:216 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libmaven-reporting-impl-java all 3.0.0-2 [14.5 kB] Get:217 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libplexus-container-default1.5-java all 2.1.0-1 [2324 B] Get:218 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libplexus-ant-factory-java all 1.0~alpha2.1-4 [11.4 kB] Get:219 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libcommons-compress-java all 1.21-1 [575 kB] Get:220 http://ftpmaster.internal/ubuntu 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http://ftpmaster.internal/ubuntu kinetic/universe amd64 maven all 3.6.3-5 [17.8 kB] Get:323 http://ftpmaster.internal/ubuntu kinetic/universe amd64 maven-repo-helper all 1.10 [137 kB] Get:324 http://ftpmaster.internal/ubuntu kinetic/universe amd64 maven-debian-helper all 2.6 [108 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 451 MB in 17s (27.0 MB/s) Selecting previously unselected package libpython3.10-minimal:amd64. 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Setting up libjni-inchi-jni (0.8+dfsg-6) ... Setting up dwz (0.14-1build2) ... Setting up libjansi-native-java (1.8-1) ... Setting up libjgraphx-java (2.1.0.7-2) ... Setting up groff-base (1.22.4-8build1) ... Setting up libhtml-parser-perl:amd64 (3.78-1) ... Setting up debugedit (1:5.0-4build1) ... Setting up libcommons-beanutils-java (1.9.4-1) ... Setting up libsnappy-java (1.1.8.3-1) ... Setting up libfontconfig1:amd64 (2.13.1-4.2ubuntu5) ... Setting up libxsom-java (2.3.0.1-10) ... Setting up libcommons-configuration-java (1.10-5) ... Setting up libwagon-file-java (3.3.4-1) ... Setting up libxml2-utils (2.9.13+dfsg-1build2) ... Setting up libcommons-codec-java (1.15-1) ... Setting up libavahi-client3:amd64 (0.8-5ubuntu5) ... Setting up libio-socket-ssl-perl (2.074-2) ... Setting up libplexus-container-default-java (2.1.0-1) ... Setting up libpython3-stdlib:amd64 (3.10.4-0ubuntu2) ... Setting up libhttp-message-perl (6.36-1) ... 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 libhttp-negotiate-perl (6.01-1) ... Setting up velocity (1.7-6) ... Setting up python3.10 (3.10.4-3) ... Setting up gpg-wks-client (2.2.27-3ubuntu2) ... Setting up libcommons-compress-java (1.21-1) ... 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 (5.07-2) ... Setting up libdistlib-java (1.0-3) ... Setting up libparams-classify-perl (0.015-1build5) ... Setting up libxmlgraphics-commons-java (2.6-1) ... Setting up python3 (3.10.4-0ubuntu2) ... Setting up man-db (2.10.2-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libguice-java (4.2.3-2) ... Setting up dh-autoreconf (20) ... Setting up libmodule-runtime-perl (0.016-1) ... Setting up libjansi-java (1.18-1) ... Setting up libplexus-i18n-java (1.0-beta-10-5) ... Setting up libplexus-container-default1.5-java (2.1.0-1) ... Setting up libcups2:amd64 (2.4.1op1-1ubuntu4) ... Setting up libplexus-interactivity-api-java (1.0-alpha-6-8) ... Setting up libhttpclient-java (4.5.13-3) ... Setting up libplexus-velocity-java (1.2-3.1) ... Setting up gnupg (2.2.27-3ubuntu2) ... Setting up liblightcouch-java (0.0.6-1.1) ... Setting up libwagon-http-java (3.3.4-1) ... Setting up libmaven-shared-utils-java (3.3.0-1) ... Setting up libfastinfoset-java (1.2.12-3) ... Setting up libhtsjdk-java (2.24.1+dfsg-3) ... Setting up libplexus-io-java (3.2.0-1.1) ... Setting up libcommons-validator-java (1:1.6-2) ... Setting up libmaven3-core-java (3.6.3-5) ... Setting up libmaven-shared-incremental-java (1.1-3) ... Setting up libmaven-shared-io-java (3.0.0-3) ... Setting up libimport-into-perl (1.002005-1) ... Setting up libbatik-java (1.14-1) ... Setting up libmoo-perl (2.005004-3) ... Setting up liblog4j2-java (2.17.1-1) ... Setting up libplexus-bsh-factory-java (1.0~alpha7-4.1) ... Setting up debhelper (13.6ubuntu1) ... Setting up libexec-maven-plugin-java (1.6.0-4.1) ... Setting up libmaven-filtering-java (3.1.1-1) ... Setting up libplexus-compiler-java (2.8.8-2) ... Setting up libmaven-compiler-plugin-java (3.8.1-4) ... Setting up libjni-inchi-java (0.8+dfsg-6) ... Setting up libdoxia-core-java (1.7-2) ... Setting up libmaven-clean-plugin-java (3.1.0-1) ... Setting up libmaven-reporting-api-java (3.0-1.1) ... Setting up libmaven-file-management-java (3.0.0-1) ... Setting up libmaven-common-artifact-filters-java (3.1.1-1) ... Setting up libplexus-archiver-java (3.6.0-2) ... Setting up libmaven-resources-plugin-java (3.1.0-1) ... Setting up libjmol-java (14.32.50+dfsg-1) ... Setting up libmaven-reporting-exec-java (1.4-3build1) ... Setting up libfop-java (1:2.6-2) ... Setting up libmaven-archiver-java (3.2.0-2.1) ... Setting up libmaven-jar-plugin-java (3.1.2-1) ... Setting up libdoxia-java (1.7-2) ... Setting up libmaven-artifact-transfer-java (0.9.1-4) ... Setting up libcommons-text-java (1.9-2) ... Setting up libmsgpack-java (0.9.1-1) ... Setting up libmmtf-java (1.0.11-1) ... Setting up libjgrapht-java (1.5.1-3) ... Setting up ca-certificates-java (20190909) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:Certigna.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Izenpe.com.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:GTS_Root_R4.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:Certigna_Root_CA.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:SecureTrust_CA.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:AffirmTrust_Networking.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:ACCVRAIZ1.pem Adding debian:AffirmTrust_Premium.pem Adding debian:EC-ACC.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:Secure_Global_CA.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:SecureSign_RootCA11.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:GTS_Root_R2.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:ISRG_Root_X1.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:GTS_Root_R3.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:GTS_Root_R1.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:TrustCor_ECA-1.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:Hongkong_Post_Root_CA_3.pem done. Setting up liblwp-protocol-https-perl (6.10-1) ... Setting up default-jre-headless (2:1.11-72build2) ... Setting up libwww-perl (6.64-1) ... Setting up antlr4 (4.7.2-5) ... Setting up maven-repo-helper (1.10) ... Setting up maven (3.6.3-5) ... update-alternatives: using /usr/share/maven/bin/mvn to provide /usr/bin/mvn (mvn) in auto mode Setting up devscripts (2.22.1ubuntu2) ... Setting up ant (1.10.12-1) ... Setting up javahelper (0.78) ... Setting up junit4 (4.13.2-1) ... Setting up libplexus-ant-factory-java (1.0~alpha2.1-4) ... Setting up ant-optional (1.10.12-1) ... Setting up junit5 (5.3.2-5) ... Setting up libistack-commons-java (3.0.6-5) ... Setting up libcodemodel-java (2.6+jaxb2.3.0.1-10) ... Setting up libtxw2-java (2.3.0.1-10) ... Setting up libjaxb-java (2.3.0.1-10) ... Setting up libbiojava5-java (5.4.0+dfsg-3) ... Setting up libsnpeff-java (5.1+dfsg-2) ... Processing triggers for libc-bin (2.35-0ubuntu3) ... Processing triggers for ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. Setting up openjdk-11-jre-headless:amd64 (11.0.15+10-0ubuntu0.22.04.1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up openjdk-11-jdk-headless:amd64 (11.0.15+10-0ubuntu0.22.04.1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jaotc to provide /usr/bin/jaotc (jaotc) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jdk-headless (2:1.11-72build2) ... Processing triggers for sgml-base (1.30) ... Setting up libvelocity-tools-java (2.0-8) ... Setting up libdoxia-sitetools-java (1.7.5-2) ... Setting