I: pbuilder: network access will be disabled during build I: Current time: Sat May 25 00:48:02 +14 2024 I: pbuilder-time-stamp: 1716547682 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [snpsift_5.1+dfsg2-2.dsc] I: copying [./snpsift_5.1+dfsg2.orig.tar.xz] I: copying [./snpsift_5.1+dfsg2-2.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Feb 28 03:43:28 2022 +14 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./snpsift_5.1+dfsg2-2.dsc: no acceptable signature found dpkg-source: info: extracting snpsift in snpsift-5.1+dfsg2 dpkg-source: info: unpacking snpsift_5.1+dfsg2.orig.tar.xz dpkg-source: info: unpacking snpsift_5.1+dfsg2-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying alter_pom_for_debian_packaging.patch dpkg-source: info: applying omit_unused_junit_classes.patch dpkg-source: info: applying Debian_specific_config_file.patch dpkg-source: info: applying test_scope_for_junit.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3683552/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 25 00:48 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/3683552/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3683552/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=612691248017461bb0454dacaaa70a01 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3683552 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.nAYN95Cx/pbuilderrc_UpoM --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.nAYN95Cx/b2 --logfile b2/build.log --extrapackages usrmerge snpsift_5.1+dfsg2-2.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-0.deb11.5-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.12-1~bpo11+1 (2023-03-05) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Feb 13 2023 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp -rwxr-xr-x 1 root root 125640 Jan 6 2023 dash -rwxr-xr-x 1 root root 121904 Sep 21 2022 date -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd -rwxr-xr-x 1 root root 102200 Sep 21 2022 df -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir -rwxr-xr-x 1 root root 88656 Mar 24 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 24 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 25 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 20 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln -rwxr-xr-x 1 root root 53024 Mar 24 2023 login -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls -rwxr-xr-x 1 root root 207168 Mar 24 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 24 2023 more -rwsr-xr-x 1 root root 59704 Mar 24 2023 mount -rwxr-xr-x 1 root root 18744 Mar 24 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Feb 13 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 6 2023 sed lrwxrwxrwx 1 root root 9 May 25 00:48 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty -rwsr-xr-x 1 root root 72000 Mar 24 2023 su -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync -rwxr-xr-x 1 root root 531984 Apr 7 2023 tar -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch -rwxr-xr-x 1 root root 35664 Sep 21 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 24 2023 umount -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 24 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/3683552/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), antlr4, antlr4-doc, javahelper, junit5, libcommons-math3-java, libcommons-math3-java-doc, libhtsjdk-java, libhtsjdk-java-doc, libmaven-assembly-plugin-java, libmaven-javadoc-plugin-java, libsnpeff-java, libsnpeff-java-doc, libtrove3-java, libtrove3-java-doc, maven-debian-helper dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on antlr4; however: Package antlr4 is not installed. pbuilder-satisfydepends-dummy depends on antlr4-doc; however: Package antlr4-doc is not installed. pbuilder-satisfydepends-dummy depends on javahelper; however: Package javahelper is not installed. pbuilder-satisfydepends-dummy depends on junit5; however: Package junit5 is not installed. pbuilder-satisfydepends-dummy depends on libcommons-math3-java; however: Package libcommons-math3-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-math3-java-doc; however: Package libcommons-math3-java-doc is not installed. pbuilder-satisfydepends-dummy depends on libhtsjdk-java; however: Package libhtsjdk-java is not installed. pbuilder-satisfydepends-dummy depends on libhtsjdk-java-doc; however: Package libhtsjdk-java-doc is not installed. pbuilder-satisfydepends-dummy depends on libmaven-assembly-plugin-java; however: Package libmaven-assembly-plugin-java is not installed. pbuilder-satisfydepends-dummy depends on libmaven-javadoc-plugin-java; however: Package libmaven-javadoc-plugin-java is not installed. pbuilder-satisfydepends-dummy depends on libsnpeff-java; however: Package libsnpeff-java is not installed. pbuilder-satisfydepends-dummy depends on libsnpeff-java-doc; however: Package libsnpeff-java-doc is not installed. pbuilder-satisfydepends-dummy depends on libtrove3-java; however: Package libtrove3-java is not installed. pbuilder-satisfydepends-dummy depends on libtrove3-java-doc; however: Package libtrove3-java-doc is not installed. pbuilder-satisfydepends-dummy depends on maven-debian-helper; however: Package maven-debian-helper is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: ant{a} ant-optional{a} antlr4{a} antlr4-doc{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} dctrl-tools{a} debhelper{a} default-jdk-doc{a} default-jdk-headless{a} default-jre-headless{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-mathjax{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gnupg-utils{a} gpg{a} gpg-agent{a} gpg-wks-client{a} gpg-wks-server{a} gpgconf{a} gpgsm{a} groff-base{a} intltool-debian{a} java-common{a} java-wrappers{a} javahelper{a} junit4{a} junit5{a} libactivation-java{a} libantlr3-runtime-java{a} libantlr4-runtime-java{a} libaopalliance-java{a} libapache-pom-java{a} libapfloat-java{a} libapiguardian-java{a} libarchive-zip-perl{a} libargs4j-java{a} libasm-java{a} libasound2{a} libasound2-data{a} libassuan0{a} libatinject-jsr330-api-java{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libb-hooks-op-check-perl{a} libbatik-java{a} libbiojava6-java{a} libbrotli1{a} libbsh-java{a} libcdi-api-java{a} libcharts4j-java{a} libciftools-java{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcodemodel-java{a} libcommons-beanutils-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-compress-java{a} libcommons-configuration-java{a} libcommons-digester-java{a} libcommons-exec-java{a} libcommons-io-java{a} libcommons-jexl2-java{a} libcommons-lang-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-math-java{a} libcommons-math3-java{a} libcommons-math3-java-doc{a} libcommons-parent-java{a} libcommons-text-java{a} libcommons-validator-java{a} libcups2{a} libdbus-1-3{a} libdebhelper-perl{a} libdevel-callchecker-perl{a} libdistlib-java{a} libdom4j-java{a} libdoxia-core-java{a} libdoxia-java{a} libdoxia-sitetools-java{a} libdtd-parser-java{a} libdynaloader-functions-perl{a} libel-api-java{a} libelf1{a} libencode-locale-perl{a} liberror-prone-java{a} libexec-maven-plugin-java{a} libexpat1{a} libfastinfoset-java{a} libfastutil-java{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} libfontbox2-java{a} libfontconfig1{a} libfop-java{a} libfreemarker-java{a} libfreetype6{a} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libglib2.0-0{a} libgoogle-gson-java{a} libgraphite2-3{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhtsjdk-java{a} libhtsjdk-java-doc{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libhttpclient-java{a} libhttpcore-java{a} libicu4j-java{a} libicu72{a} libimport-into-perl{a} libinchi1{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libistack-commons-java{a} libitext1-java{a} libitext5-java{a} libjackson2-annotations-java{a} libjackson2-core-java{a} libjackson2-databind-java{a} libjansi-java{a} libjaxb-api-java{a} libjaxb-java{a} libjaxen-java{a} libjaxp1.3-java{a} libjetty9-java{a} libjgrapht-java{a} libjgraphx-java{a} libjheaps-java{a} libjmol-java{a} libjni-inchi-java{a} libjni-inchi-jni{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-jquery-ui-theme-base{a} libjs-mathjax{a} libjson-simple-java{a} libjsonp-java{a} libjsoup-java{a} libjsp-api-java{a} libjsr305-java{a} libjtidy-java{a} libksba8{a} liblcms2-2{a} libldap-2.5-0{a} liblog4j1.2-java{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1{a} libmaven-archiver-java{a} libmaven-artifact-transfer-java{a} libmaven-assembly-plugin-java{a} libmaven-clean-plugin-java{a} libmaven-common-artifact-filters-java{a} libmaven-compiler-plugin-java{a} libmaven-file-management-java{a} libmaven-filtering-java{a} libmaven-invoker-java{a} libmaven-jar-plugin-java{a} libmaven-javadoc-plugin-java{a} libmaven-parent-java{a} libmaven-plugin-tools-java{a} libmaven-reporting-api-java{a} libmaven-reporting-exec-java{a} libmaven-reporting-impl-java{a} libmaven-resolver-java{a} libmaven-resources-plugin-java{a} libmaven-shared-incremental-java{a} libmaven-shared-io-java{a} libmaven-shared-utils-java{a} libmaven-site-plugin-java{a} libmaven3-core-java{a} libmbedcrypto7{a} libmbedtls14{a} libmbedx509-1{a} libmjson-java{a} libmmtf-java{a} libmodule-runtime-perl{a} libmoo-perl{a} libmsgpack-java{a} libnaga-java{a} libncbi-ngs3{a} libncbi-vdb3{a} libnet-http-perl{a} libnet-ssleay-perl{a} libngs-java{a} libngs-jni{a} libnpth0{a} libnspr4{a} libnss3{a} libopentest4j-java{a} libopentest4j-reporting-java{a} liboro-java{a} libparams-classify-perl{a} libpcsclite1{a} libpicocli-java{a} libpipeline1{a} libplexus-ant-factory-java{a} libplexus-archiver-java{a} libplexus-bsh-factory-java{a} libplexus-build-api-java{a} libplexus-cipher-java{a} libplexus-classworlds-java{a} libplexus-compiler-java{a} libplexus-component-annotations-java{a} libplexus-container-default-java{a} libplexus-container-default1.5-java{a} libplexus-i18n-java{a} libplexus-interactivity-api-java{a} libplexus-interpolation-java{a} libplexus-io-java{a} libplexus-languages-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libplexus-velocity-java{a} libpng16-16{a} libproc2-0{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqdox-java{a} libqdox2-java{a} libreadline8{a} libregexp-ipv6-perl{a} librelaxng-datatype-java{a} librhino-java{a} librngom-java{a} librole-tiny-perl{a} libsasl2-2{a} libsasl2-modules-db{a} libservlet-api-java{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libsnpeff-java{a} libsnpeff-java-doc{a} libstax-ex-java{a} libstreambuffer-java{a} libstringtemplate4-java{a} libsub-override-perl{a} libsub-quote-perl{a} libsurefire-java{a} libtimedate-perl{a} libtool{a} libtreelayout-java{a} libtrove3-java{a} libtrove3-java-doc{a} libtry-tiny-perl{a} libtxw2-java{a} libuchardet0{a} libunivocity-parsers-java{a} liburi-perl{a} libvecmath-java{a} libvelocity-tools-java{a} libwagon-file-java{a} libwagon-http-java{a} libwagon-http-shaded-java{a} libwagon-provider-api-java{a} libwebsocket-api-java{a} libwww-perl{a} libwww-robotrules-perl{a} libxalan2-java{a} libxbean-reflect-java{a} libxerces2-java{a} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxml2-utils{a} libxmlgraphics-commons-java{a} libxsom-java{a} libxz-java{a} m4{a} man-db{a} maven{a} maven-debian-helper{a} maven-repo-helper{a} media-types{a} ncbi-vdb-data{a} netbase{a} openjdk-17-doc{a} openjdk-17-jdk-headless{a} openjdk-17-jre-headless{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} procps{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} unzip{a} velocity{a} wdiff{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf curl dbus debian-keyring dput dput-ng dupload equivs icc-profiles-free javascript-common libarchive-cpio-perl libbiojava6-java-doc libdata-dump-perl libdistlib-java-doc libdistro-info-perl libgit-wrapper-perl libgitlab-api-v4-perl libglib2.0-data libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl libsasl2-modules libsaxon-java libsoap-lite-perl libstring-shellquote-perl libxstring-perl licensecheck lintian lynx pristine-tar psmisc python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg shared-mime-info strace wget xdg-user-dirs 0 packages upgraded, 338 newly installed, 0 to remove and 0 not upgraded. Need to get 485 MB of archives. After unpacking 1273 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 sgml-base all 1.31 [15.4 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 netbase all 6.4 [12.8 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 libproc2-0 amd64 2:4.0.2-3 [62.8 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 procps amd64 2:4.0.2-3 [709 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.8-1 [1407 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 ca-certificates-java all 20230103 [11.4 