up libmaven-javadoc-plugin-java (3.0.1-4) ... Setting up libmaven-reporting-impl-java (3.0.0-2) ... Setting up libsurefire-java (2.22.3-1) ... Setting up libmaven-plugin-tools-java (3.6.0-1) ... Setting up libmaven-assembly-plugin-java (3.1.0-1) ... Setting up libmaven-site-plugin-java (3.6-4) ... Setting up maven-debian-helper (2.6) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-109-generic #123-Ubuntu SMP Fri Apr 8 09:10:54 UTC 2022 amd64 (x86_64) Toolchain package versions: binutils_2.38-3ubuntu1 dpkg-dev_1.21.1ubuntu2 g++-11_11.3.0-1ubuntu1 gcc-11_11.3.0-1ubuntu1 libc6-dev_2.35-0ubuntu3 libstdc++-11-dev_11.3.0-1ubuntu1 libstdc++6_12-20220428-1ubuntu1 linux-libc-dev_5.15.0-28.29 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1ubuntu2 ant_1.10.12-1 ant-optional_1.10.12-1 antlr4_4.7.2-5 antlr4-doc_4.7.2-5 apt_2.4.5 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-4ubuntu4 autotools-dev_20220109.1 base-files_12ubuntu5 base-passwd_3.5.52build1 bash_5.1-6ubuntu1 binutils_2.38-3ubuntu1 binutils-common_2.38-3ubuntu1 binutils-x86-64-linux-gnu_2.38-3ubuntu1 bsdextrautils_2.37.2-4ubuntu3 bsdutils_1:2.37.2-4ubuntu3 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20211016 ca-certificates-java_20190909 coreutils_8.32-4.1ubuntu1 cpp_4:11.2.0-1ubuntu1 cpp-11_11.3.0-1ubuntu1 dash_0.5.11+git20210903+057cd650a4ed-3build1 dctrl-tools_2.24-3build2 debconf_1.5.79ubuntu1 debhelper_13.6ubuntu1 debianutils_5.5-1ubuntu2 debugedit_1:5.0-4build1 default-jdk-doc_2:1.11-72build2 default-jdk-headless_2:1.11-72build2 default-jre-headless_2:1.11-72build2 devscripts_2.22.1ubuntu2 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-0ubuntu2 dirmngr_2.2.27-3ubuntu2 dpkg_1.21.1ubuntu2 dpkg-dev_1.21.1ubuntu2 dwz_0.14-1build2 e2fsprogs_1.46.5-2ubuntu1 fakeroot_1.28-1ubuntu1 file_1:5.41-4 findutils_4.8.0-1ubuntu3 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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 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---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-23594833 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-23594833 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-23594833 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -b -rfakeroot dpkg-buildpackage: info: source package snpsift dpkg-buildpackage: info: source version 5.1+dfsg2-2 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with javahelper debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' 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 '/<>' 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=/<>/snpsift-5.1\+dfsg2/debian/maven-repo 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=/<>/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=/<>/snpsift-5.1\+dfsg2/debian -Dmaven.repo.local=/<>/snpsift-5.1\+dfsg2/debian/maven-repo --batch-mode package javadoc:jar javadoc:aggregate -DskipTests -Dnotimestamp=true -Dlocale=en_US [INFO] Scanning for projects... [INFO] [INFO] ------------------------< org.snpsift:snpsift >------------------------- [INFO] Building SnpSift 5.1 [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ snpsift --- [INFO] Using 'ISO-8859-1' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /<>/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ snpsift --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 112 source files to /<>/target/classes [WARNING] /<>/src/main/java/org/snpsift/hwe/VcfHwe.java:[116,45] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /<>/src/main/java/org/snpsift/hwe/VcfHwe.java:[116,80] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /<>/src/main/java/org/snpsift/hwe/VcfHwe.java:[116,116] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /<>/src/main/java/org/snpsift/hwe/VcfHwe.java:[116,152] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /<>/src/main/java/org/snpsift/hwe/VcfHwe.java:[117,45] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /<>/src/main/java/org/snpsift/hwe/VcfHwe.java:[117,84] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /<>/src/main/java/org/snpsift/hwe/VcfHwe.java:[117,119] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /<>/src/main/java/org/snpsift/lang/LangFactory.java:[112,25] org.antlr.v4.runtime.ANTLRInputStream in org.antlr.v4.runtime has been deprecated [WARNING] /<>/src/main/java/org/snpsift/lang/LangFactory.java:[112,54] org.antlr.v4.runtime.ANTLRInputStream in org.antlr.v4.runtime has been deprecated [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ snpsift --- [INFO] Using 'ISO-8859-1' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /<>/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1: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:3.1.2:jar (default-jar) @ snpsift --- [INFO] Building jar: /<>/target/snpsift-5.1.jar [INFO] [INFO] --- maven-javadoc-plugin:3.0.1:jar (default-cli) @ snpsift --- [INFO] Adding the --ignore-source-errors option [INFO] Loading source files for package org.snpsift... Loading source files for package org.snpsift.lang.function... Loading source files for package org.snpsift.lang... Loading source files for package org.snpsift.lang.expression... Loading source files for package org.snpsift.pedigree... Loading source files for package org.snpsift.testCases... Loading source files for package org.snpsift.testCases.unit... 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[WARNING] ^ [WARNING] symbol: class SuiteDisplayName [WARNING] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/src/main/java/org/snpsift/testCases/TestCasesZzz.java:143: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesZzz [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesGt.java:23: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesGt [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:143: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:151: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:159: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:167: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:179: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:190: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:215: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:230: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:243: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:271: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:298: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:318: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:338: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:354: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:370: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:388: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:413: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:426: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:437: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:451: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:477: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:489: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:507: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:537: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [INFO] Building jar: /<>/target/snpsift-5.1-javadoc.jar [INFO] [INFO] ------------------------< org.snpsift:snpsift >------------------------- [INFO] Building SnpSift 5.1 [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] >>> maven-javadoc-plugin:3.0.1:aggregate (default-cli) > compile @ snpsift >>> [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ snpsift --- [INFO] Using 'ISO-8859-1' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /<>/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ snpsift --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 112 source files to /<>/target/classes [WARNING] /<>/src/main/java/org/snpsift/hwe/VcfHwe.java:[116,45] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /<>/src/main/java/org/snpsift/hwe/VcfHwe.java:[116,80] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /<>/src/main/java/org/snpsift/hwe/VcfHwe.java:[116,116] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /<>/src/main/java/org/snpsift/hwe/VcfHwe.java:[116,152] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /<>/src/main/java/org/snpsift/hwe/VcfHwe.java:[117,45] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /<>/src/main/java/org/snpsift/hwe/VcfHwe.java:[117,84] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /<>/src/main/java/org/snpsift/hwe/VcfHwe.java:[117,119] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /<>/src/main/java/org/snpsift/lang/LangFactory.java:[112,25] org.antlr.v4.runtime.ANTLRInputStream in org.antlr.v4.runtime has been deprecated [WARNING] /<>/src/main/java/org/snpsift/lang/LangFactory.java:[112,54] org.antlr.v4.runtime.ANTLRInputStream in org.antlr.v4.runtime has been deprecated [INFO] [INFO] <<< maven-javadoc-plugin:3.0.1:aggregate (default-cli) < compile @ snpsift <<< [INFO] [INFO] [INFO] --- maven-javadoc-plugin:3.0.1:aggregate (default-cli) @ snpsift --- [INFO] Adding the --ignore-source-errors option [INFO] Loading source files for package org.snpsift... Loading source files for package org.snpsift.lang.function... Loading source files for package org.snpsift.lang... Loading source files for package org.snpsift.lang.expression... Loading source files for package org.snpsift.pedigree... Loading source files for package org.snpsift.testCases... Loading source files for package org.snpsift.testCases.unit... Loading source files for package org.snpsift.hwe... Loading source files for package org.snpsift.antlr... Loading source files for package org.snpsift.phatsCons... Loading source files for package org.snpsift.caseControl... Loading source files for package org.snpsift.gwasCatalog... Loading source files for package org.snpsift.fileIterator... Loading source files for package org.snpsift.util... Loading source files for package org.snpsift.annotate... Constructing Javadoc information... Standard Doclet version 11.0.15 Building tree for all the packages and classes... Generating /<>/target/site/apidocs/org/snpsift/SnpSift.html... 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import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; [WARNING] ^ [WARNING] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/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] /<>/src/main/java/org/snpsift/testCases/TestCasesZzz.java:143: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesZzz [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesGt.java:23: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesGt [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:143: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:151: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:159: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:167: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:179: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:190: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:215: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:230: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:243: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:271: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:298: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:318: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:338: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:354: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:370: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:388: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:413: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:426: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:437: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:451: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:477: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:489: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:507: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [WARNING] /<>/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:537: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 14.281 s [INFO] Finished at: 2022-04-30T12:29:40Z [INFO] ------------------------------------------------------------------------ debian/rules override_dh_auto_test make[1]: Entering directory '/<>' # 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=/<>/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=/<>/snpsift-5.1\+dfsg2/debian -Dmaven.repo.local=/<>/snpsift-5.1\+dfsg2/debian/maven-repo --batch-mode test [INFO] Scanning for projects... [INFO] [INFO] ------------------------< org.snpsift:snpsift >------------------------- [INFO] Building SnpSift 5.1 [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ snpsift --- [INFO] Using 'ISO-8859-1' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /<>/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ snpsift --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ snpsift --- [INFO] Using 'ISO-8859-1' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /<>/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ snpsift --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 26 source files to /<>/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.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: 5.619 s - in org.snpsift.testCases.unit.TestCasesDbNsfp [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: 0.001 s - in org.snpsift.testCases.unit.TestCasesSplit [INFO] Running org.snpsift.testCases.unit.TestCasesIntervals TestCasesIntervals.test_01(25): Test TestCasesIntervals.test_02(50): Test [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.snpsift.testCases.unit.TestCasesIntervals [INFO] Running org.snpsift.testCases.unit.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: 17.914 s - in org.snpsift.testCases.unit.TestCasesAnnotateMem [INFO] Running org.snpsift.testCases.unit.TestCasesExtractFields TestCasesExtractFields.test_31_ann(291): 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 4.7.2TestCasesExtractFields.test_00(71): Test TestCasesExtractFields.test_01(98): Test TestCasesExtractFields.test_02(104): Test TestCasesExtractFields.test_03(110): Test TestCasesExtractFields.test_04(116): Test TestCasesExtractFields.test_05(122): Test TestCasesExtractFields.test_06(128): Test TestCasesExtractFields.test_07(134): Test TestCasesExtractFields.test_08(140): Test TestCasesExtractFields.test_09(146): Test TestCasesExtractFields.test_10(152): Test TestCasesExtractFields.test_11(158): Test TestCasesExtractFields.test_12(164): Test TestCasesExtractFields.test_13(170): Test TestCasesExtractFields.test_14(176): Test TestCasesExtractFields.test_15(182): Test TestCasesExtractFields.test_16(188): Test TestCasesExtractFields.test_17(194): Test TestCasesExtractFields.test_18(200): Test TestCasesExtractFields.test_19(206): Test TestCasesExtractFields.test_20(212): Test TestCasesExtractFields.test_23(218): Test TestCasesExtractFields.test_24(224): Test TestCasesExtractFields.test_25(230): Test TestCasesExtractFields.test_26(236): Test TestCasesExtractFields.test_27(242): Test TestCasesExtractFields.test_28(253): Test TestCasesExtractFields.test_29(262): Test