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 java-common all 0.74 [6388 B] Get: 30 http://deb.debian.org/debian bookworm/main amd64 libavahi-common-data amd64 0.8-9 [107 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libavahi-common3 amd64 0.8-9 [41.3 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libdbus-1-3 amd64 1.14.6-1 [200 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libavahi-client3 amd64 0.8-9 [45.1 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libcups2 amd64 2.4.2-3 [244 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-4 [399 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 libnspr4 amd64 2:4.35-1 [113 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 libnss3 amd64 2:3.87.1-1 [1331 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 libasound2-data all 1.2.8-1 [20.5 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 libasound2 amd64 1.2.8-1+b1 [362 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 libpcsclite1 amd64 1.9.9-2 [49.7 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre-headless amd64 17.0.6+10-1 [43.6 MB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 default-jre-headless amd64 2:1.17-74 [2936 B] Get: 53 http://deb.debian.org/debian bookworm/main amd64 ant all 1.10.13-1 [2161 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 ant-optional all 1.10.13-1 [449 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 libantlr4-runtime-java all 4.7.2-5 [315 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libantlr3-runtime-java all 3.5.3-1 [165 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libicu4j-java all 72.1-1 [16.3 MB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libjsonp-java all 1.1.2-3 [127 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 libstringtemplate4-java all 4.0.8-2.1 [241 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 libtreelayout-java all 1.0.3-2 [27.0 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 antlr4 all 4.7.2-5 [1345 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-ui-theme-base all 1.12.1+dfsg-1.1 [44.3 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-doc all 17.0.6+10-1 [12.8 MB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 default-jdk-doc amd64 2:1.17-74 [3020 B] Get: 67 http://deb.debian.org/debian bookworm/main amd64 antlr4-doc all 4.7.2-5 [1093 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 dctrl-tools amd64 2.24-3+b1 [104 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 79 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 81 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jdk-headless amd64 17.0.6+10-1 [230 MB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 default-jdk-headless amd64 2:1.17-74 [1108 B] Get: 91 http://deb.debian.org/debian bookworm/main amd64 libassuan0 amd64 2.5.5-5 [48.5 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 gpgconf amd64 2.2.40-1.1 [564 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 libksba8 amd64 1.6.3-2 [128 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 libnpth0 amd64 1.6-3 [19.0 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 dirmngr amd64 2.2.40-1.1 [792 kB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 gnupg-l10n all 2.2.40-1.1 [1093 kB] Get: 100 http://deb.debian.org/debian bookworm/main amd64 gnupg-utils amd64 2.2.40-1.1 [927 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 gpg amd64 2.2.40-1.1 [949 kB] Get: 102 http://deb.debian.org/debian bookworm/main amd64 pinentry-curses amd64 1.2.1-1 [77.4 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 gpg-agent amd64 2.2.40-1.1 [695 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 gpg-wks-client amd64 2.2.40-1.1 [541 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 gpg-wks-server amd64 2.2.40-1.1 [531 kB] Get: 106 http://deb.debian.org/debian bookworm/main amd64 gpgsm amd64 2.2.40-1.1 [671 kB] Get: 107 http://deb.debian.org/debian bookworm/main amd64 gnupg all 2.2.40-1.1 [846 kB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 109 http://deb.debian.org/debian bookworm/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 110 http://deb.debian.org/debian bookworm/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 111 http://deb.debian.org/debian bookworm/main amd64 libfile-touch-perl all 0.12-2 [8816 B] Get: 112 http://deb.debian.org/debian bookworm/main amd64 libio-pty-perl amd64 1:1.17-1 [34.9 kB] Get: 113 http://deb.debian.org/debian bookworm/main amd64 libipc-run-perl all 20220807.0-1 [104 kB] Get: 114 http://deb.debian.org/debian bookworm/main amd64 libclass-method-modifiers-perl all 2.14-1 [18.1 kB] Get: 115 http://deb.debian.org/debian bookworm/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b1 [36.4 kB] Get: 116 http://deb.debian.org/debian bookworm/main amd64 libb-hooks-op-check-perl amd64 0.22-2+b1 [10.5 kB] Get: 117 http://deb.debian.org/debian bookworm/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 118 http://deb.debian.org/debian bookworm/main amd64 libdevel-callchecker-perl amd64 0.008-2 [15.8 kB] Get: 119 http://deb.debian.org/debian bookworm/main amd64 libparams-classify-perl amd64 0.015-2+b1 [23.1 kB] Get: 120 http://deb.debian.org/debian bookworm/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 121 http://deb.debian.org/debian bookworm/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 122 http://deb.debian.org/debian bookworm/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 123 http://deb.debian.org/debian bookworm/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 124 http://deb.debian.org/debian bookworm/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 125 http://deb.debian.org/debian bookworm/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 126 http://deb.debian.org/debian bookworm/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 127 http://deb.debian.org/debian bookworm/main amd64 libhttp-date-perl all 6.05-2 [10.5 kB] Get: 128 http://deb.debian.org/debian bookworm/main amd64 libfile-listing-perl all 6.15-1 [12.6 kB] Get: 129 http://deb.debian.org/debian bookworm/main amd64 libhtml-tagset-perl all 3.20-6 [11.7 kB] Get: 130 http://deb.debian.org/debian bookworm/main amd64 libregexp-ipv6-perl all 0.03-3 [5212 B] Get: 131 http://deb.debian.org/debian bookworm/main amd64 liburi-perl all 5.17-1 [90.4 kB] Get: 132 http://deb.debian.org/debian bookworm/main amd64 libhtml-parser-perl amd64 3.81-1 [101 kB] Get: 133 http://deb.debian.org/debian bookworm/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 134 http://deb.debian.org/debian bookworm/main amd64 libclone-perl amd64 0.46-1 [13.7 kB] Get: 135 http://deb.debian.org/debian bookworm/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 136 http://deb.debian.org/debian bookworm/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 137 http://deb.debian.org/debian bookworm/main amd64 libhttp-message-perl all 6.44-1 [81.7 kB] Get: 138 http://deb.debian.org/debian bookworm/main amd64 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get: 139 http://deb.debian.org/debian bookworm/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 140 http://deb.debian.org/debian bookworm/main amd64 perl-openssl-defaults amd64 7+b1 [7924 B] Get: 141 http://deb.debian.org/debian bookworm/main amd64 libnet-ssleay-perl amd64 1.92-2+b1 [317 kB] Get: 142 http://deb.debian.org/debian bookworm/main amd64 libio-socket-ssl-perl all 2.081-2 [219 kB] Get: 143 http://deb.debian.org/debian bookworm/main amd64 libnet-http-perl all 6.22-1 [25.3 kB] Get: 144 http://deb.debian.org/debian bookworm/main amd64 liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get: 145 http://deb.debian.org/debian bookworm/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 146 http://deb.debian.org/debian bookworm/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 147 http://deb.debian.org/debian bookworm/main amd64 libwww-perl all 6.68-1 [186 kB] Get: 148 http://deb.debian.org/debian bookworm/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get: 149 http://deb.debian.org/debian bookworm/main amd64 wdiff amd64 1.2.2-5 [119 kB] Get: 150 http://deb.debian.org/debian bookworm/main amd64 devscripts amd64 2.23.3 [1072 kB] Get: 151 http://deb.debian.org/debian bookworm/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 152 http://deb.debian.org/debian bookworm/main amd64 unzip amd64 6.0-28 [166 kB] Get: 153 http://deb.debian.org/debian bookworm/main amd64 java-wrappers all 0.4 [8916 B] Get: 154 http://deb.debian.org/debian bookworm/main amd64 javahelper all 0.78 [97.2 kB] Get: 155 http://deb.debian.org/debian bookworm/main amd64 libhamcrest-java all 2.2-1 [121 kB] Get: 156 http://deb.debian.org/debian bookworm/main amd64 junit4 all 4.13.2-3 [348 kB] Get: 157 http://deb.debian.org/debian bookworm/main amd64 libapiguardian-java all 1.1.2-1 [4656 B] Get: 158 http://deb.debian.org/debian bookworm/main amd64 libopentest4j-java all 1.2.0-4 [9516 B] Get: 159 http://deb.debian.org/debian bookworm/main amd64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 160 http://deb.debian.org/debian bookworm/main amd64 libpicocli-java all 4.6.2-2 [390 kB] Get: 161 http://deb.debian.org/debian bookworm/main amd64 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 162 http://deb.debian.org/debian bookworm/main amd64 junit5 all 5.9.2-1 [2398 kB] Get: 163 http://deb.debian.org/debian bookworm/main amd64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 164 http://deb.debian.org/debian bookworm/main amd64 libaopalliance-java all 20070526-7 [8572 B] Get: 165 http://deb.debian.org/debian bookworm/main amd64 libapache-pom-java all 29-2 [5276 B] Get: 166 http://deb.debian.org/debian bookworm/main amd64 libapfloat-java all 1.10.1-2 [620 kB] Get: 167 http://deb.debian.org/debian bookworm/main amd64 libargs4j-java all 2.33-2 [138 kB] Get: 168 http://deb.debian.org/debian bookworm/main amd64 libasm-java all 9.4-1 [389 kB] Get: 169 http://deb.debian.org/debian bookworm/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 170 http://deb.debian.org/debian bookworm/main amd64 libjaxp1.3-java all 1.3.05-6 [227 kB] Get: 171 http://deb.debian.org/debian bookworm/main amd64 libxml-commons-external-java all 1.4.01-5 [240 kB] Get: 172 http://deb.debian.org/debian bookworm/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 173 http://deb.debian.org/debian bookworm/main amd64 libcommons-io-java all 2.11.0-2 [319 kB] Get: 174 http://deb.debian.org/debian bookworm/main amd64 libcommons-logging-java all 1.2-3 [62.4 kB] Get: 175 http://deb.debian.org/debian bookworm/main amd64 libxmlgraphics-commons-java all 2.8-2 [623 kB] Get: 176 http://deb.debian.org/debian bookworm/main amd64 libbatik-java all 1.16+dfsg-1 [3908 kB] Get: 177 http://deb.debian.org/debian bookworm/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 178 http://deb.debian.org/debian bookworm/main amd64 libgoogle-gson-java all 2.10-1 [261 kB] Get: 179 http://deb.debian.org/debian bookworm/main amd64 libciftools-java all 4.0.5-1 [2139 kB] Get: 180 http://deb.debian.org/debian bookworm/main amd64 libcommons-codec-java all 1.15-1 [292 kB] Get: 181 http://deb.debian.org/debian bookworm/main amd64 libcommons-math-java all 2.2-8 [926 kB] Get: 182 http://deb.debian.org/debian bookworm/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 183 http://deb.debian.org/debian bookworm/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 184 http://deb.debian.org/debian bookworm/main amd64 libguava-java all 31.1-1 [2613 kB] Get: 185 http://deb.debian.org/debian bookworm/main amd64 libitext5-java all 5.5.13.3-2 [2665 kB] Get: 186 http://deb.debian.org/debian bookworm/main amd64 libjackson2-annotations-java all 2.14.0-1 [68.8 kB] Get: 187 http://deb.debian.org/debian bookworm/main amd64 libjackson2-core-java all 2.14.1-1 [447 kB] Get: 188 http://deb.debian.org/debian bookworm/main amd64 libjackson2-databind-java all 2.14.0-1 [1584 kB] Get: 189 http://deb.debian.org/debian bookworm/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 190 http://deb.debian.org/debian bookworm/main amd64 libjaxen-java all 1.1.6-4 [214 kB] Get: 191 http://deb.debian.org/debian bookworm/main amd64 libdom4j-java all 2.1.3-2 [310 kB] Get: 192 http://deb.debian.org/debian bookworm/main amd64 libmaven-shared-utils-java all 3.3.4-1 [138 kB] Get: 193 http://deb.debian.org/debian bookworm/main amd64 libcommons-cli-java all 1.5.0-1 [60.0 kB] Get: 194 http://deb.debian.org/debian bookworm/main amd64 libcommons-lang3-java all 3.12.0-2 [561 kB] Get: 195 http://deb.debian.org/debian bookworm/main amd64 libguice-java all 4.2.3-2 [1435 kB] Get: 196 http://deb.debian.org/debian bookworm/main amd64 libmaven-parent-java all 35-1 [6140 B] Get: 197 http://deb.debian.org/debian bookworm/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 198 http://deb.debian.org/debian bookworm/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 199 http://deb.debian.org/debian bookworm/main amd64 libmaven-resolver-java all 1.6.3-1 [548 kB] Get: 200 http://deb.debian.org/debian bookworm/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 201 http://deb.debian.org/debian bookworm/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 202 http://deb.debian.org/debian bookworm/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 203 http://deb.debian.org/debian bookworm/main amd64 libplexus-interpolation-java all 1.26-1 [76.8 kB] Get: 204 http://deb.debian.org/debian bookworm/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 205 http://deb.debian.org/debian bookworm/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 206 http://deb.debian.org/debian bookworm/main amd64 libcdi-api-java all 1.2-3 [54.3 kB] Get: 207 http://deb.debian.org/debian bookworm/main amd64 libslf4j-java all 1.7.32-1 [144 kB] Get: 208 http://deb.debian.org/debian bookworm/main amd64 libsisu-inject-java all 0.3.4-2 [347 kB] Get: 209 http://deb.debian.org/debian bookworm/main amd64 libsisu-plexus-java all 0.3.4-3 [181 kB] Get: 210 http://deb.debian.org/debian bookworm/main amd64 libmaven3-core-java all 3.8.7-1 [1572 kB] Get: 211 http://deb.debian.org/debian bookworm/main amd64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 212 http://deb.debian.org/debian bookworm/main amd64 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 213 http://deb.debian.org/debian bookworm/main amd64 libcommons-compress-java all 1.22-1 [615 kB] Get: 214 http://deb.debian.org/debian bookworm/main amd64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 215 http://deb.debian.org/debian bookworm/main amd64 libsnappy1v5 amd64 1.1.9-3 [26.0 kB] Get: 216 http://deb.debian.org/debian bookworm/main amd64 libsnappy-jni amd64 1.1.8.3-1 [7152 B] Get: 217 http://deb.debian.org/debian bookworm/main amd64 libsnappy-java all 1.1.8.3-1 [98.9 kB] Get: 218 http://deb.debian.org/debian bookworm/main amd64 libxz-java all 1.9-1 [143 kB] Get: 219 http://deb.debian.org/debian bookworm/main amd64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 220 http://deb.debian.org/debian bookworm/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 221 http://deb.debian.org/debian bookworm/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 222 http://deb.debian.org/debian bookworm/main amd64 libjsoup-java all 1.15.3-1 [431 kB] Get: 223 http://deb.debian.org/debian bookworm/main amd64 libwagon-http-java all 3.5.3-1 [49.5 kB] Get: 224 http://deb.debian.org/debian bookworm/main amd64 libistack-commons-java all 3.0.6-5 [145 kB] Get: 225 http://deb.debian.org/debian bookworm/main amd64 libcodemodel-java all 2.6+jaxb2.3.0.1-10.1 [164 kB] Get: 226 http://deb.debian.org/debian bookworm/main amd64 librelaxng-datatype-java all 1.0+ds1-3.1 [11.7 kB] Get: 227 http://deb.debian.org/debian bookworm/main amd64 librngom-java all 2.3.0.1-10.1 [290 kB] Get: 228 http://deb.debian.org/debian bookworm/main amd64 libxsom-java all 2.3.0.1-10.1 [400 kB] Get: 229 http://deb.debian.org/debian bookworm/main amd64 libtxw2-java all 2.3.0.1-10.1 [134 kB] Get: 230 http://deb.debian.org/debian bookworm/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 231 http://deb.debian.org/debian bookworm/main amd64 libdtd-parser-java all 1.2-1 [64.9 kB] Get: 232 http://deb.debian.org/debian bookworm/main amd64 libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 233 http://deb.debian.org/debian bookworm/main amd64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB] Get: 234 http://deb.debian.org/debian bookworm/main amd64 libfastinfoset-java all 1.2.12-3 [343 kB] Get: 235 http://deb.debian.org/debian bookworm/main amd64 libjaxb-java all 2.3.0.1-10.1 [1973 kB] Get: 236 http://deb.debian.org/debian bookworm/main amd64 libmaven-archiver-java all 3.6.0-1 [25.1 kB] Get: 237 http://deb.debian.org/debian bookworm/main amd64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 238 http://deb.debian.org/debian bookworm/main amd64 libcommons-text-java all 1.10.0-1 [211 kB] Get: 239 http://deb.debian.org/debian bookworm/main amd64 libfastutil-java all 8.5.11+dfsg-1 [19.6 MB] Get: 240 http://deb.debian.org/debian bookworm/main amd64 libjheaps-java all 0.14-2 [144 kB] Get: 241 http://deb.debian.org/debian bookworm/main amd64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 242 http://deb.debian.org/debian bookworm/main amd64 libjgraphx-java all 2.1.0.7-3 [807 kB] Get: 243 http://deb.debian.org/debian bookworm/main amd64 libjgrapht-java all 1.5.1-3 [1584 kB] Get: 244 http://deb.debian.org/debian bookworm/main amd64 libinchi1 amd64 1.03+dfsg-4+b2 [436 kB] Get: 245 http://deb.debian.org/debian bookworm/main amd64 libjni-inchi-jni amd64 0.8+dfsg-7 [9064 B] Get: 246 http://deb.debian.org/debian bookworm/main amd64 libcommons-exec-java all 1.3-2 [48.1 kB] Get: 247 http://deb.debian.org/debian bookworm/main amd64 libexec-maven-plugin-java all 3.1.0-1 [66.2 kB] Get: 248 http://deb.debian.org/debian bookworm/main amd64 libmaven-shared-incremental-java all 1.1-3 [9524 B] Get: 249 http://deb.debian.org/debian bookworm/main amd64 libcommons-lang-java all 2.6-10 [273 kB] Get: 250 http://deb.debian.org/debian bookworm/main amd64 libxbean-reflect-java all 4.5-8 [133 kB] Get: 251 http://deb.debian.org/debian bookworm/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 252 http://deb.debian.org/debian bookworm/main amd64 libplexus-compiler-java all 2.12.1-1 [99.8 kB] Get: 253 http://deb.debian.org/debian bookworm/main amd64 libqdox2-java all 2.0.3-1 [296 kB] Get: 254 http://deb.debian.org/debian bookworm/main amd64 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 255 http://deb.debian.org/debian bookworm/main amd64 libmaven-compiler-plugin-java all 3.10.1-2 [59.0 kB] Get: 256 http://deb.debian.org/debian bookworm/main amd64 liblog4j1.2-java all 1.2.17-11 [444 kB] Get: 257 http://deb.debian.org/debian bookworm/main amd64 libjni-inchi-java all 0.8+dfsg-7 [33.2 kB] Get: 258 http://deb.debian.org/debian bookworm/main amd64 libnaga-java all 3.0+svn80-5 [43.5 kB] Get: 259 http://deb.debian.org/debian bookworm/main amd64 libjmol-java all 14.32.83+dfsg-1 [8698 kB] Get: 260 http://deb.debian.org/debian bookworm/main amd64 libjson-simple-java all 2.3.0-1 [63.8 kB] Get: 261 http://deb.debian.org/debian bookworm/main amd64 libmsgpack-java all 0.9.3-1 [155 kB] Get: 262 http://deb.debian.org/debian bookworm/main amd64 libmmtf-java all 1.0.11-1 [187 kB] Get: 263 http://deb.debian.org/debian bookworm/main amd64 libvecmath-java all 1.5.2-7 [97.0 kB] Get: 264 http://deb.debian.org/debian bookworm/main amd64 libbiojava6-java all 6.1.0+dfsg-4 [5367 kB] Get: 265 http://deb.debian.org/debian bookworm/main amd64 libbsh-java all 2.0b4-20 [291 kB] Get: 266 http://deb.debian.org/debian bookworm/main amd64 libcharts4j-java all 1.3-4 [162 kB] Get: 267 http://deb.debian.org/debian bookworm/main amd64 libcommons-collections3-java all 3.2.2-2 [526 kB] Get: 268 http://deb.debian.org/debian bookworm/main amd64 libcommons-beanutils-java all 1.9.4-1 [232 kB] Get: 269 http://deb.debian.org/debian bookworm/main amd64 libcommons-configuration-java all 1.10-6 [347 kB] Get: 270 http://deb.debian.org/debian bookworm/main amd64 libcommons-digester-java all 1.8.1-5 [168 kB] Get: 271 http://deb.debian.org/debian bookworm/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get: 272 http://deb.debian.org/debian bookworm/main amd64 libcommons-math3-java all 3.6.1-3 [2018 kB] Get: 273 http://deb.debian.org/debian bookworm/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 274 http://deb.debian.org/debian bookworm/main amd64 libcommons-math3-java-doc all 3.6.1-3 [1560 kB] Get: 275 http://deb.debian.org/debian bookworm/main amd64 libcommons-validator-java all 1:1.7-1 [181 kB] Get: 276 http://deb.debian.org/debian bookworm/main amd64 libdistlib-java all 1.0-4 [72.1 kB] Get: 277 http://deb.debian.org/debian bookworm/main amd64 libdoxia-core-java all 1.12.0-1 [213 kB] Get: 278 http://deb.debian.org/debian bookworm/main amd64 libfontbox2-java all 2.0.27-2 [1510 kB] Get: 279 http://deb.debian.org/debian bookworm/main amd64 libqdox-java all 1.12.1-3 [172 kB] Get: 280 http://deb.debian.org/debian bookworm/main amd64 libfop-java all 1:2.8-2 [10.1 MB] Get: 281 http://deb.debian.org/debian bookworm/main amd64 libitext1-java all 1.4-7 [1257 kB] Get: 282 http://deb.debian.org/debian bookworm/main amd64 libdoxia-java all 1.12.0-1 [459 kB] Get: 283 http://deb.debian.org/debian bookworm/main amd64 libmaven-reporting-api-java all 3.1.1-1 [7240 B] Get: 284 http://deb.debian.org/debian bookworm/main amd64 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB] Get: 285 http://deb.debian.org/debian bookworm/main amd64 velocity all 1.7-6 [429 kB] Get: 286 http://deb.debian.org/debian bookworm/main amd64 libplexus-velocity-java all 1.2-3.1 [10.5 kB] Get: 287 http://deb.debian.org/debian bookworm/main amd64 liboro-java all 2.0.8a-14 [70.5 kB] Get: 288 http://deb.debian.org/debian bookworm/main amd64 libvelocity-tools-java all 2.0-8 [308 kB] Get: 289 http://deb.debian.org/debian bookworm/main amd64 libxalan2-java all 2.7.2-4 [3419 kB] Get: 290 http://deb.debian.org/debian bookworm/main amd64 libdoxia-sitetools-java all 1.11.1-1 [202 kB] Get: 291 http://deb.debian.org/debian bookworm/main amd64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 292 http://deb.debian.org/debian bookworm/main amd64 libfreemarker-java all 2.3.31-2 [1528 kB] Get: 293 http://deb.debian.org/debian bookworm/main amd64 libmjson-java all 1.4.0-3 [60.4 kB] Get: 294 http://deb.debian.org/debian bookworm/main amd64 libmbedcrypto7 amd64 2.28.3-1 [277 kB] Get: 295 http://deb.debian.org/debian bookworm/main amd64 libmbedx509-1 amd64 2.28.3-1 [128 kB] Get: 296 http://deb.debian.org/debian bookworm/main amd64 libmbedtls14 amd64 2.28.3-1 [163 kB] Get: 297 http://deb.debian.org/debian bookworm/main amd64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB] Get: 298 http://deb.debian.org/debian bookworm/main amd64 libncbi-vdb3 amd64 3.0.2+dfsg-2 [1050 kB] Get: 299 http://deb.debian.org/debian bookworm/main amd64 libncbi-ngs3 amd64 3.0.3+dfsg-5 [153 kB] Get: 300 http://deb.debian.org/debian bookworm/main amd64 libngs-jni amd64 3.0.3+dfsg-5 [23.4 kB] Get: 301 http://deb.debian.org/debian bookworm/main amd64 libngs-java amd64 3.0.3+dfsg-5 [110 kB] Get: 302 http://deb.debian.org/debian bookworm/main amd64 librhino-java all 1.7.14-2.1 [1357 kB] Get: 303 http://deb.debian.org/debian bookworm/main amd64 libhtsjdk-java all 3.0.4+dfsg-2 [1813 kB] Get: 304 http://deb.debian.org/debian bookworm/main amd64 libhtsjdk-java-doc all 3.0.4+dfsg-2 [1039 kB] Get: 305 http://deb.debian.org/debian bookworm/main amd64 libjansi-java all 2.4.0-2 [105 kB] Get: 306 http://deb.debian.org/debian bookworm/main amd64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 307 http://deb.debian.org/debian bookworm/main amd64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 308 http://deb.debian.org/debian bookworm/main amd64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 309 http://deb.debian.org/debian bookworm/main amd64 libjetty9-java all 9.4.50-3 [2962 kB] Get: 310 http://deb.debian.org/debian bookworm/main amd64 libjtidy-java all 7+svn20110807-5 [250 kB] Get: 311 http://deb.debian.org/debian bookworm/main amd64 libmaven-common-artifact-filters-java all 3.3.2-1 [48.2 kB] Get: 312 http://deb.debian.org/debian bookworm/main amd64 libmaven-artifact-transfer-java all 0.13.1-2 [158 kB] Get: 313 http://deb.debian.org/debian bookworm/main amd64 libplexus-build-api-java all 0.0.7-4 [10.3 kB] Get: 314 http://deb.debian.org/debian bookworm/main amd64 libmaven-filtering-java all 3.3.0-1 [50.2 kB] Get: 315 http://deb.debian.org/debian bookworm/main amd64 libmaven-assembly-plugin-java all 3.4.2-1 [242 kB] Get: 316 http://deb.debian.org/debian bookworm/main amd64 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB] Get: 317 http://deb.debian.org/debian bookworm/main amd64 libmaven-invoker-java all 3.2.0-1 [28.1 kB] Get: 318 http://deb.debian.org/debian bookworm/main amd64 libplexus-interactivity-api-java all 1.1-2 [11.0 kB] Get: 319 http://deb.debian.org/debian bookworm/main amd64 libmaven-javadoc-plugin-java all 3.4.1-2 [454 kB] Get: 320 http://deb.debian.org/debian bookworm/main amd64 libmaven-reporting-impl-java all 3.2.0-2 [15.2 kB] Get: 321 http://deb.debian.org/debian bookworm/main amd64 libplexus-container-default1.5-java all 2.1.1-1 [4476 B] Get: 322 http://deb.debian.org/debian bookworm/main amd64 libplexus-ant-factory-java all 1.0~alpha2.1-4 [11.4 kB] Get: 323 http://deb.debian.org/debian bookworm/main amd64 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B] Get: 324 http://deb.debian.org/debian bookworm/main amd64 libmaven-plugin-tools-java all 3.7.1-1 [265 kB] Get: 325 http://deb.debian.org/debian bookworm/main amd64 libmaven-reporting-exec-java all 1.6.0-1 [26.8 kB] Get: 326 http://deb.debian.org/debian bookworm/main amd64 libmaven-resources-plugin-java all 3.3.0-1 [28.4 kB] Get: 327 http://deb.debian.org/debian bookworm/main amd64 libmaven-site-plugin-java all 3.12.1-2 [107 kB] Get: 328 http://deb.debian.org/debian bookworm/main amd64 libtrove3-java all 3.0.3-5 [2146 kB] Get: 329 http://deb.debian.org/debian bookworm/main amd64 libsnpeff-java all 5.1+d+dfsg-3 [2150 kB] Get: 330 http://deb.debian.org/debian bookworm/main amd64 libsnpeff-java-doc all 5.1+d+dfsg-3 [760 kB] Get: 331 http://deb.debian.org/debian bookworm/main amd64 libsurefire-java all 2.22.3-2 [1169 kB] Get: 332 http://deb.debian.org/debian bookworm/main amd64 libtrove3-java-doc all 3.0.3-5 [823 kB] Get: 333 http://deb.debian.org/debian bookworm/main amd64 libwagon-file-java all 3.5.3-1 [8388 B] Get: 334 http://deb.debian.org/debian bookworm/main amd64 libwagon-http-shaded-java all 3.5.3-1 [1341 kB] Get: 335 http://deb.debian.org/debian bookworm/main amd64 libxml2-utils amd64 2.9.14+dfsg-1.1+b3 [99.0 kB] Get: 336 http://deb.debian.org/debian bookworm/main amd64 maven all 3.8.7-1 [18.9 kB] Get: 337 http://deb.debian.org/debian bookworm/main amd64 maven-repo-helper all 1.11 [142 kB] Get: 338 http://deb.debian.org/debian bookworm/main amd64 maven-debian-helper all 2.6.2 [108 kB] Fetched 485 MB in 17s (28.