TestCasesExtractFields.test_30(273): Test TestCasesExtractFields.test_31(282): Test TestCasesExtractFields.test_32(300): Test TestCasesExtractFields.test_33(312): Test TestCasesExtractFields.test_34(323): Test TestCasesExtractFields.test_35(340): Test [INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.132 s - in org.snpsift.testCases.unit.TestCasesExtractFields [INFO] Running org.snpsift.testCases.unit.TestCasesGeneSets TestCasesGeneSets.test_01(25): Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 s - in org.snpsift.testCases.unit.TestCasesGeneSets [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: 2.531 s - in org.snpsift.testCases.unit.TestCasesIndex [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: 16.453 s - in org.snpsift.testCases.unit.TestCasesAnnotateUseIndex [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: 0.013 s - in org.snpsift.testCases.unit.TestCasesPrivate [INFO] Running org.snpsift.testCases.unit.TestCasesGwasCatalog TestCasesGwasCatalog.test_01(34): Test WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '19:16185558' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs8109288' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '19:46172277' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs11671664' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '11:116648916' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs964184' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '6:161010117' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs10455872' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '1:67705957' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs11209026' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '19:45412078' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs7412' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '2:169763147' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs560887' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: Too many 'WARNING_DUPLICATE_PRIMARY_KEY' warnings, no further warnings will be shown. TestCasesGwasCatalog.test_02(50): Test [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.904 s - in org.snpsift.testCases.unit.TestCasesGwasCatalog [INFO] Running org.snpsift.testCases.unit.TestCasesDbNsfpDeleteCache TestCasesDbNsfp.test_01(113): Test TestCasesDbNsfp.test_02(138): Test TestCasesDbNsfp.test_03(160): Test TestCasesDbNsfp.test_04(179): Test TestCasesDbNsfp.test_05(200): Test TestCasesDbNsfp.test_06(223): Test [INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.179 s - in org.snpsift.testCases.unit.TestCasesDbNsfpDeleteCache [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: 16.511 s - in org.snpsift.testCases.unit.TestCasesAnnotateTabix [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.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: 14.814 s - in org.snpsift.testCases.unit.TestCasesAnnotate [INFO] Running org.snpsift.testCases.unit.TestCasesVcfCheck TestCasesVcfCheck.test_01(18): Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 s - in org.snpsift.testCases.unit.TestCasesVcfCheck [INFO] Running org.snpsift.testCases.unit.TestCasesFilter TestCasesFilter.test_57_short_circuit_AND_OR_operators(1724): Test TestCasesFilter.test_32_ann(988): Test TestCasesFilter.test_33_ann(1049): Test TestCasesFilter.test_34_ann(1108): Test TestCasesFilter.test_35_ann(1167): Test TestCasesFilter.test_01(40): Test TestCasesFilter.test_02(64): Test TestCasesFilter.test_03(86): Test TestCasesFilter.test_04(110): Test TestCasesFilter.test_05(134): Test TestCasesFilter.test_06(158): Test TestCasesFilter.test_07(182): Test TestCasesFilter.test_08(208): Test TestCasesFilter.test_09(236): Test TestCasesFilter.test_10(258): Test TestCasesFilter.test_11(281): Test TestCasesFilter.test_12(303): Test TestCasesFilter.test_13(326): Test TestCasesFilter.test_14(348): Test TestCasesFilter.test_15(381): Test TestCasesFilter.test_16(407): Test TestCasesFilter.test_17(435): Test TestCasesFilter.test_18(459): Test TestCasesFilter.test_19(483): Test TestCasesFilter.test_20(507): Test TestCasesFilter.test_21(532): Test TestCasesFilter.test_22(559): Test TestCasesFilter.test_23(615): Test TestCasesFilter.test_24(642): Test TestCasesFilter.test_25(669): Test TestCasesFilter.test_26(697): Test TestCasesFilter.test_27(748): Test TestCasesFilter.test_28(846): Test TestCasesFilter.test_29(875): Test TestCasesFilter.test_30(903): Test TestCasesFilter.test_31(932): Test TestCasesFilter.test_32(960): Test TestCasesFilter.test_33(1021): Test TestCasesFilter.test_34(1081): Test TestCasesFilter.test_35(1140): Test TestCasesFilter.test_36(1198): Test TestCasesFilter.test_37(1222): Test TestCasesFilter.test_38(1247): Test TestCasesFilter.test_39(1272): Test TestCasesFilter.test_40(1295): Test TestCasesFilter.test_41(1320): Test TestCasesFilter.test_42(1356): Test TestCasesFilter.test_43(1374): Test TestCasesFilter.test_44(1392): Test TestCasesFilter.test_45(1410): Test TestCasesFilter.test_46(1437): Test TestCasesFilter.test_47(1448): Test TestCasesFilter.test_48(1459): Test TestCasesFilter.test_49(1475): Test TestCasesFilter.test_50(1494): Test TestCasesFilter.test_51(1526): Test TestCasesFilter.test_52(1560): Test TestCasesFilter.test_53(1583): Test TestCasesFilter.test_54(1605): Test TestCasesFilter.test_55(1627): Test TestCasesFilter.test_22_3(589): Test TestCasesFilter.test_55_2(1647): Test TestCasesFilter.test_55_3(1667): Test TestCasesFilter.test_56_empty_vcf(1687): Test TestCasesFilter.test_58_rmFilter_info_field(1747): Test TestCasesFilter.test_27_ann2(812): Test TestCasesFilter.test_26_ann(721): Test TestCasesFilter.test_27_ann(778): Test [INFO] Tests run: 68, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.216 s - in org.snpsift.testCases.unit.TestCasesFilter [INFO] Running org.snpsift.testCases.unit.TestCasesGt TestCasesGt.test_01(25): Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 s - in org.snpsift.testCases.unit.TestCasesGt [INFO] Running org.snpsift.testCases.unit.TestCasesCaseControl TestCasesCaseControl.test_01(53): Test TestCasesCaseControl.test_02(65): Test TestCasesCaseControl.test_03(83): Test TestCasesCaseControl.test_04(107): Test TestCasesCaseControl.test_05(119): Test TestCasesCaseControl.test_06(125): Test TestCasesCaseControl.test_07(131): Test TestCasesCaseControl.test_08(137): Test TestCasesCaseControl.test_09(146): Test TestCasesCaseControl.test_10(222): Test TestCasesCaseControl.test_02_Str2(77): Test TestCasesCaseControl.test_03_Str2(95): Test TestCasesCaseControl.test_03_Str3(101): Test TestCasesCaseControl.test_01_Str(59): Test TestCasesCaseControl.test_02_Str(71): Test TestCasesCaseControl.test_03_Str(89): Test TestCasesCaseControl.test_04_Str(113): Test [INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.273 s - in org.snpsift.testCases.unit.TestCasesCaseControl [INFO] Running org.snpsift.testCases.unit.TestCasesSort TestCasesSort.test_01(30): Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.snpsift.testCases.unit.TestCasesSort [INFO] Running org.snpsift.testCases.unit.TestCasesVarType TestCasesVarType.test_05_multiple(82): Test TestCasesVarType.test_01_SNP(58): Test TestCasesVarType.test_02_MNP(64): Test TestCasesVarType.test_03_INS(70): Test TestCasesVarType.test_04_DEL(76): Test [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.snpsift.testCases.unit.TestCasesVarType [INFO] Running org.snpsift.testCases.unit.