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19912 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_amd64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../3-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_amd64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20346 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... 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Setting up sensible-utils (0.0.17+nmu1) ... Setting up libjsoup-java (1.15.3-1) ... Setting up libcommons-math-java (2.2-8) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libxml-commons-external-java (1.4.01-5) ... Setting up procps (2:4.0.2-3) ... Setting up libxbean-reflect-java (4.5-8) ... Setting up libasound2:amd64 (1.2.8-1+b1) ... Setting up libservlet-api-java (4.0.1-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libopentest4j-java (1.2.0-4) ... Setting up libjackson2-core-java (2.14.1-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up ncbi-vdb-data (3.0.2+dfsg-2) ... Setting up netbase (6.4) ... Setting up libcommons-math3-java (3.6.1-3) ... Setting up sgml-base (1.31) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b1) ... Setting up libwagon-http-shaded-java (3.5.3-1) ... Setting up libhttpcore-java (4.4.16-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libxerces2-java (2.12.2-1) ... Setting up libfile-dirlist-perl (0.05-3) ... Setting up libjaxp1.3-java (1.3.05-6) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up librelaxng-datatype-java (1.0+ds1-3.1) ... Setting up openssl (3.0.8-1) ... Setting up libjsonp-java (1.1.2-3) ... Setting up libcdi-api-java (1.2-3) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libsnappy-jni (1.1.8.3-1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.1+b3) ... Setting up liburi-perl (5.17-1) ... Setting up libargs4j-java (2.33-2) ... Setting up libfile-touch-perl (0.12-2) ... Setting up dctrl-tools (2.24-3+b1) ... Setting up libinchi1 (1.03+dfsg-4+b2) ... Setting up libnaga-java (3.0+svn80-5) ... Setting up libnet-ssleay-perl:amd64 (1.92-2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up pinentry-curses (1.2.1-1) ... Setting up libdom4j-java (2.1.3-2) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libwagon-provider-api-java (3.5.3-1) ... Setting up libhttp-date-perl (6.05-2) ... Setting up gettext (0.21-12) ... Setting up libjetty9-java (9.4.50-3) ... Setting up java-wrappers (0.4) ... Setting up libfile-listing-perl (6.15-1) ... Setting up libmbedx509-1:amd64 (2.28.3-1) ... Setting up libstringtemplate4-java (4.0.8-2.1) ... Setting up libplexus-languages-java (1.1.1-2) ... Setting up libmbedtls14:amd64 (2.28.3-1) ... Setting up libtool (2.4.7-5) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libstax-ex-java (1.7.8-3) ... Setting up libmaven-parent-java (35-1) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-9) ... Setting up libncbi-vdb3:amd64 (3.0.2+dfsg-2) ... Setting up libcommons-logging-java (1.2-3) ... Setting up libnet-http-perl (6.22-1) ... Setting up libsisu-inject-java (0.3.4-2) ... Setting up libnss3:amd64 (2:3.87.1-1) ... Setting up libciftools-java (4.0.5-1) ... Setting up libdevel-callchecker-perl:amd64 (0.008-2) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up libjackson2-databind-java (2.14.0-1) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up patchutils (0.4.2-1) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.4-3) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-4) ... Setting up libxalan2-java (2.7.2-4) ... Setting up libstreambuffer-java (1.5.4-1.1) ... Setting up libcommons-lang3-java (3.12.0-2) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up librngom-java (2.3.0.1-10.1) ... Setting up libjni-inchi-jni (0.8+dfsg-7) ... Setting up dwz (0.15-1) ... Setting up libmaven-common-artifact-filters-java (3.3.2-1) ... Setting up libjgraphx-java (2.1.0.7-3) ... Setting up groff-base (1.22.4-10) ... Setting up libhtml-parser-perl:amd64 (3.81-1) ... Setting up gpgconf (2.2.40-1.1) ... Setting up openjdk-17-doc (17.0.6+10-1) ... Setting up libcommons-beanutils-java (1.9.4-1) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up libsnappy-java (1.1.8.3-1) ... Setting up libfontconfig1:amd64 (2.14.1-4) ... Setting up libxsom-java (2.3.0.1-10.1) ... Setting up libcommons-configuration-java (1.10-6) ... Setting up libwagon-file-java (3.5.3-1) ... Setting up libxml2-utils (2.9.14+dfsg-1.1+b3) ... Setting up libcommons-codec-java (1.15-1) ... Setting up libavahi-client3:amd64 (0.8-9) ... Setting up libio-socket-ssl-perl (2.081-2) ... Setting up gpg (2.2.40-1.1) ... Setting up gnupg-utils (2.2.40-1.1) ... Setting up libhttp-message-perl (6.44-1) ... Setting up libncbi-ngs3:amd64 (3.0.3+dfsg-5) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up velocity (1.7-6) ... Setting up libngs-jni:amd64 (3.0.3+dfsg-5) ... Setting up gpg-agent (2.2.40-1.1) ... Setting up libcommons-compress-java (1.22-1) ... Setting up libhttp-cookies-perl (6.10-1) ... Setting up libcommons-io-java (2.11.0-2) ... Setting up libcommons-digester-java (1.8.1-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up libdistlib-java (1.0-4) ... Setting up libparams-classify-perl:amd64 (0.015-2+b1) ... Setting up gpgsm (2.2.40-1.1) ... Setting up libxmlgraphics-commons-java (2.8-2) ... Setting up default-jdk-doc (2:1.17-74) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dirmngr (2.2.40-1.1) ... Setting up libmaven-filtering-java (3.3.0-1) ... Setting up libmaven-resolver-java (1.6.3-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up antlr4-doc (4.7.2-5) ... Setting up gpg-wks-server (2.2.40-1.1) ... Setting up libcups2:amd64 (2.4.2-3) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up libwagon-http-java (3.5.3-1) ... Setting up libmaven-shared-utils-java (3.3.4-1) ... Setting up libfastinfoset-java (1.2.12-3) ... Setting up libngs-java:amd64 (3.0.3+dfsg-5) ... Setting up libmaven-resources-plugin-java (3.3.0-1) ... Setting up libhtsjdk-java (3.0.4+dfsg-2) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up gpg-wks-client (2.2.40-1.1) ... Setting up libcommons-validator-java (1:1.7-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libbatik-java (1.16+dfsg-1) ... Setting up libmoo-perl (2.005005-1) ... Setting up libmaven-invoker-java (3.2.0-1) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up libmaven-clean-plugin-java (3.2.0-2) ... Setting up gnupg (2.2.40-1.1) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libfop-java (1:2.8-2) ... Setting up libmaven-archiver-java (3.6.0-1) ... Setting up openjdk-17-jre-headless:amd64 (17.0.6+10-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up ca-certificates-java (20230103) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068_2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:E-Tugra_Global_Root_CA_ECC_v3.pem Adding debian:E-Tugra_Global_Root_CA_RSA_v3.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up junit4 (4.13.2-3) ... Setting up liblwp-protocol-https-perl (6.10-1) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up default-jre-headless (2:1.17-74) ... Setting up libwww-perl (6.68-1) ... Setting up antlr4 (4.7.2-5) ... Setting up maven-repo-helper (1.11) ... Setting up devscripts (2.23.3) ... Setting up libguava-java (31.1-1) ... Setting up openjdk-17-jdk-headless:amd64 (17.0.6+10-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up ant (1.10.13-1) ... Setting up javahelper (0.78) ... Setting up junit5 (5.9.2-1) ... Setting up libplexus-container-default-java (2.1.1-1) ... Setting up libguice-java (4.2.3-2) ... Setting up ant-optional (1.10.13-1) ... Setting up default-jdk-headless (2:1.17-74) ... Setting up libplexus-i18n-java (1.0-beta-10-6) ... Setting up libplexus-container-default1.5-java (2.1.1-1) ... Setting up libplexus-interactivity-api-java (1.1-2) ... Setting up libplexus-velocity-java (1.2-3.1) ... Setting up libmaven3-core-java (3.8.7-1) ... Setting up libmaven-shared-incremental-java (1.1-3) ... Setting up libmaven-shared-io-java (3.0.0-4) ... Setting up libplexus-bsh-factory-java (1.0~alpha7-5) ... Setting up maven (3.8.7-1) ... update-alternatives: using /usr/share/maven/bin/mvn to provide /usr/bin/mvn (mvn) in auto mode Setting up libplexus-ant-factory-java (1.0~alpha2.1-4) ... Setting up libplexus-compiler-java (2.12.1-1) ... Setting up libmaven-compiler-plugin-java (3.10.1-2) ... Setting up libjni-inchi-java (0.8+dfsg-7) ... Setting up libmaven-artifact-transfer-java (0.13.1-2) ... Setting up libmaven-file-management-java (3.0.0-1) ... Setting up libjmol-java (14.32.83+dfsg-1) ... Setting up libistack-commons-java (3.0.6-5) ... Setting up libmaven-jar-plugin-java (3.3.0-2) ... Setting up libmaven-assembly-plugin-java (3.4.2-1) ... Setting up libcommons-text-java (1.10.0-1) ... Setting up libcodemodel-java (2.6+jaxb2.3.0.1-10.1) ... Setting up libmsgpack-java (0.9.3-1) ... Setting up libtxw2-java (2.3.0.1-10.1) ... Setting up libjaxb-java (2.3.0.1-10.1) ... Setting up libmmtf-java (1.0.11-1) ... Setting up libjgrapht-java (1.5.1-3) ... Setting up libdoxia-core-java (1.12.0-1) ... Setting up libdoxia-java (1.12.0-1) ... Setting up libmaven-reporting-api-java (3.1.1-1) ... Setting up libmaven-reporting-exec-java (1.6.0-1) ... Setting up libbiojava6-java (6.1.0+dfsg-4) ... Setting up libsnpeff-java (5.1+d+dfsg-3) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for sgml-base (1.31) ... Setting up libvelocity-tools-java (2.0-8) ... Setting up libdoxia-sitetools-java (1.11.1-1) ... Setting up libmaven-site-plugin-java (3.12.1-2) ... Setting up libmaven-javadoc-plugin-java (3.4.1-2) ... Setting up libmaven-reporting-impl-java (3.2.0-2) ... Setting up libmaven-plugin-tools-java (3.7.1-1) ... Setting up libsurefire-java (2.22.3-2) ... Setting up maven-debian-helper (2.6.2) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20230103) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/3683552/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/3683552/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/snpsift-5.1+dfsg2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../snpsift_5.1+dfsg2-2_source.changes dpkg-buildpackage: info: source package snpsift dpkg-buildpackage: info: source version 5.1+dfsg2-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Pierre Gruet dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with javahelper debian/rules override_dh_auto_clean make[1]: Entering directory '/build/snpsift-5.1+dfsg2' dh_auto_clean bash -c "for dir in \$(find . -name target -type d); do if [ -f \$(echo \$dir | sed -e s/target\$/pom.xml/) ]; then rm -Rf \$dir; fi done" mh_unpatchpoms -plibsnpsift-java # Removing the unit tests we copied into a subdirectory of src/test. if [ -e src/test/java/org ]; then \ rm -f -rf src/test/java/org; \ fi make[1]: Leaving directory '/build/snpsift-5.1+dfsg2' jh_clean dh_clean debian/rules binary dh binary --with javahelper dh_update_autotools_config dh_autoreconf dh_auto_configure mh_patchpoms -plibsnpsift-java --debian-build --keep-pom-version --maven-repo=/build/snpsift-5.1\+dfsg2/debian/maven-repo Failed to parse /build/snpsift-5.1+dfsg2/debian/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) at org.debian.maven.repo.POMReader.readPom(POMReader.java:82) at org.debian.maven.repo.POMReader.readPom(POMReader.java:57) at