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: 16.107 s - in org.snpsift.testCases.unit.TestCasesAnnotateCreateIndex [INFO] Running org.snpsift.testCases.unit.TestCasesFilterChrPos Annotate: ./test/filterChrPos_01.txt ./test/filterChrPos_01.vcf Annotate: ./test/filterChrPos_02.txt ./test/filterChrPos_02.vcf Annotate: ./test/filterChrPos_03.txt ./test/filterChrPos_03.vcf [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.snpsift.testCases.unit.TestCasesFilterChrPos [INFO] Running org.snpsift.testCases.unit.TestCasesHwe [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.snpsift.testCases.unit.TestCasesHwe [INFO] Running org.snpsift.testCases.unit.TestCasesFilterALL [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 s - in org.snpsift.testCases.unit.TestCasesFilterALL [INFO] Running org.snpsift.testCases.unit.TestCasesFilterGt TestCasesFilterGt.test_01(28): Test TestCasesFilterGt.test_02(62): Test [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.snpsift.testCases.unit.TestCasesFilterGt [INFO] Running org.snpsift.testCases.unit.TestCasesConcordance TestCasesConcordance.test_01(68): Test TestCasesConcordance.test_02(74): Test TestCasesConcordance.test_03(80): Test TestCasesConcordance.test_04(91): Test TestCasesConcordance.test_05(102): Test TestCasesConcordance.test_06(113): Test TestCasesConcordance.test_07(125): Test TestCasesConcordance.test_08(131): Test TestCasesConcordance.test_09(142): Test TestCasesConcordance.test_10(153): Test TestCasesConcordance.test_11(164): Test TestCasesConcordance.test_12(181): Test [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.06 s - in org.snpsift.testCases.unit.TestCasesConcordance [INFO] [INFO] Results: [INFO] [INFO] Tests run: 403, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:52 min [INFO] Finished at: 2022-04-30T12:31:34Z [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/<>' 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=/<>/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=/<>/snpsift-5.1\+dfsg2/debian -Dmaven.repo.local=/<>/snpsift-5.1\+dfsg2/debian/maven-repo --batch-mode -Ddebian.dir=/<>/snpsift-5.1\+dfsg2/debian -Ddebian.package=libsnpsift-java -Dmaven.repo.local=/<>/snpsift-5.1\+dfsg2/debian/maven-repo -Dinstall.to.usj=true org.debian.maven:debian-maven-plugin:2.6:install [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: /<>/pom.xml.save with options: [INFO] --keep-pom-version --package=libsnpsift-java [INFO] --rules=/<>/debian/maven.rules [INFO] --ignore-rules=/<>/debian/maven.ignoreRules [INFO] --published-rules=/<>/debian/maven.publishedRules [INFO] Install jar for snpsift into /usr/share/java [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.490 s [INFO] Finished at: 2022-04-30T12:31:36Z [INFO] ------------------------------------------------------------------------ mh_resolve_dependencies --non-interactive --offline --build -plibsnpsift-java --javadoc --base-directory=/<>/snpsift-5.1\+dfsg2 --non-explore 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 dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libhtsjdk-java/api/index.html > dpkg --search /usr/share/doc/libhtsjdk-java-doc/api/index.html Found libhtsjdk-java-doc > dpkg --search /usr/share/doc/libsnpeff-java/api/index.html Found libsnpeff-java-doc > dpkg --search /usr/share/doc/libtrove3-java/api/index.html Found libtrove3-java-doc bash -c "rm -f target/apidocs/*.sh target/apidocs/options" mh_unpatchpoms -plibsnpsift-java dh_install jh_installjavadoc dh_installdocs dh_installchangelogs dh_installman dh_lintian dh_perl dh_link jh_installlibs jh_classpath jh_manifest jh_exec jh_depends dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package libsnpsift-java: substitution variable ${java:Depends} unused, but is defined dpkg-gencontrol: warning: package libsnpsift-java: substitution variable ${maven:CompileDepends} unused, but is defined dpkg-gencontrol: warning: package libsnpsift-java: substitution variable ${maven:DocDepends} unused, but is defined dpkg-gencontrol: warning: package libsnpsift-java-doc: substitution variable ${maven:CompileDepends} unused, but is defined dpkg-gencontrol: warning: package libsnpsift-java-doc: substitution variable ${maven:Depends} unused, but is defined dh_md5sums dh_builddeb INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing libsnpsift-java-doc (in debian/libsnpsift-java-doc); do_strip: , oemstrip: pkgstriptranslations: processing libsnpsift-java (in debian/libsnpsift-java); do_strip: , oemstrip: pkgstriptranslations: processing snpsift (in debian/snpsift); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libsnpsift-java-doc/DEBIAN/control, package libsnpsift-java-doc, directory debian/libsnpsift-java-doc pkgstripfiles: processing control file: debian/libsnpsift-java/DEBIAN/control, package libsnpsift-java, directory debian/libsnpsift-java INFO: pkgstripfiles: waiting for lock (libsnpsift-java-doc) ... pkgstripfiles: Running PNG optimization (using 4 cpus) for package libsnpsift-java ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libsnpsift-java' in '../libsnpsift-java_5.1+dfsg2-2_all.deb'. pkgstripfiles: processing control file: debian/snpsift/DEBIAN/control, package snpsift, directory debian/snpsift Searching for duplicated docs in dependency libsnpsift-java... symlinking changelog.Debian.gz in snpsift to file in libsnpsift-java pkgstripfiles: Running PNG optimization (using 4 cpus) for package snpsift ... pkgstripfiles: No PNG files. dpkg-deb: building package 'snpsift' in '../snpsift_5.1+dfsg2-2_all.deb'. pkgstripfiles: Disabled PNG optimization for -doc package libsnpsift-java-doc (to save build time) dpkg-deb: building package 'libsnpsift-java-doc' in '../libsnpsift-java-doc_5.1+dfsg2-2_all.deb'. dpkg-genbuildinfo --build=binary -O../snpsift_5.1+dfsg2-2_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../snpsift_5.1+dfsg2-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2022-04-30T12:32:14Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ snpsift_5.1+dfsg2-2_amd64.changes: ---------------------------------- Format: 1.8 Date: Sun, 27 Feb 2022 14:17:09 +0100 Source: snpsift Binary: libsnpsift-java libsnpsift-java-doc snpsift Built-For-Profiles: noudeb Architecture: all Version: 5.1+dfsg2-2 Distribution: kinetic-proposed Urgency: medium Maintainer: Launchpad Build Daemon 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: 28a9519875201ed1da648e314a729cf23ee5e64a 406196 libsnpsift-java-doc_5.1+dfsg2-2_all.deb 5198d3bab1309dab0a69cc769524d2e4d04157ba 305462 libsnpsift-java_5.1+dfsg2-2_all.deb 75b0d264d4d21ddce3c911021ee7786c3094adf6 4138 snpsift_5.1+dfsg2-2_all.deb f5c03538ad99a46d97258bf0dde5d6c0c3d8ee23 17106 snpsift_5.1+dfsg2-2_amd64.buildinfo Checksums-Sha256: a520c72367691b2be536ebec8f8872d9fc53b6e1e4418098c68574f0a18af145 406196 libsnpsift-java-doc_5.1+dfsg2-2_all.deb df80514883acf799dd869c0df0f773f306da341b37db73bbbcdd4318fd3e8e98 305462 libsnpsift-java_5.1+dfsg2-2_all.deb cb838fa39d0035e2e47da7f3fc71fc6e8cadb5a6fa526e4998d9bfb536228ce5 4138 snpsift_5.1+dfsg2-2_all.deb 9986adff921c9baf3adce8b6f0e42827b062a48f63ca4a5bef6e5125c95a4430 17106 snpsift_5.1+dfsg2-2_amd64.buildinfo Files: 43d188bd93dd385ff376122ec778afa5 406196 doc optional libsnpsift-java-doc_5.1+dfsg2-2_all.deb d66e8020da18d62b8cc2ab83beccb2a5 305462 java optional libsnpsift-java_5.1+dfsg2-2_all.deb 015dac3320f9e2e6fa40f46f0652bc7f 4138 java optional snpsift_5.1+dfsg2-2_all.deb 6e29fcac136af1b6b153686bfd02e217 17106 java optional snpsift_5.1+dfsg2-2_amd64.buildinfo /<>/snpsift_5.1+dfsg2-2_amd64.changes.new could not be renamed to /<>/snpsift_5.1+dfsg2-2_amd64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: snpsift Binary: libsnpsift-java libsnpsift-java-doc snpsift Architecture: all Version: 5.1+dfsg2-2 Checksums-Md5: 43d188bd93dd385ff376122ec778afa5 406196 libsnpsift-java-doc_5.1+dfsg2-2_all.deb d66e8020da18d62b8cc2ab83beccb2a5 305462 libsnpsift-java_5.1+dfsg2-2_all.deb 015dac3320f9e2e6fa40f46f0652bc7f 4138 snpsift_5.1+dfsg2-2_all.deb Checksums-Sha1: 28a9519875201ed1da648e314a729cf23ee5e64a 406196 libsnpsift-java-doc_5.1+dfsg2-2_all.deb 5198d3bab1309dab0a69cc769524d2e4d04157ba 305462 libsnpsift-java_5.1+dfsg2-2_all.deb 75b0d264d4d21ddce3c911021ee7786c3094adf6 4138 snpsift_5.1+dfsg2-2_all.deb Checksums-Sha256: a520c72367691b2be536ebec8f8872d9fc53b6e1e4418098c68574f0a18af145 406196 libsnpsift-java-doc_5.1+dfsg2-2_all.deb df80514883acf799dd869c0df0f773f306da341b37db73bbbcdd4318fd3e8e98 305462 libsnpsift-java_5.1+dfsg2-2_all.deb cb838fa39d0035e2e47da7f3fc71fc6e8cadb5a6fa526e4998d9bfb536228ce5 4138 snpsift_5.1+dfsg2-2_all.