org.debian.maven.repo.Repository.scan(Repository.java:397) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:201) at org.debian.maven.repo.Repository.scanOnce(Repository.java:196) at org.debian.maven.repo.POMTransformer.usePluginVersionsFromRepository(POMTransformer.java:107) at org.debian.maven.repo.POMTransformer.main(POMTransformer.java:779) Failed to parse /build/snpsift-5.1+dfsg2/debian/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) at org.debian.maven.repo.POMReader.readPom(POMReader.java:82) at org.debian.maven.repo.POMReader.readPom(POMReader.java:57) at org.debian.maven.repo.Repository.scan(Repository.java:397) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:201) at org.debian.maven.repo.Repository.scanOnce(Repository.java:196) at org.debian.maven.repo.POMTransformer.usePluginVersionsFromRepository(POMTransformer.java:107) at org.debian.maven.repo.POMTransformer.main(POMTransformer.java:779) jh_linkjars dh_auto_build /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/snpsift-5.1\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/snpsift-5.1\+dfsg2/debian -Dmaven.repo.local=/build/snpsift-5.1\+dfsg2/debian/maven-repo --batch-mode package javadoc:jar javadoc:aggregate -DskipTests -Dnotimestamp=true -Dlocale=en_US OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release. [INFO] Scanning for projects... [INFO] [INFO] ------------------------< org.snpsift:snpsift >------------------------- [INFO] Building SnpSift 5.1 [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The artifact org.apache.maven.plugins:maven-surefire-plugin:jar:2.12.4 has been relocated to org.apache.maven.plugins:maven-surefire-plugin:jar:2.22.3 [WARNING] The artifact org.apache.maven.plugins:maven-jar-plugin:jar:2.4 has been relocated to org.apache.maven.plugins:maven-jar-plugin:jar:3.3.0 [WARNING] The POM for org.biojava:biojava-structure:jar:6.x is invalid, transitive dependencies (if any) will not be available, enable debug logging for more details [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ snpsift --- [INFO] skip non existing resourceDirectory /build/snpsift-5.1+dfsg2/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ snpsift --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 112 source files to /build/snpsift-5.1+dfsg2/target/classes [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/lang/LangFactory.java:[112,25] org.antlr.v4.runtime.ANTLRInputStream in org.antlr.v4.runtime has been deprecated [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/lang/LangFactory.java:[112,54] org.antlr.v4.runtime.ANTLRInputStream in org.antlr.v4.runtime has been deprecated [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/hwe/VcfHwe.java:[116,45] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/hwe/VcfHwe.java:[116,80] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/hwe/VcfHwe.java:[116,116] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/hwe/VcfHwe.java:[116,152] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/hwe/VcfHwe.java:[117,45] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/hwe/VcfHwe.java:[117,84] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/hwe/VcfHwe.java:[117,119] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ snpsift --- [INFO] skip non existing resourceDirectory /build/snpsift-5.1+dfsg2/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ snpsift --- [INFO] Changes detected - recompiling the module! [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ snpsift --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ snpsift --- [INFO] Building jar: /build/snpsift-5.1+dfsg2/target/snpsift-5.1.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ snpsift --- [INFO] Adding the --ignore-source-errors option [INFO] No previous run data found, generating javadoc. [WARNING] Javadoc Warnings [WARNING] Loading source files for package org.snpsift... [WARNING] Loading source files for package org.snpsift.util... [WARNING] Loading source files for package org.snpsift.testCases.unit... [WARNING] Loading source files for package org.snpsift.testCases... [WARNING] Loading source files for package org.snpsift.phatsCons... [WARNING] Loading source files for package org.snpsift.pedigree... [WARNING] Loading source files for package org.snpsift.lang.function... [WARNING] Loading source files for package org.snpsift.lang.expression... [WARNING] Loading source files for package org.snpsift.lang... [WARNING] Loading source files for package org.snpsift.hwe... [WARNING] Loading source files for package org.snpsift.gwasCatalog... [WARNING] Loading source files for package org.snpsift.fileIterator... [WARNING] Loading source files for package org.snpsift.caseControl... [WARNING] Loading source files for package org.snpsift.antlr... [WARNING] Loading source files for package org.snpsift.annotate... [WARNING] Constructing Javadoc information... [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVcfCheck.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:9: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:9: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:10: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:10: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:12: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertFalse; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:12: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertFalse; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:13: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:13: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesLd.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesLd.java:6: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesLd.java:6: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIntervals.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:15: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:15: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:7: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:7: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGwasCatalog.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGwasCatalog.java:13: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGwasCatalog.java:13: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGt.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGt.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGt.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGeneSets.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGeneSets.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGeneSets.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterGt.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterGt.java:12: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterGt.java:12: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterChrPos.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterChrPos.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:10: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:10: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilter.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilter.java:17: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:13: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:13: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:14: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:14: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:15: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesConcordance.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesConcordance.java:9: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesConcordance.java:9: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:12: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:12: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:16: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotateTabix.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:3: error: package org.junit.platform.suite.api does not exist [WARNING] import org.junit.platform.suite.api.SelectPackages; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:4: error: package org.junit.platform.suite.api does not exist [WARNING] import org.junit.platform.suite.api.Suite; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:5: error: package org.junit.platform.suite.api does not exist [WARNING] import org.junit.platform.suite.api.SuiteDisplayName; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:13: error: cannot find symbol [WARNING] @Suite [WARNING] ^ [WARNING] symbol: class Suite [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:14: error: cannot find symbol [WARNING] @SuiteDisplayName("Unit test cases") [WARNING] ^ [WARNING] symbol: class SuiteDisplayName [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:15: error: cannot find symbol [WARNING] @SelectPackages({"org.snpsift.testCases.unit"}) [WARNING] ^ [WARNING] symbol: class SelectPackages [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestCasesZzz.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestCasesZzz.java:13: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVcfCheck.java:16: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesVcfCheck [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:56: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesVarType [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:62: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesVarType [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:68: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesVarType [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:74: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesVarType [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:80: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesVarType [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:26: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesSplit [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:56: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesSplit [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:82: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesSplit [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:28: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesSort [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:46: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:57: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:68: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:79: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:87: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:93: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:99: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:105: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesLd.java:22: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesLd [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIntervals.java:23: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesIntervals [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIntervals.java:48: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesIntervals [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:30: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesIndex [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:82: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesIndex [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:21: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesHwe [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:33: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesHwe [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:45: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesHwe [WARNING] Building index for all the packages and classes... 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[WARNING] Generating /build/snpsift-5.1+dfsg2/target/apidocs/overview-summary.html... [WARNING] Generating /build/snpsift-5.1+dfsg2/target/apidocs/help-doc.html... [WARNING] 100 warnings [INFO] Building jar: /build/snpsift-5.1+dfsg2/target/snpsift-5.1-javadoc.jar [INFO] [INFO] ------------------------< org.snpsift:snpsift >------------------------- [INFO] Building SnpSift 5.1 [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] >>> maven-javadoc-plugin:3.4.1:aggregate (default-cli) > compile @ snpsift >>> [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ snpsift --- [INFO] skip non existing resourceDirectory /build/snpsift-5.1+dfsg2/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ snpsift --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 112 source files to /build/snpsift-5.1+dfsg2/target/classes [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/lang/LangFactory.java:[112,25] org.antlr.v4.runtime.ANTLRInputStream in org.antlr.v4.runtime has been deprecated [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/lang/LangFactory.java:[112,54] org.antlr.v4.runtime.ANTLRInputStream in org.antlr.v4.runtime has been deprecated [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/hwe/VcfHwe.java:[116,45] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/hwe/VcfHwe.java:[116,80] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/hwe/VcfHwe.java:[116,116] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/hwe/VcfHwe.java:[116,152] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/hwe/VcfHwe.java:[117,45] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/hwe/VcfHwe.java:[117,84] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/hwe/VcfHwe.java:[117,119] factorialLog(int) in org.apache.commons.math3.util.ArithmeticUtils has been deprecated [INFO] [INFO] <<< maven-javadoc-plugin:3.4.1:aggregate (default-cli) < compile @ snpsift <<< [INFO] [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:aggregate (default-cli) @ snpsift --- [INFO] Adding the --ignore-source-errors option [INFO] Configuration changed, re-generating javadoc. [WARNING] Javadoc Warnings [WARNING] Loading source files for package org.snpsift... [WARNING] Loading source files for package org.snpsift.util... [WARNING] Loading source files for package org.snpsift.testCases.unit... [WARNING] Loading source files for package org.snpsift.testCases... [WARNING] Loading source files for package org.snpsift.phatsCons... [WARNING] Loading source files for package org.snpsift.pedigree... [WARNING] Loading source files for package org.snpsift.lang.function... [WARNING] Loading source files for package org.snpsift.lang.expression... [WARNING] Loading source files for package org.snpsift.lang... [WARNING] Loading source files for package org.snpsift.hwe... [WARNING] Loading source files for package org.snpsift.gwasCatalog... [WARNING] Loading source files for package org.snpsift.fileIterator... [WARNING] Loading source files for package org.snpsift.caseControl... [WARNING] Loading source files for package org.snpsift.antlr... [WARNING] Loading source files for package org.snpsift.annotate... [WARNING] Constructing Javadoc information... [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVcfCheck.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:9: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:9: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:10: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:10: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:12: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertFalse; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:12: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertFalse; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:13: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:13: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesLd.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesLd.java:6: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesLd.java:6: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIntervals.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:15: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:15: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:7: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:7: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGwasCatalog.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGwasCatalog.java:13: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGwasCatalog.java:13: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGt.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGt.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGt.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGeneSets.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGeneSets.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGeneSets.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterGt.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterGt.java:12: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterGt.java:12: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterChrPos.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterChrPos.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:10: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:10: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilter.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilter.java:17: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:13: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:13: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:14: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:14: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:15: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesConcordance.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesConcordance.java:9: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesConcordance.java:9: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:12: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:12: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:16: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotateTabix.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:3: error: package org.junit.platform.suite.api does not exist [WARNING] import org.junit.platform.suite.api.SelectPackages; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:4: error: package org.junit.platform.suite.api does not exist [WARNING] import org.junit.platform.suite.api.Suite; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:5: error: package org.junit.platform.suite.api does not exist [WARNING] import org.junit.platform.suite.api.SuiteDisplayName; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:13: error: cannot find symbol [WARNING] @Suite [WARNING] ^ [WARNING] symbol: class Suite [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:14: error: cannot find symbol [WARNING] @SuiteDisplayName("Unit test cases") [WARNING] ^ [WARNING] symbol: class SuiteDisplayName [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:15: error: cannot find symbol [WARNING] @SelectPackages({"org.snpsift.testCases.unit"}) [WARNING] ^ [WARNING] symbol: class SelectPackages [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestCasesZzz.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestCasesZzz.java:13: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVcfCheck.java:16: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesVcfCheck [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:56: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesVarType [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:62: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesVarType [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:68: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesVarType [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:74: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesVarType [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:80: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesVarType [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:26: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesSplit [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:56: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesSplit [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:82: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesSplit [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:28: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesSort [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:46: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:57: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:68: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:79: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:87: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:93: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:99: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:105: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesPrivate [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesLd.java:22: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesLd [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIntervals.java:23: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesIntervals [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIntervals.java:48: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesIntervals [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:30: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesIndex [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:82: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesIndex [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:21: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesHwe [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:33: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesHwe [WARNING] /build/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:45: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesHwe [WARNING] Building index for all the packages and classes... 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[WARNING] 100 warnings [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 59.187 s [INFO] Finished at: 2024-05-25T00:55:53+14:00 [INFO] ------------------------------------------------------------------------  debian/rules override_dh_auto_test make[1]: Entering directory '/build/snpsift-5.1+dfsg2' # Moving the unit tests into a subdir of src/test so that Maven sees them. mkdir -p src/test/java/org/snpsift/testCases cp -a src/main/java/org/snpsift/testCases/unit src/test/java/org/snpsift/testCases dh_auto_test /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/snpsift-5.1\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/snpsift-5.1\+dfsg2/debian -Dmaven.repo.local=/build/snpsift-5.1\+dfsg2/debian/maven-repo --batch-mode test OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release. [INFO] Scanning for projects... [INFO] [INFO] ------------------------< org.snpsift:snpsift >------------------------- [INFO] Building SnpSift 5.1 [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The artifact org.apache.maven.plugins:maven-surefire-plugin:jar:2.12.4 has been relocated to org.apache.maven.plugins:maven-surefire-plugin:jar:2.22.3 [WARNING] The POM for org.biojava:biojava-structure:jar:6.x is invalid, transitive dependencies (if any) will not be available, enable debug logging for more details [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ snpsift --- [INFO] skip non existing resourceDirectory /build/snpsift-5.1+dfsg2/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ snpsift --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ snpsift --- [INFO] skip non existing resourceDirectory /build/snpsift-5.1+dfsg2/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ snpsift --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 26 source files to /build/snpsift-5.1+dfsg2/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ snpsift --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.snpsift.testCases.unit.TestCasesFilterChrPos Annotate: ./test/filterChrPos_01.txt ./test/filterChrPos_01.vcf Annotate: ./test/filterChrPos_02.txt ./test/filterChrPos_02.vcf Annotate: ./test/filterChrPos_03.txt ./test/filterChrPos_03.vcf [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.513 s - in org.snpsift.testCases.unit.TestCasesFilterChrPos [INFO] Running org.snpsift.testCases.unit.TestCasesGt TestCasesGt.test_01(25): Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.05 s - in org.snpsift.testCases.unit.TestCasesGt [INFO] Running org.snpsift.testCases.unit.TestCasesGeneSets TestCasesGeneSets.test_01(25): Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.255 s - in org.snpsift.testCases.unit.TestCasesGeneSets [INFO] Running org.snpsift.testCases.unit.TestCasesAnnotateTabix TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test TestCasesAnnotate.test_29_repeated_IDs(618): Test TestCasesAnnotate.test_01(145): Test TestCasesAnnotate.test_02(153): Test TestCasesAnnotate.test_03(161): Test TestCasesAnnotate.test_04(169): Test TestCasesAnnotate.test_05(181): Test TestCasesAnnotate.test_06(192): Test TestCasesAnnotate.test_07(217): Test TestCasesAnnotate.test_08(232): Test TestCasesAnnotate.test_09(245): Test TestCasesAnnotate.test_11(273): Test TestCasesAnnotate.test_12(300): Test TestCasesAnnotate.test_13(320): Test TestCasesAnnotate.test_14(340): Test TestCasesAnnotate.test_15(356): Test TestCasesAnnotate.test_16(372): Test TestCasesAnnotate.test_17(390): Test TestCasesAnnotate.test_18(415): Test TestCasesAnnotate.test_19(428): Test