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Sat, 30 Apr 2022 12:32:14 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: adduser (= 3.118ubuntu5), ant (= 1.10.12-1), ant-optional (= 1.10.12-1), antlr4 (= 4.7.2-5), antlr4-doc (= 4.7.2-5), autoconf (= 2.71-2), automake (= 1:1.16.5-1.3), autopoint (= 0.21-4ubuntu4), autotools-dev (= 20220109.1), base-files (= 12ubuntu5), base-passwd (= 3.5.52build1), bash (= 5.1-6ubuntu1), binutils (= 2.38-3ubuntu1), binutils-common (= 2.38-3ubuntu1), binutils-x86-64-linux-gnu (= 2.38-3ubuntu1), bsdextrautils (= 2.37.2-4ubuntu3), bsdutils (= 1:2.37.2-4ubuntu3), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), ca-certificates (= 20211016), ca-certificates-java (= 20190909), coreutils (= 8.32-4.1ubuntu1), cpp (= 4:11.2.0-1ubuntu1), cpp-11 (= 11.3.0-1ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-3build1), dctrl-tools (= 2.24-3build2), debconf (= 1.5.79ubuntu1), debhelper (= 13.6ubuntu1), debianutils (= 5.5-1ubuntu2), debugedit (= 1:5.0-4build1), default-jdk-doc (= 2:1.11-72build2), default-jdk-headless (= 2:1.11-72build2), default-jre-headless (= 2:1.11-72build2), devscripts (= 2.22.1ubuntu2), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.0-1), diffutils (= 1:3.8-0ubuntu2), dirmngr (= 2.2.27-3ubuntu2), dpkg (= 1.21.1ubuntu2), dpkg-dev (= 1.21.1ubuntu2), dwz (= 0.14-1build2), fakeroot (= 1.28-1ubuntu1), file (= 1:5.41-4), findutils (= 4.8.0-1ubuntu3), fontconfig-config (= 2.13.1-4.2ubuntu5), fonts-dejavu-core (= 2.37-2build1), fonts-mathjax (= 2.7.9+dfsg-1), g++ (= 4:11.2.0-1ubuntu1), g++-11 (= 11.3.0-1ubuntu1), gcc (= 4:11.2.0-1ubuntu1), gcc-11 (= 11.3.0-1ubuntu1), gcc-11-base (= 11.3.0-1ubuntu1), gcc-12-base (= 12-20220428-1ubuntu1), gettext (= 0.21-4ubuntu4), gettext-base (= 0.21-4ubuntu4), gnupg (= 2.2.27-3ubuntu2), gnupg-l10n (= 2.2.27-3ubuntu2), gnupg-utils (= 2.2.27-3ubuntu2), gpg (= 2.2.27-3ubuntu2), gpg-agent (= 2.2.27-3ubuntu2), gpg-wks-client (= 2.2.27-3ubuntu2), gpg-wks-server (= 2.2.27-3ubuntu2), gpgconf (= 2.2.27-3ubuntu2), gpgsm (= 2.2.27-3ubuntu2), gpgv (= 2.2.27-3ubuntu2), grep (= 3.7-1build1), groff-base (= 1.22.4-8build1), gzip (= 1.10-4ubuntu4), hostname (= 3.23ubuntu2), init-system-helpers (= 1.62), intltool-debian (= 0.35.0+20060710.5), java-common (= 0.72build2), java-wrappers (= 0.3), javahelper (= 0.78), junit4 (= 4.13.2-1), junit5 (= 5.3.2-5), libacl1 (= 2.3.1-1), libactivation-java (= 1.2.0-2), libantlr3-runtime-java (= 3.5.2-9), libantlr4-runtime-java (= 4.7.2-5), libaopalliance-java (= 20070526-6), libapache-pom-java (= 18-1), libapfloat-java (= 1.10.1-2), libapiguardian-java (= 1.1.0-3), libarchive-zip-perl (= 1.68-1), libargs4j-java (= 2.33-1.1), libasan6 (= 11.3.0-1ubuntu1), libasm-java (= 9.2-1), libasound2 (= 1.2.6.1-1ubuntu1), libasound2-data (= 1.2.6.1-1ubuntu1), libassuan0 (= 2.5.5-1build1), libatinject-jsr330-api-java (= 1.0+ds1-5), libatomic1 (= 12-20220428-1ubuntu1), libattr1 (= 1:2.5.1-1build1), libaudit-common (= 1:3.0.7-1build1), libaudit1 (= 1:3.0.7-1build1), libavahi-client3 (= 0.8-5ubuntu5), libavahi-common-data (= 0.8-5ubuntu5), libavahi-common3 (= 0.8-5ubuntu5), libb-hooks-op-check-perl (= 0.22-1build5), libbatik-java (= 1.14-1), libbinutils (= 2.38-3ubuntu1), libbiojava5-java (= 5.4.0+dfsg-3), libblkid1 (= 2.37.2-4ubuntu3), libbrotli1 (= 1.0.9-2build6), libbsh-java (= 2.0b4-20), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.35-0ubuntu3), libc-dev-bin (= 2.35-0ubuntu3), libc6 (= 2.35-0ubuntu3), libc6-dev (= 2.35-0ubuntu3), libcap-ng0 (= 0.7.9-2.2build3), libcap2 (= 1:2.44-1build3), libcc1-0 (= 12-20220428-1ubuntu1), libcdi-api-java (= 1.2-3), libcharts4j-java (= 1.3-4), libciftools-java (= 3.0.1-1), libclass-method-modifiers-perl (= 2.13-1), libclass-xsaccessor-perl (= 1.19-3build9), libcodemodel-java (= 2.6+jaxb2.3.0.1-10), libcom-err2 (= 1.46.5-2ubuntu1), libcommons-beanutils-java (= 1.9.4-1), libcommons-cli-java (= 1.4-2), libcommons-codec-java (= 1.15-1), libcommons-collections3-java (= 3.2.2-2), libcommons-compress-java (= 1.21-1), libcommons-configuration-java (= 1.10-5), libcommons-digester-java (= 1.8.1-5), libcommons-exec-java (= 1.3-2), libcommons-io-java (= 2.11.0-2), libcommons-jexl2-java (= 2.1.1-5), libcommons-lang-java (= 2.6-9), libcommons-lang3-java (= 3.11-1), libcommons-logging-java (= 1.2-3), libcommons-math-java (= 2.2-8), libcommons-math3-java (= 3.6.1-3), libcommons-math3-java-doc (= 3.6.1-3), libcommons-parent-java (= 43-1), libcommons-text-java (= 1.9-2), libcommons-validator-java (= 1:1.6-2), libcrypt-dev (= 1:4.4.27-1), libcrypt1 (= 1:4.4.27-1), libctf-nobfd0 (= 2.38-3ubuntu1), libctf0 (= 2.38-3ubuntu1), libcups2 (= 2.4.1op1-1ubuntu4), libdb5.3 (= 5.3.28+dfsg1-0.8ubuntu3), libdbus-1-3 (= 1.12.20-2ubuntu4), libdebconfclient0 (= 0.261ubuntu1), libdebhelper-perl (= 13.6ubuntu1), libdevel-callchecker-perl (= 0.008-1ubuntu4), libdistlib-java (= 1.0-3), libdom4j-java (= 2.1.3-1), libdoxia-core-java (= 1.7-2), libdoxia-java (= 1.7-2), libdoxia-sitetools-java (= 1.7.5-2), libdpkg-perl (= 1.21.1ubuntu2), libdtd-parser-java (= 1.2-1), libdw1 (= 0.186-1build1), libdynaloader-functions-perl (= 0.003-1.1), libel-api-java (= 3.0.0-3), libelf1 (= 0.186-1build1), libencode-locale-perl (= 1.05-1.1), libexec-maven-plugin-java (= 1.6.0-4.1), libexpat1 (= 2.4.8-1), libfakeroot (= 1.28-1ubuntu1), libfastinfoset-java (= 1.2.12-3), libfastutil-java (= 8.5.8+dfsg-1), libffi8 (= 3.4.2-4), libfile-dirlist-perl (= 0.05-2), libfile-homedir-perl (= 1.006-1), libfile-listing-perl (= 6.15-1), libfile-stripnondeterminism-perl (= 1.13.0-1), libfile-touch-perl (= 0.12-1), libfile-which-perl (= 1.27-1), libfontbox2-java (= 2.0.26-1), libfontconfig1 (= 2.13.1-4.2ubuntu5), libfop-java (= 1:2.6-2), libfreemarker-java (= 2.3.23-11), libfreetype6 (= 2.11.1+dfsg-2), libgcc-11-dev (= 11.3.0-1ubuntu1), libgcc-s1 (= 12-20220428-1ubuntu1), libgcrypt20 (= 1.9.4-3ubuntu3), libgdbm-compat4 (= 1.23-1), libgdbm6 (= 1.23-1), libgeronimo-annotation-1.3-spec-java (= 1.3-1), libgeronimo-interceptor-3.0-spec-java (= 1.0.1-4fakesync), libglib2.0-0 (= 2.72.1-1), libgmp10 (= 2:6.2.1+dfsg-3ubuntu1), libgnutls30 (= 3.7.4-2ubuntu1), libgomp1 (= 12-20220428-1ubuntu1), libgoogle-gson-java (= 2.8.8-1), libgpg-error0 (= 1.45-2), libgraphite2-3 (= 1.3.14-1build2), libgssapi-krb5-2 (= 1.19.2-2), libguava-java (= 29.0-6), libguice-java (= 4.2.3-2), libhamcrest-java (= 1.3-9), libharfbuzz0b (= 2.7.4-1ubuntu4), libhawtjni-runtime-java (= 1.17-1), libhogweed6 (= 3.7.3-1build2), libhtml-parser-perl (= 3.78-1), libhtml-tagset-perl (= 3.20-4), libhtml-tree-perl (= 5.07-2), libhtsjdk-java (= 2.24.1+dfsg-3), libhtsjdk-java-doc (= 2.24.1+dfsg-3), libhttp-cookies-perl (= 6.10-1), libhttp-date-perl (= 6.05-1), libhttp-message-perl (= 6.36-1), libhttp-negotiate-perl (= 