TestCasesAnnotate.test_20(439): Test TestCasesAnnotate.test_21(453): Test TestCasesAnnotate.test_22(479): Test TestCasesAnnotate.test_24(509): Test TestCasesAnnotate.test_25(539): Test TestCasesAnnotate.test_35(693): Test TestCasesAnnotate.test_36(711): Test TestCasesAnnotate.test_38(732): Test TestCasesAnnotate.test_39(743): Test TestCasesAnnotate.test_40(762): Test TestCasesAnnotate.test_41(770): Test TestCasesAnnotate.test_42(781): Test TestCasesAnnotate.test_43(809): Test TestCasesAnnotate.test_44(835): Test TestCasesAnnotate.test_45(861): Test TestCasesAnnotate.test_33_empty_db(665): Test TestCasesAnnotate.test_26_repeat_db_entry(568): Test TestCasesAnnotate.test_32_annotate_minimal_representation_input(654): Test TestCasesAnnotate.test_28_exists(596): Test TestCasesAnnotate.test_34_dbStartsOnDifferentChromo(676): Test TestCasesAnnotate.test_23_allele_specific_annotation_missing_R(491): Test TestCasesAnnotate.test_27_repeat_db_entry(580): Test [INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 71.893 s - in org.snpsift.testCases.unit.TestCasesAnnotateTabix [INFO] Running org.snpsift.testCases.unit.TestCasesVcfCheck TestCasesVcfCheck.test_01(18): Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.snpsift.testCases.unit.TestCasesVcfCheck [INFO] Running org.snpsift.testCases.unit.TestCasesAnnotateUseIndex TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test TestCasesAnnotate.test_29_repeated_IDs(618): Test TestCasesAnnotate.test_01(145): Test TestCasesAnnotate.test_02(153): Test TestCasesAnnotate.test_03(161): Test TestCasesAnnotate.test_04(169): Test TestCasesAnnotate.test_05(181): Test TestCasesAnnotate.test_06(192): Test TestCasesAnnotate.test_07(217): Test TestCasesAnnotate.test_08(232): Test TestCasesAnnotate.test_09(245): Test TestCasesAnnotate.test_11(273): Test TestCasesAnnotate.test_12(300): Test TestCasesAnnotate.test_13(320): Test TestCasesAnnotate.test_14(340): Test TestCasesAnnotate.test_15(356): Test TestCasesAnnotate.test_16(372): Test TestCasesAnnotate.test_17(390): Test TestCasesAnnotate.test_18(415): Test TestCasesAnnotate.test_19(428): Test TestCasesAnnotate.test_20(439): Test TestCasesAnnotate.test_21(453): Test TestCasesAnnotate.test_22(479): Test TestCasesAnnotate.test_24(509): Test TestCasesAnnotate.test_25(539): Test TestCasesAnnotate.test_35(693): Test TestCasesAnnotate.test_36(711): Test TestCasesAnnotate.test_38(732): Test TestCasesAnnotate.test_39(743): Test TestCasesAnnotate.test_40(762): Test TestCasesAnnotate.test_41(770): Test TestCasesAnnotate.test_42(781): Test TestCasesAnnotate.test_43(809): Test TestCasesAnnotate.test_44(835): Test TestCasesAnnotate.test_45(861): Test TestCasesAnnotate.test_33_empty_db(665): Test TestCasesAnnotate.test_26_repeat_db_entry(568): Test TestCasesAnnotate.test_32_annotate_minimal_representation_input(654): Test TestCasesAnnotate.test_28_exists(596): Test TestCasesAnnotate.test_34_dbStartsOnDifferentChromo(676): Test TestCasesAnnotate.test_23_allele_specific_annotation_missing_R(491): Test TestCasesAnnotate.test_27_repeat_db_entry(580): Test [INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 38.295 s - in org.snpsift.testCases.unit.TestCasesAnnotateUseIndex [INFO] Running org.snpsift.testCases.unit.TestCasesLd [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpsift.testCases.unit.TestCasesLd [INFO] Running org.snpsift.testCases.unit.TestCasesSplit TestCasesSplit.test_01(28): Test TestCasesSplit.test_02(58): Test TestCasesSplit.test_03(84): Test [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpsift.testCases.unit.TestCasesSplit [INFO] Running org.snpsift.testCases.unit.TestCasesHwe [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 s - in org.snpsift.testCases.unit.TestCasesHwe [INFO] Running org.snpsift.testCases.unit.TestCasesAnnotateCreateIndex TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test TestCasesAnnotate.test_29_repeated_IDs(618): Test TestCasesAnnotate.test_01(145): Test TestCasesAnnotate.test_02(153): Test TestCasesAnnotate.test_03(161): Test TestCasesAnnotate.test_04(169): Test TestCasesAnnotate.test_05(181): Test TestCasesAnnotate.test_06(192): Test TestCasesAnnotate.test_07(217): Test TestCasesAnnotate.test_08(232): Test TestCasesAnnotate.test_09(245): Test TestCasesAnnotate.test_11(273): Test TestCasesAnnotate.test_12(300): Test TestCasesAnnotate.test_13(320): Test TestCasesAnnotate.test_14(340): Test TestCasesAnnotate.test_15(356): Test TestCasesAnnotate.test_16(372): Test TestCasesAnnotate.test_17(390): Test TestCasesAnnotate.test_18(415): Test TestCasesAnnotate.test_19(428): Test TestCasesAnnotate.test_20(439): Test TestCasesAnnotate.test_21(453): Test TestCasesAnnotate.test_22(479): Test TestCasesAnnotate.test_24(509): Test TestCasesAnnotate.test_25(539): Test TestCasesAnnotate.test_35(693): Test TestCasesAnnotate.test_36(711): Test TestCasesAnnotate.test_38(732): Test TestCasesAnnotate.test_39(743): Test TestCasesAnnotate.test_40(762): Test TestCasesAnnotate.test_41(770): Test TestCasesAnnotate.test_42(781): Test TestCasesAnnotate.test_43(809): Test TestCasesAnnotate.test_44(835): Test TestCasesAnnotate.test_45(861): Test TestCasesAnnotate.test_33_empty_db(665): Test TestCasesAnnotate.test_26_repeat_db_entry(568): Test TestCasesAnnotate.test_32_annotate_minimal_representation_input(654): Test TestCasesAnnotate.test_28_exists(596): Test TestCasesAnnotate.test_34_dbStartsOnDifferentChromo(676): Test TestCasesAnnotate.test_23_allele_specific_annotation_missing_R(491): Test TestCasesAnnotate.test_27_repeat_db_entry(580): Test [INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 43.257 s - in org.snpsift.testCases.unit.TestCasesAnnotateCreateIndex [INFO] Running org.snpsift.testCases.unit.TestCasesGwasCatalog TestCasesGwasCatalog.test_01(34): Test WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '19:16185558' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs8109288' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '19:46172277' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs11671664' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '11:116648916' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs964184' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '6:161010117' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs10455872' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '1:67705957' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs11209026' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '19:45412078' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs7412' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '2:169763147' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs560887' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: Too many 'WARNING_DUPLICATE_PRIMARY_KEY' warnings, no further warnings will be shown. TestCasesGwasCatalog.test_02(50): Test [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.859 s - in org.snpsift.testCases.unit.TestCasesGwasCatalog [INFO] Running org.snpsift.testCases.unit.TestCasesCaseControl TestCasesCaseControl.test_01(53): Test TestCasesCaseControl.test_02(65): Test TestCasesCaseControl.test_03(83): Test TestCasesCaseControl.test_04(107): Test TestCasesCaseControl.test_05(119): Test TestCasesCaseControl.test_06(125): Test TestCasesCaseControl.test_07(131): Test TestCasesCaseControl.test_08(137): Test TestCasesCaseControl.test_09(146): Test TestCasesCaseControl.test_10(222): Test TestCasesCaseControl.test_02_Str2(77): Test TestCasesCaseControl.test_03_Str2(95): Test TestCasesCaseControl.test_03_Str3(101): Test TestCasesCaseControl.test_01_Str(59): Test TestCasesCaseControl.test_02_Str(71): Test TestCasesCaseControl.test_03_Str(89): Test TestCasesCaseControl.test_04_Str(113): Test [INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.635 s - in org.snpsift.testCases.unit.TestCasesCaseControl [INFO] Running org.snpsift.testCases.unit.TestCasesVarType TestCasesVarType.test_05_multiple(82): Test TestCasesVarType.test_01_SNP(58): Test TestCasesVarType.test_02_MNP(64): Test TestCasesVarType.test_03_INS(70): Test TestCasesVarType.test_04_DEL(76): Test [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 s - in org.snpsift.testCases.unit.TestCasesVarType [INFO] Running org.snpsift.testCases.unit.TestCasesConcordance TestCasesConcordance.test_01(68): Test TestCasesConcordance.test_02(74): Test TestCasesConcordance.test_03(80): Test TestCasesConcordance.test_04(91): Test TestCasesConcordance.test_05(102): Test TestCasesConcordance.test_06(113): Test TestCasesConcordance.test_07(125): Test TestCasesConcordance.test_08(131): Test TestCasesConcordance.test_09(142): Test TestCasesConcordance.test_10(153): Test TestCasesConcordance.test_11(164): Test TestCasesConcordance.test_12(181): Test [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.125 s - in org.snpsift.testCases.unit.TestCasesConcordance [INFO] Running org.snpsift.testCases.unit.TestCasesAnnotateMem TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test TestCasesAnnotate.test_29_repeated_IDs(618): Test TestCasesAnnotate.test_01(145): Test TestCasesAnnotate.test_02(153): Test TestCasesAnnotate.test_03(161): Test TestCasesAnnotate.test_04(169): Test TestCasesAnnotate.test_05(181): Test TestCasesAnnotate.test_06(192): Test TestCasesAnnotate.test_07(217): Test TestCasesAnnotate.test_08(232): Test TestCasesAnnotate.test_09(245): Test TestCasesAnnotate.test_11(273): Test TestCasesAnnotate.test_12(300): Test TestCasesAnnotate.test_13(320): Test TestCasesAnnotate.test_14(340): Test TestCasesAnnotate.test_15(356): Test TestCasesAnnotate.test_16(372): Test TestCasesAnnotate.test_17(390): Test TestCasesAnnotate.test_18(415): Test TestCasesAnnotate.test_19(428): Test TestCasesAnnotate.test_20(439): Test TestCasesAnnotate.test_21(453): Test TestCasesAnnotate.test_22(479): Test TestCasesAnnotate.test_24(509): Test TestCasesAnnotate.test_25(539): Test TestCasesAnnotate.test_35(693): Test TestCasesAnnotate.test_36(711): Test TestCasesAnnotate.test_38(732): Test TestCasesAnnotate.test_39(743): Test TestCasesAnnotate.test_40(762): Test TestCasesAnnotate.test_41(770): Test TestCasesAnnotate.test_42(781): Test TestCasesAnnotate.test_43(809): Test TestCasesAnnotate.test_44(835): Test TestCasesAnnotate.test_45(861): Test TestCasesAnnotate.test_33_empty_db(665): Test TestCasesAnnotate.test_26_repeat_db_entry(568): Test TestCasesAnnotate.test_32_annotate_minimal_representation_input(654): Test TestCasesAnnotate.test_28_exists(596): Test TestCasesAnnotate.test_34_dbStartsOnDifferentChromo(676): Test TestCasesAnnotate.test_23_allele_specific_annotation_missing_R(491): Test TestCasesAnnotate.test_27_repeat_db_entry(580): Test [INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 41.324 s - in org.snpsift.testCases.unit.TestCasesAnnotateMem [INFO] Running org.snpsift.testCases.unit.TestCasesFilterGt TestCasesFilterGt.test_01(28): Test ANTLR Tool version 4.9.3 used for code generation does not match the current runtime version 4.7.2ANTLR Tool version 4.9.3 used for code generation does not match the current runtime version 4.7.2TestCasesFilterGt.test_02(62): Test [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.113 s - in org.snpsift.testCases.unit.TestCasesFilterGt [INFO] Running org.snpsift.testCases.unit.TestCasesSort TestCasesSort.test_01(30): Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpsift.testCases.unit.TestCasesSort [INFO] Running org.snpsift.testCases.unit.TestCasesFilterALL [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.133 s - in org.snpsift.testCases.unit.TestCasesFilterALL [INFO] Running org.snpsift.testCases.unit.TestCasesExtractFields TestCasesExtractFields.test_31_ann(291): Test TestCasesExtractFields.test_00(71): Test TestCasesExtractFields.test_01(98): Test TestCasesExtractFields.test_02(104): Test TestCasesExtractFields.test_03(110): Test TestCasesExtractFields.test_04(116): Test TestCasesExtractFields.test_05(122): Test TestCasesExtractFields.test_06(128): Test TestCasesExtractFields.test_07(134): Test TestCasesExtractFields.test_08(140): Test TestCasesExtractFields.test_09(146): Test TestCasesExtractFields.test_10(152): Test TestCasesExtractFields.test_11(158): Test TestCasesExtractFields.test_12(164): Test TestCasesExtractFields.test_13(170): Test TestCasesExtractFields.test_14(176): Test TestCasesExtractFields.test_15(182): Test TestCasesExtractFields.test_16(188): Test TestCasesExtractFields.test_17(194): Test TestCasesExtractFields.test_18(200): Test TestCasesExtractFields.test_19(206): Test TestCasesExtractFields.test_20(212): Test TestCasesExtractFields.test_23(218): Test TestCasesExtractFields.test_24(224): Test TestCasesExtractFields.test_25(230): Test TestCasesExtractFields.test_26(236): Test TestCasesExtractFields.test_27(242): Test