6.01-1), libhttpclient-java (= 4.5.13-3), libhttpcore-java (= 4.4.14-2), libicu4j-java (= 68.2-2), libicu71 (= 71.1-2), libidn2-0 (= 2.3.2-2build1), libimport-into-perl (= 1.002005-1), libinchi1 (= 1.03+dfsg-4), libio-html-perl (= 1.004-3), libio-pty-perl (= 1:1.15-2build2), libio-socket-ssl-perl (= 2.074-2), libipc-run-perl (= 20200505.0-1), libisl23 (= 0.24-2build1), libistack-commons-java (= 3.0.6-5), libitext1-java (= 1.4-7), libitext5-java (= 5.5.13.2-1), libitm1 (= 12-20220428-1ubuntu1), libjackson2-annotations-java (= 2.13.0-1), libjackson2-core-java (= 2.13.0-2), libjackson2-databind-java (= 2.13.0-2), libjansi-java (= 1.18-1), libjansi-native-java (= 1.8-1), libjaxb-api-java (= 2.3.1-1), libjaxb-java (= 2.3.0.1-10), libjaxen-java (= 1.1.6-4), libjaxp1.3-java (= 1.3.05-6), libjetty9-java (= 9.4.45-1), libjgrapht-java (= 1.5.1-3), libjgraphx-java (= 2.1.0.7-2), libjheaps-java (= 0.14-2), libjmol-java (= 14.32.50+dfsg-1), libjni-inchi-java (= 0.8+dfsg-6), libjni-inchi-jni (= 0.8+dfsg-6), libjpeg-turbo8 (= 2.1.2-0ubuntu1), libjpeg8 (= 8c-2ubuntu10), libjs-mathjax (= 2.7.9+dfsg-1), libjson-simple-java (= 2.3.0-1), libjsonp-java (= 1.1.2-3), libjsoup-java (= 1.14.3-1), libjsp-api-java (= 2.3.4-3), libjsr305-java (= 0.1~+svn49-11), libjtidy-java (= 7+svn20110807-5), libk5crypto3 (= 1.19.2-2), libkeyutils1 (= 1.6.1-2ubuntu3), libkrb5-3 (= 1.19.2-2), libkrb5support0 (= 1.19.2-2), libksba8 (= 1.6.0-2build1), liblcms2-2 (= 2.12~rc1-2build2), libldap-2.5-0 (= 2.5.11+dfsg-1~exp1ubuntu3), liblightcouch-java (= 0.0.6-1.1), liblog4j1.2-java (= 1.2.17-11), liblog4j2-java (= 2.17.1-1), liblsan0 (= 12-20220428-1ubuntu1), liblwp-mediatypes-perl (= 6.04-1), liblwp-protocol-https-perl (= 6.10-1), liblz4-1 (= 1.9.3-2build2), liblzma5 (= 5.2.5-2ubuntu1), libmagic-mgc (= 1:5.41-4), libmagic1 (= 1:5.41-4), libmaven-archiver-java (= 3.2.0-2.1), libmaven-artifact-transfer-java (= 0.9.1-4), libmaven-assembly-plugin-java (= 3.1.0-1), libmaven-clean-plugin-java (= 3.1.0-1), libmaven-common-artifact-filters-java (= 3.1.1-1), libmaven-compiler-plugin-java (= 3.8.1-4), libmaven-file-management-java (= 3.0.0-1), libmaven-filtering-java (= 3.1.1-1), libmaven-invoker-java (= 3.0.0-1), libmaven-jar-plugin-java (= 3.1.2-1), libmaven-javadoc-plugin-java (= 3.0.1-4), libmaven-parent-java (= 31-2), libmaven-plugin-tools-java (= 3.6.0-1), libmaven-reporting-api-java (= 3.0-1.1), libmaven-reporting-exec-java (= 1.4-3build1), libmaven-reporting-impl-java (= 3.0.0-2), libmaven-resolver-java (= 1.4.2-3build1), libmaven-resources-plugin-java (= 3.1.0-1), libmaven-shared-incremental-java (= 1.1-3), libmaven-shared-io-java (= 3.0.0-3), libmaven-shared-utils-java (= 3.3.0-1), libmaven-site-plugin-java (= 3.6-4), libmaven3-core-java (= 3.6.3-5), libmmtf-java (= 1.0.11-1), libmodule-runtime-perl (= 0.016-1), libmongodb-java (= 3.6.3-2), libmoo-perl (= 2.005004-3), libmount1 (= 2.37.2-4ubuntu3), libmpc3 (= 1.2.1-2build1), libmpdec3 (= 2.5.1-2build2), libmpfr6 (= 4.1.0-3build3), libmsgpack-java (= 0.9.1-1), libnaga-java (= 3.0+svn80-4), libncurses6 (= 6.3+20220423-1), libncursesw6 (= 6.3+20220423-1), libnet-http-perl (= 6.22-1), libnet-ssleay-perl (= 1.92-1build2), libnettle8 (= 3.7.3-1build2), libngs-java (= 2.11.2-3), libngs-sdk-dev (= 2.11.2-3), libngs-sdk2 (= 2.11.2-3), libnpth0 (= 1.6-3build2), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libnspr4 (= 2:4.33-1), libnss3 (= 2:3.68.2-0ubuntu1), libopentest4j-java (= 1.2.0-3), liboro-java (= 2.0.8a-14), libp11-kit0 (= 0.24.1-1), libpam-modules (= 1.4.0-13ubuntu1), libpam-modules-bin (= 1.4.0-13ubuntu1), libpam-runtime (= 1.4.0-13ubuntu1), libpam0g (= 1.4.0-13ubuntu1), libparams-classify-perl (= 0.015-1build5), libparboiled-java (= 1.1.7-2.1), libpcre2-8-0 (= 10.40-1), libpcre3 (= 2:8.39-14), libpcsclite1 (= 1.9.5-3), libpegdown-java (= 1.6.0-1.1), libperl5.34 (= 5.34.0-3ubuntu1), libpicocli-java (= 3.9.6-3), libpipeline1 (= 1.5.5-1), libplexus-ant-factory-java (= 1.0~alpha2.1-4), libplexus-archiver-java (= 3.6.0-2), libplexus-bsh-factory-java (= 1.0~alpha7-4.1), libplexus-build-api-java (= 0.0.7-4), libplexus-cipher-java (= 1.8-2), libplexus-classworlds-java (= 2.6.0-1), libplexus-compiler-java (= 2.8.8-2), libplexus-component-annotations-java (= 2.1.0-1), libplexus-container-default-java (= 2.1.0-1), libplexus-container-default1.5-java (= 2.1.0-1), libplexus-i18n-java (= 1.0-beta-10-5), libplexus-interactivity-api-java (= 1.0-alpha-6-8), libplexus-interpolation-java (= 1.26-1), libplexus-io-java (= 3.2.0-1.1), libplexus-languages-java (= 0.9.10-2), libplexus-sec-dispatcher-java (= 1.4-4), libplexus-utils2-java (= 3.3.0-1), libplexus-velocity-java (= 1.2-3.1), libpng16-16 (= 1.6.37-5), libprocps8 (= 2:3.3.17-6ubuntu2), libpython3-stdlib (= 3.10.4-0ubuntu2), libpython3.10-minimal (= 3.10.4-3), libpython3.10-stdlib (= 3.10.4-3), libqdox-java (= 1.12.1-3), libqdox2-java (= 2.0.0-1), libquadmath0 (= 12-20220428-1ubuntu1), libreadline8 (= 8.1.2-1.2), librelaxng-datatype-java (= 1.0+ds1-3.1), librngom-java (= 2.3.0.1-10), librole-tiny-perl (= 2.002004-1), libsasl2-2 (= 2.1.27+dfsg2-3ubuntu1), libsasl2-modules-db (= 2.1.27+dfsg2-3ubuntu1), libseccomp2 (= 2.5.3-2ubuntu2), libselinux1 (= 3.3-1build2), libsemanage-common (= 3.3-1build2), libsemanage2 (= 3.3-1build2), libsepol2 (= 3.3-1build1), libservlet-api-java (= 4.0.1-2), libsigsegv2 (= 2.13-1ubuntu3), libsisu-inject-java (= 0.3.4-2), libsisu-plexus-java (= 0.3.4-3), libslf4j-java (= 1.7.32-1), libsmartcols1 (= 2.37.2-4ubuntu3), libsnappy-java (= 1.1.8.3-1), libsnappy-jni (= 1.1.8.3-1), libsnappy1v5 (= 1.1.8-1build3), libsnpeff-java (= 5.1+dfsg-2), libsnpeff-java-doc (= 5.1+dfsg-2), libsqlite3-0 (= 3.38.2-1), libssl3 (= 3.0.2-0ubuntu1), libstax-ex-java (= 1.7.8-3), libstdc++-11-dev (= 11.3.0-1ubuntu1), libstdc++6 (= 12-20220428-1ubuntu1), libstreambuffer-java (= 1.5.4-1.1), libstringtemplate4-java (= 4.0.8-2.1), libsub-override-perl (= 0.09-2), libsub-quote-perl (= 2.006006-1), libsurefire-java (= 2.22.3-1), libsystemd0 (= 249.11-0ubuntu3.1), libtasn1-6 (= 4.18.0-4build1), libtimedate-perl (= 2.3300-2), libtinfo6 (= 6.3+20220423-1), libtirpc-common (= 1.3.2-2build1), libtirpc-dev (= 1.3.2-2build1), libtirpc3 (= 1.3.2-2build1), libtool (= 2.4.7-3), libtreelayout-java (= 1.0.3-2), libtrove3-java (= 3.0.3-5), libtrove3-java-doc (= 3.0.3-5), libtry-tiny-perl (= 0.31-1), libtsan0 (= 11.3.0-1ubuntu1), libtxw2-java (= 2.3.0.1-10), libubsan1 (= 12-20220428-1ubuntu1), libuchardet0 (= 0.0.7-1build2), libudev1 (= 249.11-0ubuntu3.1), libunistring2 (= 1.0-1), libunivocity-parsers-java (= 2.8.3-2), liburi-perl (= 5.10-1), libuuid1 (= 2.37.2-4ubuntu3), libvecmath-java (= 1.5.2-7), libvelocity-tools-java (= 2.0-8), libwagon-file-java (= 3.3.4-1), libwagon-http-java (= 3.3.4-1), libwagon-http-shaded-java (= 3.3.4-1), libwagon-provider-api-java (= 3.3.4-1), libwebsocket-api-java (= 1.1-2), libwww-perl (= 6.64-1), libwww-robotrules-perl (= 6.02-1), libxalan2-java (= 2.7.2-4), libxbean-reflect-java (= 4.5-8), libxerces2-java (= 2.12.1-1), libxml-commons-external-java (= 1.4.01-5), libxml-commons-resolver1.1-java (= 1.2-11), libxml2 (= 2.9.13+dfsg-1build2), libxml2-utils (= 2.9.13+dfsg-1build2), libxmlgraphics-commons-java (= 2.6-1), libxsom-java (= 2.3.0.1-10), libxz-java (= 1.9-1), libzstd1 (= 1.5.2+dfsg-1), linux-libc-dev (= 5.15.0-28.29), login (= 1:4.8.1-2ubuntu2), lsb-base (= 11.1.0ubuntu4), lto-disabled-list (= 25), m4 (= 1.4.18-5ubuntu2), make (= 4.3-4.1build1), man-db (= 2.10.2-1), maven (= 3.6.3-5), maven-debian-helper (= 2.6), maven-repo-helper (= 1.10), mawk (= 1.3.4.20200120-3), media-types (= 7.1.0), ncurses-base (= 6.3+20220423-1), ncurses-bin (= 6.3+20220423-1), netbase (= 6.3), openjdk-11-doc (= 11.0.15+10-0ubuntu0.22.04.1), openjdk-11-jdk-headless (= 11.0.15+10-0ubuntu0.22.04.1), openjdk-11-jre-headless (= 11.0.15+10-0ubuntu0.22.04.1), openssl (= 3.0.2-0ubuntu1), passwd (= 1:4.8.1-2ubuntu2), patch (= 2.7.6-7build2), patchutils (= 0.4.2-1build2), perl (= 5.34.0-3ubuntu1), perl-base (= 5.34.0-3ubuntu1), perl-modules-5.34 (= 5.34.0-3ubuntu1), perl-openssl-defaults (= 5build2), pinentry-curses (= 1.2.0-1), po-debconf (= 1.0.21+nmu1), procps (= 2:3.3.17-6ubuntu2), python3 (= 3.10.4-0ubuntu2), python3-minimal (= 3.10.4-0ubuntu2), python3.10 (= 3.10.4-3), python3.10-minimal (= 3.10.4-3), readline-common (= 8.1.2-1.2), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.8-1ubuntu2), sensible-utils (= 0.0.17), sgml-base (= 1.30), sysvinit-utils (= 3.01-1ubuntu1), tar (= 1.34+dfsg-1build3), ucf (= 3.0043), unzip (= 6.0-26ubuntu3), util-linux (= 2.37.2-4ubuntu3), velocity (= 1.7-6), wdiff (= 1.2.2-2build3), xz-utils (= 5.2.5-2ubuntu1), zlib1g (= 1:1.2.11.dfsg-2ubuntu9) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1645967829" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ libsnpsift-java-doc_5.1+dfsg2-2_all.deb --------------------------------------- new Debian package, version 2.0. size 406196 bytes: control archive=11093 bytes. 1095 bytes, 22 lines control 48070 bytes, 425 lines md5sums Package: libsnpsift-java-doc Source: snpsift Version: 5.1+dfsg2-2 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 7008 Recommends: antlr4-doc, default-jdk-doc, libcommons-math3-java-doc, libhtsjdk-java-doc, libsnpeff-java-doc, libtrove3-java-doc Suggests: libsnpsift-java Section: doc Priority: optional Multi-Arch: foreign Homepage: https://pcingola.github.io/SnpEff/ss_introduction/ Description: Documentation for SnpSift SnpSift is a toolbox that allows one to filter and manipulate annotated files. Once the genomic variants have been annotated, one needs to filter them out in order to find the "interesting / relevant variants". Given the large data files, this is not a trivial task (e.g. one cannot load all the variants into XLS spreadsheet). SnpSift helps to perform this VCF file manipulation and filtering required at this stage in data processing pipelines. . 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2022-02-27 13:17 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 286 2022-02-26 14:07 ./usr/share/lintian/overrides/libsnpsift-java-doc libsnpsift-java_5.1+dfsg2-2_all.deb ----------------------------------- new Debian package, version 2.0. size 305462 bytes: control archive=942 bytes. 1027 bytes, 20 lines control 415 bytes, 5 lines md5sums Package: libsnpsift-java Source: snpsift Version: 5.1+dfsg2-2 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 341 Depends: antlr4, libcommons-math3-java (>= 3.6.1), libhtsjdk-java (>= 2.23.0), libsnpeff-java, libtrove3-java Section: java Priority: optional Homepage: https://pcingola.github.io/SnpEff/ss_introduction/ Description: tool to annotate and manipulate genome variants - lib SnpSift is a toolbox that allows one to filter and manipulate annotated files. Once the genomic variants have been annotated, one needs to filter them out in order to find the "interesting / relevant variants". Given the large data files, this is not a trivial task (e.g. one cannot load all the variants into XLS spreadsheet). SnpSift helps to perform this VCF file manipulation and filtering required at this stage in data processing pipelines. . This package contains the library. drwxr-xr-x root/root 0 2022-02-27 13:17 ./ drwxr-xr-x root/root 0 2022-02-27 13:17 ./usr/ drwxr-xr-x root/root 0 2022-02-27 13:17 ./usr/share/ drwxr-xr-x root/root 0 2022-02-27 13:17 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-02-27 13:17 ./usr/share/doc/libsnpsift-java/ -rw-r--r-- root/root 196 2022-02-27 13:17 ./usr/share/doc/libsnpsift-java/changelog.Debian.gz -rw-r--r-- root/root 1598 2022-02-26 20:33 ./usr/share/doc/libsnpsift-java/copyright drwxr-xr-x root/root 0 2022-02-27 13:17 ./usr/share/java/ lrwxrwxrwx root/root 0 2022-02-27 13:17 ./usr/share/java/snpsift-5.1.jar -> snpsift.jar -rw-r--r-- root/root 322613 2022-02-27 13:17 ./usr/share/java/snpsift.jar drwxr-xr-x root/root 0 2022-02-27 13:17 ./usr/share/maven-repo/ drwxr-xr-x root/root 0 2022-02-27 13:17 ./usr/share/maven-repo/org/ drwxr-xr-x root/root 0 2022-02-27 13:17 ./usr/share/maven-repo/org/snpsift/ drwxr-xr-x root/root 0 2022-02-27 13:17 ./usr/share/maven-repo/org/snpsift/snpsift/ drwxr-xr-x root/root 0 2022-02-27 13:17 ./usr/share/maven-repo/org/snpsift/snpsift/5.1/ lrwxrwxrwx root/root 0 2022-02-27 13:17 ./usr/share/maven-repo/org/snpsift/snpsift/5.1/snpsift-5.1.jar -> ../../../../../java/snpsift.jar -rw-r--r-- root/root 2483 2022-02-27 13:17 ./usr/share/maven-repo/org/snpsift/snpsift/5.1/snpsift-5.1.pom drwxr-xr-x root/root 0 2022-02-27 13:17 ./usr/share/maven-repo/org/snpsift/snpsift/debian/ lrwxrwxrwx root/root 0 2022-02-27 13:17 ./usr/share/maven-repo/org/snpsift/snpsift/debian/snpsift-debian.jar -> ../../../../../java/snpsift.jar -rw-r--r-- root/root 2486 2022-02-27 13:17 ./usr/share/maven-repo/org/snpsift/snpsift/debian/snpsift-debian.pom snpsift_5.1+dfsg2-2_all.deb --------------------------- new Debian package, version 2.0. size 4138 bytes: control archive=818 bytes. 974 bytes, 20 lines control 182 bytes, 3 lines md5sums Package: snpsift Version: 5.1+dfsg2-2 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 15 Depends: default-jre, libsnpsift-java (= 5.1+dfsg2-2) Suggests: snpeff Section: java Priority: optional Homepage: https://pcingola.github.io/SnpEff/ss_introduction/ Description: tool to annotate and manipulate genome variants - tool SnpSift is a toolbox that allows one to filter and manipulate annotated files. Once the genomic variants have been annotated, one needs to filter them out in order to find the "interesting / relevant variants". Given the large data files, this is not a trivial task (e.g. one cannot load all the variants into XLS spreadsheet). SnpSift helps to perform this VCF file manipulation and filtering required at this stage in data processing pipelines. . This package contains the command line tool. drwxr-xr-x root/root 0 2022-02-27 13:17 ./ drwxr-xr-x root/root 0 2022-02-27 13:17 ./usr/ drwxr-xr-x root/root 0 2022-02-27 13:17 ./usr/bin/ -rwxr-xr-x root/root 559 2022-02-26 14:15 ./usr/bin/snpSift drwxr-xr-x root/root 0 2022-02-27 13:17 ./usr/share/ drwxr-xr-x root/root 0 2022-02-27 13:17 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-02-27 13:17 ./usr/share/doc/snpsift/ lrwxrwxrwx root/root 0 2022-02-27 13:17 ./usr/share/doc/snpsift/changelog.Debian.gz -> ../libsnpsift-java/changelog.Debian.gz -rw-r--r-- root/root 1598 2022-02-26 20:33 ./usr/share/doc/snpsift/copyright drwxr-xr-x root/root 0 2022-02-27 13:17 ./usr/share/man/ drwxr-xr-x root/root 0 2022-02-27 13:17 ./usr/share/man/man1/ -rw-r--r-- root/root 1528 2022-02-27 13:17 ./usr/share/man/man1/snpSift.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 63688 Build-Time: 176 Distribution: kinetic-proposed Host Architecture: amd64 Install-Time: 45 Job: snpsift_5.1+dfsg2-2.dsc Machine Architecture: amd64 Package: snpsift Package-Time: 223 Source-Version: 5.1+dfsg2-2 Space: 63688 Status: successful Version: 5.1+dfsg2-2 -------------------------------------------------------------------------------- Finished at 2022-04-30T12:32:14Z Build needed 00:03:43, 63688k disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-23594833 Scanning for processes to kill in build PACKAGEBUILD-23594833