TestCasesExtractFields.test_28(253): Test TestCasesExtractFields.test_29(262): Test TestCasesExtractFields.test_30(273): Test TestCasesExtractFields.test_31(282): Test TestCasesExtractFields.test_32(300): Test TestCasesExtractFields.test_33(312): Test TestCasesExtractFields.test_34(323): Test TestCasesExtractFields.test_35(340): Test [INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.154 s - in org.snpsift.testCases.unit.TestCasesExtractFields [INFO] Running org.snpsift.testCases.unit.TestCasesDbNsfp TestCasesDbNsfp.test_01(113): Test TestCasesDbNsfp.test_02(138): Test TestCasesDbNsfp.test_03(160): Test TestCasesDbNsfp.test_04(179): Test TestCasesDbNsfp.test_05(200): Test TestCasesDbNsfp.test_06(223): Test [INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 11.551 s - in org.snpsift.testCases.unit.TestCasesDbNsfp [INFO] Running org.snpsift.testCases.unit.TestCasesDbNsfpDeleteCache TestCasesDbNsfp.test_01(113): Test TestCasesDbNsfp.test_02(138): Test TestCasesDbNsfp.test_03(160): Test TestCasesDbNsfp.test_04(179): Test TestCasesDbNsfp.test_05(200): Test TestCasesDbNsfp.test_06(223): Test [INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 35.244 s - in org.snpsift.testCases.unit.TestCasesDbNsfpDeleteCache [INFO] Running org.snpsift.testCases.unit.TestCasesPrivate TestCasesPrivate.test_01(48): Test TestCasesPrivate.test_02(59): Test TestCasesPrivate.test_03(70): Test TestCasesPrivate.test_04(81): Test TestCasesPrivate.test_05(89): Test TestCasesPrivate.test_06(95): Test TestCasesPrivate.test_07(101): Test TestCasesPrivate.test_08(107): Test [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.snpsift.testCases.unit.TestCasesPrivate [INFO] Running org.snpsift.testCases.unit.TestCasesAnnotate TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test TestCasesAnnotate.test_29_repeated_IDs(618): Test TestCasesAnnotate.test_01(145): Test TestCasesAnnotate.test_02(153): Test TestCasesAnnotate.test_03(161): Test TestCasesAnnotate.test_04(169): Test TestCasesAnnotate.test_05(181): Test TestCasesAnnotate.test_06(192): Test TestCasesAnnotate.test_07(217): Test TestCasesAnnotate.test_08(232): Test TestCasesAnnotate.test_09(245): Test TestCasesAnnotate.test_11(273): Test TestCasesAnnotate.test_12(300): Test TestCasesAnnotate.test_13(320): Test TestCasesAnnotate.test_14(340): Test TestCasesAnnotate.test_15(356): Test TestCasesAnnotate.test_16(372): Test TestCasesAnnotate.test_17(390): Test TestCasesAnnotate.test_18(415): Test TestCasesAnnotate.test_19(428): Test TestCasesAnnotate.test_20(439): Test TestCasesAnnotate.test_21(453): Test TestCasesAnnotate.test_22(479): Test TestCasesAnnotate.test_24(509): Test TestCasesAnnotate.test_25(539): Test TestCasesAnnotate.test_35(693): Test TestCasesAnnotate.test_36(711): Test TestCasesAnnotate.test_38(732): Test TestCasesAnnotate.test_39(743): Test TestCasesAnnotate.test_40(762): Test TestCasesAnnotate.test_41(770): Test TestCasesAnnotate.test_42(781): Test TestCasesAnnotate.test_43(809): Test TestCasesAnnotate.test_44(835): Test TestCasesAnnotate.test_45(861): Test TestCasesAnnotate.test_33_empty_db(665): Test TestCasesAnnotate.test_26_repeat_db_entry(568): Test TestCasesAnnotate.test_32_annotate_minimal_representation_input(654): Test TestCasesAnnotate.test_28_exists(596): Test TestCasesAnnotate.test_34_dbStartsOnDifferentChromo(676): Test TestCasesAnnotate.test_23_allele_specific_annotation_missing_R(491): Test TestCasesAnnotate.test_27_repeat_db_entry(580): Test [INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 107.038 s - in org.snpsift.testCases.unit.TestCasesAnnotate [INFO] Running org.snpsift.testCases.unit.TestCasesIndex TestCasesIndex.test_01(32): Test TestCasesIndex.test_02(84): Test [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 10.365 s - in org.snpsift.testCases.unit.TestCasesIndex [INFO] Running org.snpsift.testCases.unit.TestCasesIntervals TestCasesIntervals.test_01(25): Test TestCasesIntervals.test_02(50): Test [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.snpsift.testCases.unit.TestCasesIntervals [INFO] Running org.snpsift.testCases.unit.TestCasesFilter TestCasesFilter.test_57_short_circuit_AND_OR_operators(1724): Test TestCasesFilter.test_32_ann(988): Test TestCasesFilter.test_33_ann(1049): Test TestCasesFilter.test_34_ann(1108): Test TestCasesFilter.test_35_ann(1167): Test TestCasesFilter.test_01(40): Test TestCasesFilter.test_02(64): Test TestCasesFilter.test_03(86): Test TestCasesFilter.test_04(110): Test TestCasesFilter.test_05(134): Test TestCasesFilter.test_06(158): Test TestCasesFilter.test_07(182): Test TestCasesFilter.test_08(208): Test TestCasesFilter.test_09(236): Test TestCasesFilter.test_10(258): Test TestCasesFilter.test_11(281): Test TestCasesFilter.test_12(303): Test TestCasesFilter.test_13(326): Test TestCasesFilter.test_14(348): Test TestCasesFilter.test_15(381): Test TestCasesFilter.test_16(407): Test TestCasesFilter.test_17(435): Test TestCasesFilter.test_18(459): Test TestCasesFilter.test_19(483): Test TestCasesFilter.test_20(507): Test TestCasesFilter.test_21(532): Test TestCasesFilter.test_22(559): Test TestCasesFilter.test_23(615): Test TestCasesFilter.test_24(642): Test TestCasesFilter.test_25(669): Test TestCasesFilter.test_26(697): Test TestCasesFilter.test_27(748): Test TestCasesFilter.test_28(846): Test TestCasesFilter.test_29(875): Test TestCasesFilter.test_30(903): Test TestCasesFilter.test_31(932): Test TestCasesFilter.test_32(960): Test TestCasesFilter.test_33(1021): Test TestCasesFilter.test_34(1081): Test TestCasesFilter.test_35(1140): Test TestCasesFilter.test_36(1198): Test TestCasesFilter.test_37(1222): Test TestCasesFilter.test_38(1247): Test TestCasesFilter.test_39(1272): Test TestCasesFilter.test_40(1295): Test TestCasesFilter.test_41(1320): Test TestCasesFilter.test_42(1356): Test TestCasesFilter.test_43(1374): Test TestCasesFilter.test_44(1392): Test TestCasesFilter.test_45(1410): Test TestCasesFilter.test_46(1437): Test TestCasesFilter.test_47(1448): Test TestCasesFilter.test_48(1459): Test TestCasesFilter.test_49(1475): Test TestCasesFilter.test_50(1494): Test TestCasesFilter.test_51(1526): Test TestCasesFilter.test_52(1560): Test TestCasesFilter.test_53(1583): Test TestCasesFilter.test_54(1605): Test TestCasesFilter.test_55(1627): Test TestCasesFilter.test_22_3(589): Test TestCasesFilter.test_55_2(1647): Test TestCasesFilter.test_55_3(1667): Test TestCasesFilter.test_56_empty_vcf(1687): Test TestCasesFilter.test_58_rmFilter_info_field(1747): Test TestCasesFilter.test_27_ann2(812): Test TestCasesFilter.test_26_ann(721): Test TestCasesFilter.test_27_ann(778): Test [INFO] Tests run: 68, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.144 s - in org.snpsift.testCases.unit.TestCasesFilter [INFO] [INFO] Results: [INFO] [INFO] Tests run: 403, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 06:30 min [INFO] Finished at: 2024-05-25T01:02:31+14:00 [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/snpsift-5.1+dfsg2' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/snpsift-5.1\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/snpsift-5.1\+dfsg2/debian -Dmaven.repo.local=/build/snpsift-5.1\+dfsg2/debian/maven-repo --batch-mode -Ddebian.dir=/build/snpsift-5.1\+dfsg2/debian -Ddebian.package=libsnpsift-java -Dmaven.repo.local=/build/snpsift-5.1\+dfsg2/debian/maven-repo -Dinstall.to.usj=true org.debian.maven:debian-maven-plugin:2.6:install OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release. [INFO] Scanning for projects... [INFO] [INFO] ------------------------< org.snpsift:snpsift >------------------------- [INFO] Building SnpSift 5.1 [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ snpsift --- [INFO] Cleaning pom file: /build/snpsift-5.1+dfsg2/pom.xml.save with options: [INFO] --keep-pom-version --package=libsnpsift-java [INFO] --rules=/build/snpsift-5.1+dfsg2/debian/maven.rules [INFO] --ignore-rules=/build/snpsift-5.1+dfsg2/debian/maven.ignoreRules [INFO] --published-rules=/build/snpsift-5.1+dfsg2/debian/maven.publishedRules [INFO] Install jar for snpsift into /usr/share/java [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 1.117 s [INFO] Finished at: 2024-05-25T01:02:37+14:00 [INFO] ------------------------------------------------------------------------  mh_resolve_dependencies --non-interactive --offline --build -plibsnpsift-java --javadoc --base-directory=/build/snpsift-5.1\+dfsg2 --non-explore Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) at org.debian.maven.repo.POMReader.readPom(POMReader.java:82) at org.debian.maven.repo.POMReader.readPom(POMReader.java:57) at org.debian.maven.repo.Repository.scan(Repository.java:397) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:201) at org.debian.maven.repo.Repository.scanOnce(Repository.java:196) at org.debian.maven.repo.POMTransformer.usePluginVersionsFromRepository(POMTransformer.java:107) at org.debian.maven.packager.DependenciesSolver.main(DependenciesSolver.java:907) Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) at org.debian.maven.repo.POMReader.readPom(POMReader.java:82) at org.debian.maven.repo.POMReader.readPom(POMReader.java:57) at org.debian.maven.repo.Repository.scan(Repository.java:397) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:201) at org.debian.maven.repo.Repository.scanOnce(Repository.java:196) at org.debian.maven.repo.POMTransformer.usePluginVersionsFromRepository(POMTransformer.java:107) at org.debian.maven.packager.DependenciesSolver.main(DependenciesSolver.java:907) Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) at org.debian.maven.repo.POMReader.readPom(POMReader.java:82) at org.debian.maven.repo.POMReader.readPom(POMReader.java:57) at org.debian.maven.repo.Repository.scan(Repository.java:397) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:201) at org.debian.maven.packager.DependenciesSolver.getRepository(DependenciesSolver.java:231) at org.debian.maven.packager.DependenciesSolver.solveDependencies(DependenciesSolver.java:237) at org.debian.maven.packager.DependenciesSolver.main(DependenciesSolver.java:922) Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) at org.debian.maven.repo.POMReader.readPom(POMReader.java:82) at org.debian.maven.repo.POMReader.readPom(POMReader.java:57) at org.debian.maven.repo.Repository.scan(Repository.java:397) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:394) at org.debian.maven.repo.Repository.scan(Repository.java:201) at org.debian.maven.packager.DependenciesSolver.getRepository(DependenciesSolver.java:231) at org.debian.maven.packager.DependenciesSolver.solveDependencies(DependenciesSolver.java:237) at org.debian.maven.packager.DependenciesSolver.main(DependenciesSolver.java:922) Analysing pom.xml... Checking dependencies for documentation packages... > dpkg --search /usr/share/doc/antlr4/api/index.html Found antlr4-doc > dpkg --search /usr/share/doc/libcommons-math3-java/api/index.html Found libcommons-math3-java-doc > dpkg --search /usr/share/doc/libhtsjdk-java/api/index.html Found libhtsjdk-java-doc > dpkg --search /usr/share/doc/libsnpeff-java/api/index.html Found libsnpeff-java-doc > dpkg --search /usr/share/doc/libtrove3-java/api/index.html Found libtrove3-java-doc bash -c "rm -f target/apidocs/*.sh target/apidocs/options" mh_unpatchpoms -plibsnpsift-java dh_install jh_installjavadoc dh_installdocs dh_installchangelogs dh_installman dh_lintian dh_perl dh_link jh_installlibs jh_classpath jh_manifest jh_exec jh_depends dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package libsnpsift-java: substitution variable ${java:Depends} unused, but is defined dpkg-gencontrol: warning: package libsnpsift-java: substitution variable ${maven:CompileDepends} unused, but is defined dpkg-gencontrol: warning: package libsnpsift-java: substitution variable ${maven:DocDepends} unused, but is defined dpkg-gencontrol: warning: package libsnpsift-java-doc: substitution variable ${maven:CompileDepends} unused, but is defined dpkg-gencontrol: warning: package libsnpsift-java-doc: substitution variable ${maven:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'libsnpsift-java' in '../libsnpsift-java_5.1+dfsg2-2_all.deb'. dpkg-deb: building package 'libsnpsift-java-doc' in '../libsnpsift-java-doc_5.1+dfsg2-2_all.deb'. dpkg-deb: building package 'snpsift' in '../snpsift_5.1+dfsg2-2_all.deb'. dpkg-genbuildinfo --build=binary -O../snpsift_5.1+dfsg2-2_amd64.buildinfo dpkg-genchanges --build=binary -O../snpsift_5.1+dfsg2-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3683552/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3683552/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3683552 and its subdirectories I: Current time: Sat May 25 01:03:17 +14 2024 I: pbuilder-time-stamp: 1716548597